Starting phenix.real_space_refine on Thu Mar 13 12:43:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ezm_31389/03_2025/7ezm_31389.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ezm_31389/03_2025/7ezm_31389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ezm_31389/03_2025/7ezm_31389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ezm_31389/03_2025/7ezm_31389.map" model { file = "/net/cci-nas-00/data/ceres_data/7ezm_31389/03_2025/7ezm_31389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ezm_31389/03_2025/7ezm_31389.cif" } resolution = 2.9 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= 0.002 sd= 0.032 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 69 5.16 5 C 5748 2.51 5 N 1524 2.21 5 O 1667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9008 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1850 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2362 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 291} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 44 Chain: "G" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 421 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1736 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "P" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 4.63, per 1000 atoms: 0.51 Number of scatterers: 9008 At special positions: 0 Unit cell: (104.5, 120.175, 121.22, 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 69 16.00 O 1667 8.00 N 1524 7.00 C 5748 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 114 " - pdb=" SG CYS D 196 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.2 seconds 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 40.1% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 6 through 38 Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 212 through 221 removed outlier: 4.595A pdb=" N ILE A 217 " --> pdb=" O ARG A 214 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N HIS A 218 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 246 through 261 Processing helix chain 'A' and resid 262 through 266 removed outlier: 3.550A pdb=" N GLN A 265 " --> pdb=" O PRO A 262 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN A 266 " --> pdb=" O TRP A 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 262 through 266' Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 301 through 315 Processing helix chain 'A' and resid 335 through 356 Processing helix chain 'B' and resid 6 through 26 removed outlier: 4.209A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'D' and resid 39 through 69 Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 74 through 105 Proline residue: D 96 - end of helix Proline residue: D 101 - end of helix Processing helix chain 'D' and resid 110 through 145 Processing helix chain 'D' and resid 147 through 152 Processing helix chain 'D' and resid 154 through 173 Processing helix chain 'D' and resid 174 through 180 removed outlier: 3.595A pdb=" N ILE D 178 " --> pdb=" O THR D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 218 through 248 Processing helix chain 'D' and resid 301 through 339 Proline residue: D 328 - end of helix Processing helix chain 'D' and resid 339 through 348 Processing helix chain 'D' and resid 349 through 371 removed outlier: 4.019A pdb=" N SER D 363 " --> pdb=" O SER D 359 " (cutoff:3.500A) Proline residue: D 367 - end of helix Processing helix chain 'D' and resid 374 through 383 Processing helix chain 'G' and resid 9 through 25 removed outlier: 3.849A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 52 through 56 removed outlier: 4.106A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 196 removed outlier: 6.662A pdb=" N LEU A 40 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL A 204 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU A 42 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER A 225 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE A 226 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE A 272 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE A 228 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN A 274 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL A 230 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.882A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.675A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.354A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.814A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.649A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.827A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 