Starting phenix.real_space_refine on Fri Jun 13 03:50:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7toe_26030/06_2025/7toe_26030_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7toe_26030/06_2025/7toe_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_26030/06_2025/7toe_26030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7toe_26030/06_2025/7toe_26030.map" model { file = "/net/cci-nas-00/data/ceres_data/7toe_26030/06_2025/7toe_26030_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7toe_26030/06_2025/7toe_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.46, per 1000 atoms: 0.63 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: 3.68 Conformation dependent library (CDL) restraints added in 2.0 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: 1.74 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: 4.80 Time building geometry restraints manager: 4.35 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: 0.04 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: 0.590 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: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 36.440 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.980 ------------------------------------------------------------------------------- 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= 0.172 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 Details of bonding type rmsd hydrogen bonds : bond 0.16978 ( 678) hydrogen bonds : angle 7.60923 ( 1950) covalent geometry : bond 0.00325 (15452) covalent geometry : angle 0.58771 (20896) *********************** 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 : 1.832 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: 1.2321 time to fit residues: 397.6074 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 : 1.679 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.165235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.125017 restraints weight = 17920.065| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.07 r_work: 0.3339 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 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= 0.154 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 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 678) hydrogen bonds : angle 5.94524 ( 1950) covalent geometry : bond 0.00355 (15452) covalent geometry : angle 0.58600 (20896) *********************** 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 : 1.673 Fit side-chains REVERT: A 152 LYS cc_start: 0.7268 (tmmt) cc_final: 0.7025 (tttt) REVERT: B 30 ASP cc_start: 0.7330 (t0) cc_final: 0.6581 (OUTLIER) REVERT: B 130 LEU cc_start: 0.8227 (tp) cc_final: 0.7903 (tp) REVERT: B 171 LYS cc_start: 0.7700 (ptmm) cc_final: 0.7396 (pttp) REVERT: B 249 TYR cc_start: 0.7571 (t80) cc_final: 0.7089 (t80) REVERT: B 389 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7832 (mt-10) REVERT: B 446 CYS cc_start: 0.8361 (m) cc_final: 0.8064 (m) REVERT: B 497 LYS cc_start: 0.8658 (tptt) cc_final: 0.8268 (tttp) REVERT: C 130 LEU cc_start: 0.8454 (tp) cc_final: 0.8098 (tt) REVERT: C 405 MET cc_start: 0.8487 (mmm) cc_final: 0.7807 (mmt) REVERT: C 475 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7995 (tm-30) REVERT: D 37 MET cc_start: 0.8676 (mmm) cc_final: 0.8176 (mmt) REVERT: D 95 LYS cc_start: 0.7498 (tmmt) cc_final: 0.6861 (tmmt) REVERT: D 99 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: D 135 ASN cc_start: 0.8407 (m-40) cc_final: 0.7987 (m110) REVERT: D 140 LEU cc_start: 0.8098 (mp) cc_final: 0.7795 (mt) outliers start: 21 outliers final: 12 residues processed: 227 average time/residue: 1.1160 time to fit residues: 283.1320 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 15 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 154 optimal weight: 0.2980 chunk 10 optimal weight: 20.0000 chunk 172 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.163637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.121365 restraints weight = 17765.835| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.21 r_work: 0.3307 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15452 Z= 0.186 Angle : 0.591 7.592 20896 Z= 0.304 Chirality : 0.045 0.171 2240 Planarity : 0.004 0.053 2732 Dihedral : 4.428 19.814 2056 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.56 % Favored : 96.38 % Rotamer: Outliers : 2.39 % Allowed : 12.50 % 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: -0.28 (0.19), residues: 1852 helix: 0.44 (0.20), residues: 696 sheet: -0.83 (0.23), residues: 432 loop : -0.15 (0.23), residues: 724 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 0.017 0.002 PHE B 102 TYR 0.019 0.002 TYR