184 through 186 Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.063A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.507A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.93 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2088 1.33 - 1.46: 2829 1.46 - 1.60: 4172 1.60 - 1.73: 1 1.73 - 1.86: 106 Bond restraints: 9196 Sorted by residual: bond pdb=" O1 TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.462 1.636 -0.174 2.00e-02 2.50e+03 7.56e+01 bond pdb=" OH TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.679 1.526 0.153 2.00e-02 2.50e+03 5.81e+01 bond pdb=" CA SER B 281 " pdb=" CB SER B 281 " ideal model delta sigma weight residual 1.532 1.465 0.066 1.78e-02 3.16e+03 1.39e+01 bond pdb=" N VAL A 240 " pdb=" CA VAL A 240 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.60e+00 bond pdb=" N GLY B 41 " pdb=" CA GLY B 41 " ideal model delta sigma weight residual 1.448 1.492 -0.044 1.88e-02 2.83e+03 5.56e+00 ... (remaining 9191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 11457 1.81 - 3.62: 914 3.62 - 5.43: 91 5.43 - 7.24: 18 7.24 - 9.05: 4 Bond angle restraints: 12484 Sorted by residual: angle pdb=" C ARG D 139 " pdb=" CA ARG D 139 " pdb=" CB ARG D 139 " ideal model delta sigma weight residual 110.68 118.72 -8.04 1.70e+00 3.46e-01 2.23e+01 angle pdb=" C ARG D 345 " pdb=" CA ARG D 345 " pdb=" CB ARG D 345 " ideal model delta sigma weight residual 110.88 103.83 7.05 1.57e+00 4.06e-01 2.02e+01 angle pdb=" N VAL A 238 " pdb=" CA VAL A 238 " pdb=" C VAL A 238 " ideal model delta sigma weight residual 109.20 102.41 6.79 1.55e+00 4.16e-01 1.92e+01 angle pdb=" N ALA H 136 " pdb=" CA ALA H 136 " pdb=" C ALA H 136 " ideal model delta sigma weight residual 113.02 107.99 5.03 1.20e+00 6.94e-01 1.75e+01 angle pdb=" CA VAL A 238 " pdb=" C VAL A 238 " pdb=" O VAL A 238 " ideal model delta sigma weight residual 121.92 117.04 4.88 1.17e+00 7.31e-01 1.74e+01 ... (remaining 12479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 4939 16.36 - 32.71: 413 32.71 - 49.06: 76 49.06 - 65.42: 22 65.42 - 81.77: 5 Dihedral angle restraints: 5455 sinusoidal: 2051 harmonic: 3404 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 156.95 -63.95 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 151.59 28.41 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 152.84 27.16 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 5452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1137 0.081 - 0.163: 272 0.163 - 0.244: 23 0.244 - 0.325: 3 0.325 - 0.407: 2 Chirality restraints: 1437 Sorted by residual: chirality pdb=" CA ARG A 210 " pdb=" N ARG A 210 " pdb=" C ARG A 210 " pdb=" CB ARG A 210 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CA ARG D 345 " pdb=" N ARG D 345 " pdb=" C ARG D 345 " pdb=" CB ARG D 345 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CG LEU A 316 " pdb=" CB LEU A 316 " pdb=" CD1 LEU A 316 " pdb=" CD2 LEU A 316 " both_signs ideal model delta sigma weight residual False -2.59 -2.86 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1434 not shown) Planarity restraints: 1576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 313 " 0.048 9.50e-02 1.11e+02 4.23e-02 1.69e+01 pdb=" NE ARG D 313 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG D 313 " 0.070 2.00e-02 2.50e+03 pdb=" NH1 ARG D 313 " -0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG D 313 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 367 " -0.020 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" C PRO D 367 " 0.071 2.00e-02 2.50e+03 pdb=" O PRO D 367 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE D 368 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 202 " -0.006 9.50e-02 1.11e+02 3.17e-02 1.25e+01 pdb=" NE ARG A 202 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 202 " -0.061 2.00e-02 2.50e+03 pdb=" NH1 ARG A 202 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG A 202 " 0.020 2.00e-02 2.50e+03 ... (remaining 1573 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1292 2.76 - 3.30: 9206 3.30 - 3.83: 15416 3.83 - 4.37: 19126 4.37 - 4.90: 32178 Nonbonded interactions: 77218 Sorted by model distance: nonbonded pdb=" OH TYR A 356 " pdb=" OE1 GLN D 153 " model vdw 2.228 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.239 3.040 nonbonded pdb=" O TYR D 360 " pdb=" OG SER D 363 " model vdw 2.247 3.040 nonbonded pdb=" O MET D 72 " pdb=" ND2 ASN D 77 " model vdw 2.248 3.120 nonbonded pdb=" OD1 ASN D 98 " pdb=" OH TYR D 360 " model vdw 2.260 3.040 ... (remaining 77213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.300 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:84.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 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 : 0.011 0.174 9196 Z= 0.684 Angle : 1.074 9.054 12484 Z= 0.645 Chirality : 0.068 0.407 1437 Planarity : 0.009 0.102 1576 Dihedral : 13.160 81.772 3241 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.94 % Allowed : 3.34 % Favored : 95.72 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.78 % 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: -0.87 (0.23), residues: 1150 helix: -0.43 (0.23), residues: 404 sheet: -0.10 (0.30), residues: 278 loop : -0.83 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.008 TRP B 82 HIS 0.019 0.006 HIS D 157 PHE 0.025 0.006 PHE B 241 TYR 0.046 0.009 TYR H 175 ARG 0.071 0.009 ARG D 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 308 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 SER cc_start: 0.7426 (p) cc_final: 0.6994 (p) REVERT: A 9 ASP cc_start: 0.6886 (m-30) cc_final: 0.6420 (m-30) REVERT: A 39 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6529 (mt-10) REVERT: A 237 GLN cc_start: 0.7324 (mt0) cc_final: 0.7086 (mt0) REVERT: A 275 LYS cc_start: 0.7832 (mttt) cc_final: 0.7625 (mttt) REVERT: B 67 SER cc_start: 0.7986 (m) cc_final: 0.7689 (t) REVERT: B 74 SER cc_start: 0.7782 (t) cc_final: 0.7454 (t) REVERT: B 98 SER cc_start: 0.7826 (p) cc_final: 0.7445 (t) REVERT: B 118 ASP cc_start: 0.6246 (p0) cc_final: 0.5987 (p0) REVERT: B 184 THR cc_start: 0.8506 (p) cc_final: 0.8296 (t) REVERT: B 220 GLN cc_start: 0.8247 (mt0) cc_final: 0.7890 (mt0) REVERT: B 221 THR cc_start: 0.7915 (m) cc_final: 0.7714 (t) REVERT: B 277 SER cc_start: 0.8359 (t) cc_final: 0.8149 (t) REVERT: B 334 SER cc_start: 0.7768 (m) cc_final: 0.7554 (p) REVERT: D 76 THR cc_start: 0.7375 (m) cc_final: 0.7143 (m) REVERT: D 111 SER cc_start: 0.8252 (t) cc_final: 0.8007 (p) REVERT: H 141 THR cc_start: 0.7753 (m) cc_final: 0.7420 (p) REVERT: H 180 ARG cc_start: 0.8180 (mtt180) cc_final: 0.7688 (mtt180) outliers start: 9 outliers final: 4 residues processed: 315 average time/residue: 1.0801 time to fit residues: 364.8825 Evaluate side-chains 277 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 273 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain H residue 135 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN D 131 ASN G 18 GLN H 142 GLN H 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.133810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.120146 restraints weight = 12156.226| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.89 r_work: 0.3370 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9196 Z= 0.266 Angle : 0.631 6.782 12484 Z= 0.334 Chirality : 0.045 0.161 1437 Planarity : 0.005 0.041 1576 Dihedral : 6.869 70.680 1271 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.70 % Allowed : 13.67 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.51 (0.25), residues: 1150 helix: 1.32 (0.26), residues: 409 sheet: -0.25 (0.29), residues: 282 loop : -0.01 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 339 HIS 0.006 0.001 HIS B 62 PHE 0.031 0.002 PHE A 55 TYR 0.015 0.002 TYR H 190 ARG 0.008 0.001 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 275 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 SER cc_start: 0.8297 (p) cc_final: 0.8003 (p) REVERT: A 39 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7323 (mt-10) REVERT: A 201 PHE cc_start: 0.8355 (m-80) cc_final: 0.7849 (m-80) REVERT: A 212 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7692 (mt-10) REVERT: A 276 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7460 (ptpp) REVERT: A 290 ASP cc_start: 0.7660 (m-30) cc_final: 0.7435 (m-30) REVERT: B 68 ARG cc_start: 0.8120 (ttt180) cc_final: 0.7743 (ttt180) REVERT: B 98 SER cc_start: 0.7751 (p) cc_final: 0.7390 (t) REVERT: B 170 ASP cc_start: 0.7775 (t70) cc_final: 0.7395 (t0) REVERT: B 186 ASP cc_start: 0.7104 (t0) cc_final: 0.6879 (t0) REVERT: B 214 ARG cc_start: 0.7748 (mtm180) cc_final: 0.7521 (mtm-85) REVERT: B 268 ASN cc_start: 0.7639 (p0) cc_final: 0.7425 (p0) REVERT: B 271 CYS