A 308 ARG 0.005 0.000 ARG D 459 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 678) hydrogen bonds : angle 5.62323 ( 1950) covalent geometry : bond 0.00444 (15452) covalent geometry : angle 0.59066 (20896) *********************** 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 248 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 1.766 Fit side-chains REVERT: A 152 LYS cc_start: 0.7196 (tmmt) cc_final: 0.6993 (tttt) REVERT: A 159 MET cc_start: 0.8009 (tpp) cc_final: 0.7780 (tpp) REVERT: A 175 ARG cc_start: 0.8276 (ptm160) cc_final: 0.7698 (ptm160) REVERT: A 258 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8131 (t70) REVERT: A 398 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8138 (tt0) REVERT: B 30 ASP cc_start: 0.7441 (t0) cc_final: 0.6657 (OUTLIER) REVERT: B 97 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.6992 (ttpp) REVERT: B 130 LEU cc_start: 0.8212 (tp) cc_final: 0.7926 (tp) REVERT: B 249 TYR cc_start: 0.7604 (t80) cc_final: 0.7109 (t80) REVERT: B 389 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7768 (mt-10) REVERT: B 395 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7894 (pt0) REVERT: B 446 CYS cc_start: 0.8429 (m) cc_final: 0.8101 (m) REVERT: B 497 LYS cc_start: 0.8611 (tptt) cc_final: 0.8219 (tttp) REVERT: C 130 LEU cc_start: 0.8408 (tp) cc_final: 0.8207 (tp) REVERT: C 317 GLU cc_start: 0.6340 (OUTLIER) cc_final: 0.6001 (tt0) REVERT: C 475 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7908 (tm-30) REVERT: D 37 MET cc_start: 0.8591 (mmm) cc_final: 0.7790 (mmt) REVERT: D 66 PHE cc_start: 0.8053 (m-80) cc_final: 0.7792 (m-80) REVERT: D 95 LYS cc_start: 0.7439 (tmmt) cc_final: 0.6883 (tmmt) REVERT: D 99 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: D 135 ASN cc_start: 0.8458 (m-40) cc_final: 0.8111 (m110) outliers start: 39 outliers final: 16 residues processed: 237 average time/residue: 1.2176 time to fit residues: 320.1446 Evaluate side-chains 217 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 1.719 ------------------------------------------------------------------------------- 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 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 94 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 170 optimal weight: 0.9980 chunk 141 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.162579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.121804 restraints weight = 17796.621| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.19 r_work: 0.3297 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1893 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= 0.195 Angle : 0.592 7.416 20896 Z= 0.304 Chirality : 0.045 0.190 2240 Planarity : 0.004 0.053 2732 Dihedral : 4.485 19.182 2056 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.73 % Favored : 96.22 % Rotamer: Outliers : 2.27 % Allowed : 15.32 % Favored : 82.41 % 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: -0.39 (0.20), residues: 1852 helix: 0.25 (0.19), residues: 744 sheet: -0.89 (0.23), residues: 444 loop : -0.09 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 164 HIS 0.005 0.001 HIS A 124 PHE 0.020 0.001 PHE C 241 TYR 0.019 0.002 TYR A 308 ARG 0.007 0.000 ARG C 246 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 678) hydrogen bonds : angle 5.47612 ( 1950) covalent geometry : bond 0.00467 (15452) covalent geometry : angle 0.59186 (20896) *********************** 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 244 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 1.656 Fit side-chains revert: symmetry clash REVERT: A 159 MET cc_start: 0.8027 (tpp) cc_final: 0.7764 (tpp) REVERT: A 258 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8161 (t70) REVERT: B 97 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7007 (ttpp) REVERT: B 130 LEU cc_start: 0.8194 (tp) cc_final: 0.7903 (tp) REVERT: B 249 TYR cc_start: 0.7575 (t80) cc_final: 0.7091 (t80) REVERT: B 389 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7765 (mt-10) REVERT: B 395 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7828 (pt0) REVERT: B 446 CYS cc_start: 0.8453 (m) cc_final: 0.8108 (m) REVERT: B 497 LYS cc_start: 0.8647 (tptt) cc_final: 0.8269 (tttp) REVERT: C 89 LYS cc_start: 0.8850 (ttpt) cc_final: 0.8392 (mptt) REVERT: C 166 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.7416 (mpp80) REVERT: C 317 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.6083 (tt0) REVERT: C 466 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8254 (m) REVERT: C 475 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7934 (tm-30) REVERT: D 37 MET cc_start: 0.8618 (mmm) cc_final: 0.7813 (mmt) REVERT: D 66 PHE cc_start: 0.8063 (m-80) cc_final: 0.7829 (m-80) REVERT: D 95 LYS cc_start: 0.7351 (tmmt) cc_final: 0.6831 (tmmt) REVERT: D 99 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: D 135 ASN cc_start: 0.8537 (m-40) cc_final: 0.8217 (m110) outliers start: 37 outliers final: 19 residues processed: 230 average time/residue: 1.1869 time to fit residues: 303.2823 Evaluate side-chains 222 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 1.689 ------------------------------------------------------------------------------- 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 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 260 MET 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 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 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 19 optimal weight: 0.1980 chunk 162 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 174 optimal weight: 6.9990 chunk 156 optimal weight: 0.7980 chunk 181 optimal weight: 0.0770 chunk 108 optimal weight: 0.9990 chunk 167 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 overall best weight: 0.6142 ------------------------------------------------------------------------------- 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 384 GLN ** 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 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN D 451 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.166903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.126464 restraints weight = 18096.633| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.25 r_work: 0.3363 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15452 Z= 0.108 Angle : 0.521 7.754 20896 Z= 0.271 Chirality : 0.042 0.185 2240 Planarity : 0.004 0.052 2732 Dihedral : 4.227 17.892 2056 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.46 % Favored : 96.49 % Rotamer: Outliers : 2.27 % Allowed : 16.91 % Favored : 80.82 % 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: -0.03 (0.20), residues: 1852 helix: 0.80 (0.21), residues: 692 sheet: -0.86 (0.23), residues: 452 loop : -0.03 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 164 HIS 0.004 0.001 HIS D 451 PHE 0.017 0.001 PHE B 87 TYR 0.019 0.001 TYR A 308 ARG 0.007 0.000 ARG D 459 Details of bonding type rmsd hydrogen bonds : bond 0.03214 ( 678) hydrogen bonds : angle 5.14156 ( 1950) covalent geometry : bond 0.00241 (15452) covalent geometry : angle 0.52084 (20896) *********************** 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 258 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 221 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.8020 (ttp-110) cc_final: 0.7244 (ttp-110) REVERT: A 159 MET cc_start: 0.7822 (tpp) cc_final: 0.7606 (tpp) REVERT: A 258 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8000 (m-30) REVERT: A 398 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7729 (tt0) REVERT: A 470 HIS cc_start: 0.8063 (OUTLIER) cc_final: 0.7842 (m-70) REVERT: B 63 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: B 88 PHE cc_start: 0.8103 (m-80) cc_final: 0.7260 (m-80) REVERT: B 97 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7203 (ttpt) REVERT: B 130 LEU cc_start: 0.8124 (tp) cc_final: 0.7861 (tp) REVERT: B 192 ARG cc_start: 0.8097 (ptt-90) cc_final: 0.7886 (ptt90) REVERT: B 249 TYR cc_start: 0.7585 (t80) cc_final: 0.7071 (t80) REVERT: B 258 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8083 (m-30) REVERT: B 395 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7714 (pt0) REVERT: B 446 CYS cc_start: 0.8355 (m) cc_final: 0.8076 (m) REVERT: B 450 MET cc_start: 0.8481 (ttm) cc_final: 0.8271 (ttm) REVERT: B 497 LYS cc_start: 0.8503 (tptt) cc_final: 0.7779 (mptt) REVERT: C 89 LYS cc_start: 0.8858 (ttpt) cc_final: 0.8373 (mptt) REVERT: C 120 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7525 (ptp90) REVERT: C 130 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7875 (tt) REVERT: C 166 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.7474 (mtp85) REVERT: C 317 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.6063 (tt0) REVERT: C 466 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8167 (m) REVERT: C 475 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7895 (tm-30) REVERT: D 37 MET cc_start: 0.8576 (mmm) cc_final: 0.7835 (mmt) REVERT: D 66 PHE cc_start: 0.7990 (m-80) cc_final: 0.7464 (m-80) REVERT: D 135 ASN cc_start: 0.8426 (m-40) cc_final: 0.8194 (m110) outliers start: 37 outliers final: 10 residues processed: 246 average time/residue: 1.2103 time to fit residues: 330.3193 Evaluate side-chains 222 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 470 HIS 