cc_start: 0.7888 (m) cc_final: 0.7539 (p) REVERT: D 126 SER cc_start: 0.8644 (OUTLIER) cc_final: 0.8394 (m) REVERT: D 202 ASN cc_start: 0.7898 (OUTLIER) cc_final: 0.7558 (p0) REVERT: D 308 LYS cc_start: 0.8258 (mmtp) cc_final: 0.8005 (mttm) REVERT: D 344 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7615 (mt-10) REVERT: H 78 THR cc_start: 0.8450 (t) cc_final: 0.7823 (m) REVERT: H 141 THR cc_start: 0.8048 (m) cc_final: 0.7658 (p) REVERT: H 180 ARG cc_start: 0.8402 (mtt180) cc_final: 0.8063 (mtt180) REVERT: P 8 PHE cc_start: 0.8430 (m-10) cc_final: 0.8185 (m-10) outliers start: 45 outliers final: 19 residues processed: 291 average time/residue: 1.0861 time to fit residues: 338.1843 Evaluate side-chains 259 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 20 optimal weight: 0.9980 chunk 102 optimal weight: 0.0870 chunk 46 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 58 optimal weight: 0.0670 chunk 33 optimal weight: 0.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 ASN H 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.136101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.121919 restraints weight = 12261.187| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.95 r_work: 0.3347 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9196 Z= 0.207 Angle : 0.572 7.186 12484 Z= 0.299 Chirality : 0.043 0.148 1437 Planarity : 0.004 0.042 1576 Dihedral : 5.531 70.999 1263 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.91 % Allowed : 16.70 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.74 (0.25), residues: 1150 helix: 1.63 (0.25), residues: 417 sheet: -0.20 (0.29), residues: 280 loop : 0.02 (0.32), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 339 HIS 0.004 0.001 HIS B 62 PHE 0.026 0.002 PHE A 55 TYR 0.016 0.001 TYR D 179 ARG 0.008 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 245 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 SER cc_start: 0.8371 (p) cc_final: 0.8032 (p) REVERT: A 9 ASP cc_start: 0.7975 (m-30) cc_final: 0.7624 (m-30) REVERT: A 39 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7380 (mt-10) REVERT: A 201 PHE cc_start: 0.8405 (m-80) cc_final: 0.7677 (m-80) REVERT: A 212 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7803 (mt-10) REVERT: A 276 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7478 (ptpp) REVERT: A 290 ASP cc_start: 0.7672 (m-30) cc_final: 0.7422 (m-30) REVERT: A 307 GLU cc_start: 0.7981 (tp30) cc_final: 0.7681 (tp30) REVERT: A 326 SER cc_start: 0.8631 (p) cc_final: 0.8419 (t) REVERT: B 33 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7608 (mt) REVERT: B 98 SER cc_start: 0.7888 (p) cc_final: 0.7575 (t) REVERT: B 170 ASP cc_start: 0.7898 (t70) cc_final: 0.7492 (t0) REVERT: B 212 ASP cc_start: 0.7694 (t70) cc_final: 0.7430 (t0) REVERT: B 214 ARG cc_start: 0.7684 (mtm180) cc_final: 0.7460 (mtm180) REVERT: B 227 SER cc_start: 0.8479 (t) cc_final: 0.8125 (t) REVERT: B 268 ASN cc_start: 0.7659 (p0) cc_final: 0.7455 (p0) REVERT: B 271 CYS cc_start: 0.8010 (m) cc_final: 0.7680 (p) REVERT: B 274 THR cc_start: 0.7900 (m) cc_final: 0.7644 (p) REVERT: B 289 TYR cc_start: 0.7480 (m-10) cc_final: 0.7007 (m-80) REVERT: D 126 SER cc_start: 0.8632 (t) cc_final: 0.8398 (m) REVERT: D 202 ASN cc_start: 0.8050 (OUTLIER) cc_final: 0.7753 (p0) REVERT: D 308 LYS cc_start: 0.8217 (mmtp) cc_final: 0.7964 (mttp) REVERT: D 336 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7928 (ttt180) REVERT: D 344 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7617 (mt-10) REVERT: H 63 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8149 (t) REVERT: H 154 SER cc_start: 0.8557 (OUTLIER) cc_final: 0.8338 (p) REVERT: P 8 PHE cc_start: 0.8408 (m-10) cc_final: 0.8187 (m-10) outliers start: 47 outliers final: 23 residues processed: 267 average time/residue: 1.0981 time to fit residues: 314.4274 Evaluate side-chains 279 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 250 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 105 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.128559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.114080 restraints weight = 12090.940| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.93 r_work: 0.3323 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9196 Z= 0.242 Angle : 0.568 6.850 12484 Z= 0.297 Chirality : 0.043 0.159 1437 Planarity : 0.004 0.042 1576 Dihedral : 5.330 70.106 1262 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 5.11 % Allowed : 17.01 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.84 (0.25), residues: 1150 helix: 1.86 (0.25), residues: 409 sheet: -0.23 (0.29), residues: 285 loop : 0.01 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 339 HIS 0.004 0.001 HIS D 210 PHE 0.023 0.002 PHE A 55 TYR 0.016 0.002 TYR D 179 ARG 0.007 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 238 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 6 SER cc_start: 0.8405 (p) cc_final: 0.8034 (p) REVERT: A 9 ASP cc_start: 0.7974 (m-30) cc_final: 0.7636 (m-30) REVERT: A 39 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7372 (mt-10) REVERT: A 201 PHE cc_start: 0.8462 (m-80) cc_final: 0.7848 (m-80) REVERT: A 276 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7567 (ttpp) REVERT: A 290 ASP cc_start: 0.7676 (m-30) cc_final: 0.7358 (m-30) REVERT: A 307 GLU cc_start: 0.8106 (tp30) cc_final: 0.7733 (tp30) REVERT: A 322 LYS cc_start: 0.8035 (ttmt) cc_final: 0.7740 (ttmm) REVERT: A 326 SER cc_start: 0.8641 (p) cc_final: 0.8438 (t) REVERT: A 354 LYS cc_start: 0.8157 (mmmt) cc_final: 0.7883 (mmmt) REVERT: B 98 SER cc_start: 0.7991 (p) cc_final: 0.7621 (t) REVERT: B 170 ASP cc_start: 0.7939 (t70) cc_final: 0.7544 (t0) REVERT: B 212 ASP cc_start: 0.7673 (t70) cc_final: 0.7419 (t0) REVERT: B 271 CYS cc_start: 0.8043 (m) cc_final: 0.7751 (p) REVERT: B 274 THR cc_start: 0.7886 (m) cc_final: 0.7628 (p) REVERT: B 289 TYR cc_start: 0.7625 (m-10) cc_final: 0.7198 (m-80) REVERT: D 74 THR cc_start: 0.8046 (t) cc_final: 0.7626 (p) REVERT: D 75 VAL cc_start: 0.8123 (p) cc_final: 0.7630 (t) REVERT: D 202 ASN cc_start: 0.8106 (p0) cc_final: 0.7888 (p0) REVERT: D 296 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7330 (tp) REVERT: D 336 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7909 (ttt180) REVERT: D 344 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7671 (mt-10) REVERT: H 20 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7644 (pp) REVERT: H 30 SER cc_start: 0.8413 (OUTLIER) cc_final: 0.8185 (t) REVERT: H 63 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8138 (t) outliers start: 49 outliers final: 22 residues processed: 262 average time/residue: 1.2277 time to fit residues: 344.3877 Evaluate side-chains 263 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 235 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 23 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 59 optimal weight: 0.5980 chunk 25 optimal weight: 0.0270 chunk 67 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 112 optimal weight: 0.0770 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 22 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 overall best weight: 0.2934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 GLN D 374 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.135038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.120550 restraints weight = 12090.772| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.95 r_work: 0.3354 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9196 Z= 0.164 Angle : 0.540 9.864 12484 Z= 0.280 Chirality : 0.041 0.143 1437 Planarity : 0.004 0.040 1576 Dihedral : 5.154 71.074 1262 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.76 % Allowed : 19.73 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.87 (0.25), residues: 1150 helix: 1.96 (0.26), residues: 416 sheet: -0.20 (0.29), residues: 291 loop : -0.09 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 339 HIS 0.002 0.001 HIS D 210 PHE 0.023 0.001 PHE A 55 TYR 0.017 0.001 TYR D 179 ARG 0.008 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 6 SER cc_start: 0.8430 (p) cc_final: 0.8197 (p) REVERT: A 9 ASP cc_start: 0.7933 (m-30) cc_final: 0.7658 (m-30) REVERT: A 39 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7314 (mt-10) REVERT: A 201 PHE cc_start: 0.8442 (m-80) cc_final: 0.7664 (m-80) REVERT: A 276 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7510 (ttpp) REVERT: A 290 ASP cc_start: 0.7684 (m-30) cc_final: 0.7357 (m-30) REVERT: A 307 GLU cc_start: 0.8083 (tp30) cc_final: 0.7752 (tp30) REVERT: A 322 LYS cc_start: 0.8035 (ttmt) cc_final: 0.7791 (ttmm) REVERT: B 33 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7661 (mt) REVERT: B 52 ARG cc_start: 0.7968 (ptp90) cc_final: 0.7706 (ptp90) REVERT: B 87 THR cc_start: 0.8270 (m) cc_final: 0.7953 (t) REVERT: B 98 SER cc_start: 