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 97 LYS Chi-restraints excluded: chain B residue 258 ASP 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 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 411 MET 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 112 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 65 optimal weight: 0.0060 chunk 167 optimal weight: 20.0000 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 HIS ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN C 64 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 ASN C 372 GLN C 451 HIS D 451 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.162631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.122262 restraints weight = 17817.827| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.16 r_work: 0.3319 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15452 Z= 0.160 Angle : 0.562 7.317 20896 Z= 0.286 Chirality : 0.044 0.173 2240 Planarity : 0.004 0.052 2732 Dihedral : 4.281 17.870 2056 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.67 % Favored : 96.27 % Rotamer: Outliers : 2.27 % Allowed : 18.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1852 helix: 0.60 (0.20), residues: 720 sheet: -0.87 (0.23), residues: 452 loop : -0.03 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 53 HIS 0.004 0.001 HIS D 451 PHE 0.020 0.001 PHE C 241 TYR 0.018 0.001 TYR A 308 ARG 0.008 0.000 ARG D 459 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 678) hydrogen bonds : angle 5.19744 ( 1950) covalent geometry : bond 0.00383 (15452) covalent geometry : angle 0.56156 (20896) *********************** 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: 37 poor density : 218 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8250 (pt0) REVERT: A 258 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.8065 (t70) REVERT: A 398 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: B 63 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: B 88 PHE cc_start: 0.8107 (m-80) cc_final: 0.7198 (m-80) REVERT: B 130 LEU cc_start: 0.8110 (tp) cc_final: 0.7835 (tp) REVERT: B 192 ARG cc_start: 0.8090 (ptt-90) cc_final: 0.7869 (ptt90) REVERT: B 249 TYR cc_start: 0.7591 (t80) cc_final: 0.7106 (t80) REVERT: B 258 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8018 (m-30) REVERT: B 446 CYS cc_start: 0.8336 (m) cc_final: 0.8022 (m) REVERT: B 497 LYS cc_start: 0.8509 (tptt) cc_final: 0.8112 (tttp) REVERT: C 89 LYS cc_start: 0.8859 (ttpt) cc_final: 0.8371 (mptt) REVERT: C 120 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7797 (ptp90) REVERT: C 130 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7914 (tt) REVERT: C 166 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.7293 (mtp85) REVERT: C 317 GLU cc_start: 0.6250 (OUTLIER) cc_final: 0.5952 (tt0) REVERT: C 466 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8186 (m) REVERT: C 475 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7881 (tm-30) REVERT: D 37 MET cc_start: 0.8541 (mmm) cc_final: 0.7869 (mmt) REVERT: D 66 PHE cc_start: 0.7979 (m-80) cc_final: 0.7421 (m-80) REVERT: D 135 ASN cc_start: 0.8382 (m-40) cc_final: 0.8165 (m110) outliers start: 37 outliers final: 12 residues processed: 244 average time/residue: 1.2588 time to fit residues: 338.8664 Evaluate side-chains 222 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 1.651 ------------------------------------------------------------------------------- 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 258 ASP Chi-restraints excluded: chain A residue 398 GLU 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 40 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 160 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 113 optimal weight: 0.0040 chunk 101 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 164 optimal weight: 0.0270 overall best weight: 2.0056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** C 105 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.164730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.124095 restraints weight = 18022.393| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.21 r_work: 0.3329 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15452 Z= 0.134 Angle : 0.549 7.445 20896 Z= 0.281 Chirality : 0.043 0.187 2240 Planarity : 0.004 0.052 2732 Dihedral : 4.244 18.060 2056 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.89 % Favored : 96.06 % Rotamer: Outliers : 2.33 % Allowed : 18.87 % Favored : 78.80 % 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: -0.02 (0.20), residues: 1852 helix: 0.78 (0.20), residues: 696 sheet: -0.86 (0.23), residues: 452 loop : -0.00 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 53 HIS 0.005 0.001 HIS D 451 PHE 0.021 0.001 PHE C 56 TYR 0.019 0.001 TYR A 308 ARG 0.012 0.000 ARG B 439 Details of bonding type rmsd hydrogen bonds : bond 0.03278 ( 678) hydrogen bonds : angle 5.12611 ( 1950) covalent geometry : bond 0.00317 (15452) covalent geometry : angle 0.54865 (20896) *********************** 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 246 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 208 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8240 (pt0) REVERT: A 120 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7883 (ttp80) REVERT: A 258 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.7980 (m-30) REVERT: A 470 HIS cc_start: 0.8087 (OUTLIER) cc_final: 0.7870 (m-70) REVERT: B 63 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: B 88 PHE cc_start: 0.8132 (m-80) cc_final: 0.7234 (m-80) REVERT: B 130 LEU cc_start: 0.8129 (tp) cc_final: 0.7858 (tp) REVERT: B 249 TYR cc_start: 0.7589 (t80) cc_final: 0.7102 (t80) REVERT: B 258 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8112 (m-30) REVERT: B 280 ASN cc_start: 0.8123 (m-40) cc_final: 0.7858 (m-40) REVERT: B 395 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7740 (pt0) REVERT: B 446 CYS cc_start: 0.8396 (m) cc_final: 0.8115 (m) REVERT: B 497 LYS cc_start: 0.8499 (tptt) cc_final: 0.7749 (mptt) REVERT: C 89 LYS cc_start: 0.8865 (ttpt) cc_final: 0.8393 (mptt) REVERT: C 120 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8136 (ptp90) REVERT: C 130 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7977 (tt) REVERT: C 166 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.7384 (mtp85) REVERT: C 317 GLU cc_start: 0.6346 (OUTLIER) cc_final: 0.6051 (tt0) REVERT: C 379 ASP cc_start: 0.7571 (p0) cc_final: 0.7368 (t0) REVERT: C 466 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8212 (m) REVERT: C 475 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7888 (tm-30) REVERT: D 37 MET cc_start: 0.8611 (mmm) cc_final: 0.8028 (mmt) REVERT: D 66 PHE cc_start: 0.8027 (m-80) cc_final: 0.7478 (m-80) REVERT: D 99 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7597 (mm-30) outliers start: 38 outliers final: 14 residues processed: 237 average time/residue: 1.1954 time to fit residues: 313.9389 Evaluate side-chains 220 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 1.613 ------------------------------------------------------------------------------- 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 258 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 470 HIS 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 395 GLN Chi-restraints excluded: chain B residue 423 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 203 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 115 optimal weight: 0.0370 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.165343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124050 restraints weight = 17831.269| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.25 r_work: 0.3331 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15452 Z= 0.121 Angle : 0.541 8.564 20896 Z= 0.277 Chirality : 0.043 0.178 2240 Planarity : 0.004 0.052 2732 Dihedral : 4.201 19.253 2056 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.78 % Favored : 96.17 % Rotamer: Outliers : 1.96 % Allowed : 19.30 % Favored : 78.74 % 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: 0.00 (0.20), residues: 1852 helix: 0.82 (0.20), residues: 696 sheet: -0.92 (0.22), residues: 472 loop : 0.09 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 53 HIS 0.005 0.001 HIS D 451 PHE 0.021 0.001 PHE C 241 TYR 0.020 0.001 TYR A 308 ARG 0.009 0.000 ARG B 439 Details of bonding type rmsd hydrogen bonds : bond 0.03169 ( 678) hydrogen bonds : angle 5.06402 ( 1950) covalent geometry : bond 0.00284 (15452) covalent geometry : angle 0.54058 (20896) *********************** 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 242 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 1.