0.7871 (p) cc_final: 0.7513 (t) REVERT: B 170 ASP cc_start: 0.7939 (t70) cc_final: 0.7509 (t0) REVERT: B 212 ASP cc_start: 0.7683 (t70) cc_final: 0.7429 (t0) REVERT: B 227 SER cc_start: 0.8536 (m) cc_final: 0.8117 (t) REVERT: B 271 CYS cc_start: 0.8046 (m) cc_final: 0.7823 (p) REVERT: B 289 TYR cc_start: 0.7537 (m-10) cc_final: 0.7231 (m-80) REVERT: D 74 THR cc_start: 0.8070 (t) cc_final: 0.7735 (p) REVERT: D 75 VAL cc_start: 0.8117 (OUTLIER) cc_final: 0.7564 (t) REVERT: D 126 SER cc_start: 0.8604 (t) cc_final: 0.8356 (m) REVERT: D 170 PHE cc_start: 0.6922 (m-10) cc_final: 0.6615 (m-10) REVERT: D 202 ASN cc_start: 0.8122 (p0) cc_final: 0.7870 (p0) REVERT: D 213 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8074 (mp) REVERT: D 296 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.7254 (tp) REVERT: D 323 PHE cc_start: 0.8574 (m-80) cc_final: 0.8198 (m-80) REVERT: D 329 ILE cc_start: 0.8457 (tp) cc_final: 0.8242 (tt) REVERT: D 336 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7860 (ttt180) REVERT: H 67 ARG cc_start: 0.8161 (ttp80) cc_final: 0.7863 (ttp80) outliers start: 36 outliers final: 19 residues processed: 259 average time/residue: 1.3817 time to fit residues: 382.1964 Evaluate side-chains 259 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 234 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 32 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.129515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.115446 restraints weight = 12033.263| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.90 r_work: 0.3346 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9196 Z= 0.255 Angle : 0.562 8.989 12484 Z= 0.293 Chirality : 0.043 0.193 1437 Planarity : 0.004 0.040 1576 Dihedral : 5.180 69.794 1262 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.80 % Allowed : 20.04 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.85 (0.25), residues: 1150 helix: 2.01 (0.26), residues: 411 sheet: -0.25 (0.29), residues: 297 loop : -0.12 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 339 HIS 0.004 0.001 HIS D 210 PHE 0.021 0.002 PHE A 55 TYR 0.015 0.002 TYR D 179 ARG 0.007 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 247 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 6 SER cc_start: 0.8479 (p) cc_final: 0.8241 (p) REVERT: A 9 ASP cc_start: 0.7946 (m-30) cc_final: 0.7690 (m-30) REVERT: A 39 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7298 (mt-10) REVERT: A 201 PHE cc_start: 0.8501 (m-80) cc_final: 0.7710 (m-80) REVERT: A 290 ASP cc_start: 0.7719 (m-30) cc_final: 0.7374 (m-30) REVERT: A 307 GLU cc_start: 0.8050 (tp30) cc_final: 0.7723 (tp30) REVERT: A 322 LYS cc_start: 0.8023 (ttmt) cc_final: 0.7778 (ttmm) REVERT: B 52 ARG cc_start: 0.8090 (ptp90) cc_final: 0.7865 (ptp90) REVERT: B 87 THR cc_start: 0.8244 (m) cc_final: 0.8017 (t) REVERT: B 88 ASN cc_start: 0.8191 (m-40) cc_final: 0.7912 (m110) REVERT: B 98 SER cc_start: 0.8008 (p) cc_final: 0.7668 (t) REVERT: B 212 ASP cc_start: 0.7684 (t70) cc_final: 0.7445 (t0) REVERT: B 271 CYS cc_start: 0.8062 (m) cc_final: 0.7766 (p) REVERT: B 289 TYR cc_start: 0.7701 (m-10) cc_final: 0.7140 (m-80) REVERT: B 312 ASP cc_start: 0.7619 (t0) cc_final: 0.7367 (t70) REVERT: B 327 VAL cc_start: 0.8439 (t) cc_final: 0.8225 (t) REVERT: D 74 THR cc_start: 0.8070 (t) cc_final: 0.7701 (p) REVERT: D 75 VAL cc_start: 0.8200 (p) cc_final: 0.7744 (t) REVERT: D 126 SER cc_start: 0.8620 (t) cc_final: 0.8376 (m) REVERT: D 202 ASN cc_start: 0.8167 (p0) cc_final: 0.7949 (p0) REVERT: D 213 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8063 (mp) REVERT: D 296 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7267 (tp) REVERT: D 323 PHE cc_start: 0.8571 (m-80) cc_final: 0.8155 (m-80) REVERT: D 329 ILE cc_start: 0.8449 (tp) cc_final: 0.8238 (tt) REVERT: D 336 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7917 (ttt180) REVERT: H 30 SER cc_start: 0.8415 (OUTLIER) cc_final: 0.8200 (t) REVERT: H 67 ARG cc_start: 0.8212 (ttp80) cc_final: 0.7746 (ttp80) REVERT: H 199 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8108 (m) REVERT: H 215 THR cc_start: 0.8262 (p) cc_final: 0.8057 (p) REVERT: P 8 PHE cc_start: 0.8523 (m-10) cc_final: 0.8264 (m-10) outliers start: 46 outliers final: 24 residues processed: 271 average time/residue: 1.1533 time to fit residues: 334.9340 Evaluate side-chains 271 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 242 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 241 LYS Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 199 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 56 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 16 optimal weight: 0.0060 chunk 32 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.135351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.121382 restraints weight = 12237.324| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.93 r_work: 0.3326 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9196 Z= 0.224 Angle : 0.558 8.556 12484 Z= 0.288 Chirality : 0.043 0.168 1437 Planarity : 0.004 0.040 1576 Dihedral : 5.178 69.820 1262 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.76 % Allowed : 21.19 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.88 (0.25), residues: 1150 helix: 2.01 (0.25), residues: 411 sheet: -0.20 (0.29), residues: 287 loop : -0.12 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.003 0.001 HIS D 210 PHE 0.025 0.001 PHE A 55 TYR 0.018 0.001 TYR D 179 ARG 0.007 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 6 SER cc_start: 0.8481 (p) cc_final: 0.8190 (p) REVERT: A 9 ASP cc_start: 0.7951 (m-30) cc_final: 0.7665 (m-30) REVERT: A 10 LYS cc_start: 0.8451 (mtmm) cc_final: 0.8170 (mtmm) REVERT: A 39 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7183 (mt-10) REVERT: A 201 PHE cc_start: 0.8531 (m-80) cc_final: 0.7648 (m-80) REVERT: A 290 ASP cc_start: 0.7729 (m-30) cc_final: 0.7394 (m-30) REVERT: A 307 GLU cc_start: 0.8035 (tp30) cc_final: 0.7715 (tp30) REVERT: A 322 LYS cc_start: 0.8067 (ttmt) cc_final: 0.7822 (ttmm) REVERT: B 52 ARG cc_start: 0.8060 (ptp90) cc_final: 0.7789 (ptp90) REVERT: B 87 THR cc_start: 0.8254 (m) cc_final: 0.8033 (t) REVERT: B 88 ASN cc_start: 0.8187 (m-40) cc_final: 0.7934 (m110) REVERT: B 98 SER cc_start: 0.8124 (p) cc_final: 0.7785 (t) REVERT: B 212 ASP cc_start: 0.7682 (t70) cc_final: 0.7415 (t0) REVERT: B 227 SER cc_start: 0.8565 (m) cc_final: 0.8028 (t) REVERT: B 271 CYS cc_start: 0.8040 (m) cc_final: 0.7770 (p) REVERT: B 289 TYR cc_start: 0.7659 (m-10) cc_final: 0.7156 (m-80) REVERT: B 327 VAL cc_start: 0.8364 (t) cc_final: 0.8146 (t) REVERT: D 74 THR cc_start: 0.8028 (t) cc_final: 0.7746 (p) REVERT: D 75 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7724 (t) REVERT: D 213 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8060 (mp) REVERT: D 296 ILE cc_start: 0.7497 (OUTLIER) cc_final: 0.7256 (tp) REVERT: D 323 PHE cc_start: 0.8601 (m-80) cc_final: 0.8139 (m-80) REVERT: D 329 ILE cc_start: 0.8442 (tp) cc_final: 0.8225 (tt) REVERT: D 336 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7885 (ttt180) REVERT: H 30 SER cc_start: 0.8423 (OUTLIER) cc_final: 0.8211 (t) REVERT: H 67 ARG cc_start: 0.8188 (ttp80) cc_final: 0.7705 (ttp80) REVERT: H 215 THR cc_start: 0.8277 (p) cc_final: 0.8046 (p) REVERT: P 8 PHE cc_start: 0.8533 (m-10) cc_final: 0.8281 (m-10) outliers start: 36 outliers final: 25 residues processed: 262 average time/residue: 1.1349 time to fit residues: 317.6535 Evaluate side-chains 266 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 236 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 241 LYS Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 199 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 58 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.133787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.119944 restraints weight = 12247.317| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.91 r_work: 0.3338 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9196 Z= 0.258 Angle : 0.581 9.286 12484 Z= 0.296 Chirality : 0.044 0.210 1437 Planarity : 0.004 0.040 1576 Dihedral : 5.219 69.658 1262 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.28 % Allowed : 20.67 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.83 (0.25), residues: 1150 helix: 1.97 (0.25), residues: 411 sheet: -0.23 (0.29), residues: 287 loop : -0.13 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.004 0.001 HIS D 210 PHE 0.026 0.002 PHE A 55 TYR 0.017 0.002 TYR D 179 ARG 0.008 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 244 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 6 SER cc_start: 0.8502 (p) cc_final: 0.8270 (p) REVERT: A 9 ASP cc_start: 0.7979 (m-30) cc_final: 0.7732 (m-30) REVERT: A 39 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7241 (mt-10) REVERT: A 194 PHE cc_start: 