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8243 (pt0) REVERT: A 258 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.7997 (m-30) REVERT: A 470 HIS cc_start: 0.8050 (OUTLIER) cc_final: 0.7811 (m-70) REVERT: B 63 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: B 88 PHE cc_start: 0.8117 (m-80) cc_final: 0.7246 (m-80) REVERT: B 130 LEU cc_start: 0.8104 (tp) cc_final: 0.7830 (tp) REVERT: B 249 TYR cc_start: 0.7583 (t80) cc_final: 0.7112 (t80) REVERT: B 258 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.8185 (m-30) REVERT: B 280 ASN cc_start: 0.8130 (m-40) cc_final: 0.7869 (m-40) REVERT: B 395 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7772 (pt0) REVERT: B 446 CYS cc_start: 0.8324 (m) cc_final: 0.8041 (m) REVERT: B 497 LYS cc_start: 0.8501 (tptt) cc_final: 0.7768 (mptt) REVERT: C 89 LYS cc_start: 0.8819 (ttpt) cc_final: 0.8362 (mptt) REVERT: C 120 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8107 (ptp90) REVERT: C 130 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7872 (tt) REVERT: C 166 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.7359 (mtp85) REVERT: C 317 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.6046 (tt0) REVERT: C 466 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.8187 (m) REVERT: D 37 MET cc_start: 0.8617 (mmm) cc_final: 0.8005 (mmt) REVERT: D 66 PHE cc_start: 0.7935 (m-80) cc_final: 0.7354 (m-80) REVERT: D 99 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7777 (mm-30) outliers start: 32 outliers final: 15 residues processed: 231 average time/residue: 1.1841 time to fit residues: 304.4958 Evaluate side-chains 222 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 1.786 ------------------------------------------------------------------------------- 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 258 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 470 HIS 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 395 GLN Chi-restraints excluded: chain B residue 423 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 203 LEU Chi-restraints excluded: chain C residue 262 ASN 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 79 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS B 165 ASN B 397 ASN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN D 266 GLN D 451 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.160681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.119751 restraints weight = 17891.809| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.20 r_work: 0.3273 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 15452 Z= 0.246 Angle : 0.652 10.127 20896 Z= 0.328 Chirality : 0.046 0.190 2240 Planarity : 0.005 0.052 2732 Dihedral : 4.567 19.763 2056 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.00 % Favored : 95.95 % Rotamer: Outliers : 2.21 % Allowed : 19.85 % Favored : 77.94 % 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: -0.36 (0.19), residues: 1852 helix: 0.35 (0.19), residues: 736 sheet: -1.02 (0.22), residues: 452 loop : -0.05 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 53 HIS 0.006 0.001 HIS D 451 PHE 0.019 0.002 PHE A 413 TYR 0.018 0.002 TYR A 308 ARG 0.012 0.001 ARG A 175 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 678) hydrogen bonds : angle 5.40690 ( 1950) covalent geometry : bond 0.00597 (15452) covalent geometry : angle 0.65191 (20896) *********************** 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 239 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8224 (pt0) REVERT: A 258 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8161 (t70) REVERT: B 88 PHE cc_start: 0.8175 (m-80) cc_final: 0.7320 (m-80) REVERT: B 130 LEU cc_start: 0.8173 (tp) cc_final: 0.7920 (tp) REVERT: B 249 TYR cc_start: 0.7620 (t80) cc_final: 0.7154 (t80) REVERT: B 258 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8079 (m-30) REVERT: B 280 ASN cc_start: 0.8113 (m-40) cc_final: 0.7825 (m-40) REVERT: B 446 CYS cc_start: 0.8411 (m) cc_final: 0.8044 (m) REVERT: C 89 LYS cc_start: 0.8858 (ttpt) cc_final: 0.8392 (mptt) REVERT: C 120 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8064 (ptp90) REVERT: C 130 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8084 (tt) REVERT: C 166 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.7446 (mpp80) REVERT: C 317 GLU cc_start: 0.6464 (OUTLIER) cc_final: 0.6172 (tt0) REVERT: C 466 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8242 (m) REVERT: C 475 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7825 (tm-30) REVERT: D 37 MET cc_start: 0.8623 (mmm) cc_final: 0.8013 (mmt) REVERT: D 66 PHE cc_start: 0.7962 (m-80) cc_final: 0.7386 (m-80) REVERT: D 99 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7693 (mm-30) outliers start: 36 outliers final: 16 residues processed: 228 average time/residue: 1.1890 time to fit residues: 301.8488 Evaluate side-chains 215 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 1.882 ------------------------------------------------------------------------------- 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 258 ASP 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 423 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 135 ASN 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 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 41 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 81 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS B 395 GLN B 397 ASN ** C 105 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.160447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.119540 restraints weight = 18001.911| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.17 r_work: 0.3267 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15452 Z= 0.245 Angle : 0.652 11.520 20896 Z= 0.330 Chirality : 0.046 0.227 2240 Planarity : 0.005 0.062 2732 Dihedral : 4.676 21.757 2056 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.84 % Allowed : 20.34 % Favored : 77.82 % 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: -0.52 (0.19), residues: 1852 helix: 0.21 (0.19), residues: 728 sheet: -1.08 (0.22), residues: 452 loop : -0.14 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 53 HIS 0.005 0.001 HIS D 451 PHE 0.031 0.002 PHE C 56 TYR 0.019 0.002 TYR A 308 ARG 0.013 0.001 ARG A 175 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 678) hydrogen bonds : angle 5.44041 ( 1950) covalent geometry : bond 0.00595 (15452) covalent geometry : angle 0.65165 (20896) ********************** 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 224 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8240 (pt0) REVERT: A 125 MET cc_start: 0.8714 (mmm) cc_final: 0.8486 (mmm) REVERT: A 258 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8185 (t70) REVERT: B 88 PHE cc_start: 0.8157 (m-80) cc_final: 0.7361 (m-80) REVERT: B 130 LEU cc_start: 0.8188 (tp) cc_final: 0.7967 (tp) REVERT: B 249 TYR cc_start: 0.7607 (t80) cc_final: 0.7121 (t80) REVERT: B 258 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8115 (m-30) REVERT: B 280 ASN cc_start: 0.8100 (m-40) cc_final: 0.7832 (m-40) REVERT: B 446 CYS cc_start: 0.8401 (m) cc_final: 0.8029 (m) REVERT: C 80 ILE cc_start: 0.8512 (mm) cc_final: 0.8293 (mp) REVERT: C 89 LYS cc_start: 0.8851 (ttpt) cc_final: 0.8381 (mptt) REVERT: C 120 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7475 (ptp90) REVERT: C 130 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8046 (tt) REVERT: C 166 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7361 (mpp80) REVERT: C 317 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.6193 (tt0) REVERT: C 466 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8250 (m) REVERT: C 475 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7870 (tm-30) REVERT: D 37 MET cc_start: 0.8620 (mmm) cc_final: 0.7968 (mmt) REVERT: D 66 PHE cc_start: 0.7980 (m-80) cc_final: 0.7374 (m-80) REVERT: D 99 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7677 (mm-30) outliers start: 30 outliers final: 17 residues processed: 219 average time/residue: 1.1669 time to fit residues: 284.7579 Evaluate side-chains 213 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 1.803 ------------------------------------------------------------------------------- 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 258 ASP 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 423 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 C residue 480 ILE Chi-restraints excluded: chain D residue 135 ASN 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 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 130 optimal weight: 0.9990 chunk 153 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 171 optimal weight: 0.0670 chunk 93 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 136 optimal weight: 0.0980 overall best weight: 1.0324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN D 451 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.163012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.124050 restraints weight = 17849.097| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.13 r_work: 0.3341 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15452 Z= 0.117 Angle : 0.557 10.921 20896 Z= 0.285 Chirality : 0.043 0.217 2240 Planarity : 0.004 0.057 2732 Dihedral : 4.382 20.029 2056 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.72 % Allowed : 20.53 % Favored : 77.76 % 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: 0.77 (0.20), residues: 688 sheet: -1.04 (0.22), residues: 472 loop : -0.10 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 53 HIS 0.006 0.001 HIS D 451 PHE 0.036 0.001 PHE C 56 TYR 0.022 0.001 TYR A 308 ARG 0.013 0.000 ARG A 175 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 678) hydrogen bonds : angle 5.12060 ( 1950) covalent geometry : bond 0.00268 (15452) covalent geometry : angle 0.55669 (20896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12208.51 seconds wall clock time: 210 minutes 46.01 seconds (12646.01 seconds total)