0.7636 (m-80) cc_final: 0.7429 (m-10) REVERT: A 201 PHE cc_start: 0.8549 (m-80) cc_final: 0.7636 (m-80) REVERT: A 290 ASP cc_start: 0.7750 (m-30) cc_final: 0.7424 (m-30) REVERT: A 294 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7555 (mm-30) REVERT: A 307 GLU cc_start: 0.8040 (tp30) cc_final: 0.7723 (tp30) REVERT: A 322 LYS cc_start: 0.8034 (ttmt) cc_final: 0.7749 (ttmm) REVERT: B 52 ARG cc_start: 0.8130 (ptp90) cc_final: 0.7847 (ptp90) REVERT: B 87 THR cc_start: 0.8259 (m) cc_final: 0.8040 (t) REVERT: B 88 ASN cc_start: 0.8213 (m-40) cc_final: 0.7929 (m110) REVERT: B 98 SER cc_start: 0.8168 (p) cc_final: 0.7843 (t) REVERT: B 212 ASP cc_start: 0.7683 (t70) cc_final: 0.7432 (t0) REVERT: B 227 SER cc_start: 0.8594 (m) cc_final: 0.8071 (t) REVERT: B 271 CYS cc_start: 0.8056 (m) cc_final: 0.7769 (p) REVERT: B 289 TYR cc_start: 0.7728 (m-10) cc_final: 0.7312 (m-80) REVERT: B 327 VAL cc_start: 0.8410 (t) cc_final: 0.8192 (t) REVERT: D 74 THR cc_start: 0.8050 (t) cc_final: 0.7766 (p) REVERT: D 75 VAL cc_start: 0.8265 (OUTLIER) cc_final: 0.7832 (t) REVERT: D 213 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8076 (mp) REVERT: D 296 ILE cc_start: 0.7486 (OUTLIER) cc_final: 0.7246 (tp) REVERT: D 323 PHE cc_start: 0.8598 (m-80) cc_final: 0.8151 (m-80) REVERT: D 329 ILE cc_start: 0.8437 (tp) cc_final: 0.8223 (tt) REVERT: D 336 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7968 (ttt180) REVERT: H 30 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.8206 (t) REVERT: H 67 ARG cc_start: 0.8198 (ttp80) cc_final: 0.7720 (ttp80) REVERT: H 215 THR cc_start: 0.8262 (p) cc_final: 0.8048 (p) outliers start: 41 outliers final: 29 residues processed: 264 average time/residue: 1.1056 time to fit residues: 312.3541 Evaluate side-chains 276 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 242 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 241 LYS Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 199 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 22 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 19 optimal weight: 0.0000 chunk 31 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 16 optimal weight: 0.0000 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 ASN D 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.129334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.115316 restraints weight = 12094.879| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.89 r_work: 0.3341 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9196 Z= 0.243 Angle : 0.590 11.921 12484 Z= 0.300 Chirality : 0.044 0.211 1437 Planarity : 0.004 0.040 1576 Dihedral : 5.193 69.943 1262 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.97 % Allowed : 21.40 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.81 (0.25), residues: 1150 helix: 1.94 (0.25), residues: 410 sheet: -0.28 (0.30), residues: 288 loop : -0.10 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.004 0.001 HIS D 210 PHE 0.018 0.002 PHE A 339 TYR 0.017 0.002 TYR D 179 ARG 0.008 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 243 time to evaluate : 2.161 Fit side-chains revert: symmetry clash REVERT: A 6 SER cc_start: 0.8522 (p) cc_final: 0.8241 (p) REVERT: A 9 ASP cc_start: 0.7903 (m-30) cc_final: 0.7622 (m-30) REVERT: A 10 LYS cc_start: 0.8458 (mtmm) cc_final: 0.8181 (mtmm) REVERT: A 201 PHE cc_start: 0.8516 (m-80) cc_final: 0.7668 (m-80) REVERT: A 290 ASP cc_start: 0.7726 (m-30) cc_final: 0.7400 (m-30) REVERT: A 307 GLU cc_start: 0.8035 (tp30) cc_final: 0.7718 (tp30) REVERT: A 322 LYS cc_start: 0.8081 (ttmt) cc_final: 0.7812 (ttmm) REVERT: B 52 ARG cc_start: 0.8104 (ptp90) cc_final: 0.7893 (ptp90) REVERT: B 88 ASN cc_start: 0.8200 (m-40) cc_final: 0.7935 (m110) REVERT: B 98 SER cc_start: 0.8172 (p) cc_final: 0.7841 (t) REVERT: B 212 ASP cc_start: 0.7704 (t70) cc_final: 0.7438 (t0) REVERT: B 221 THR cc_start: 0.8259 (t) cc_final: 0.8053 (m) REVERT: B 227 SER cc_start: 0.8489 (m) cc_final: 0.8127 (t) REVERT: B 228 ASP cc_start: 0.7956 (p0) cc_final: 0.7608 (p0) REVERT: B 271 CYS cc_start: 0.8037 (m) cc_final: 0.7773 (p) REVERT: B 289 TYR cc_start: 0.7706 (m-10) cc_final: 0.7220 (m-80) REVERT: D 74 THR cc_start: 0.8036 (t) cc_final: 0.7750 (p) REVERT: D 75 VAL cc_start: 0.8265 (OUTLIER) cc_final: 0.7828 (t) REVERT: D 115 LYS cc_start: 0.8458 (mmmt) cc_final: 0.7629 (mmpt) REVERT: D 296 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.7204 (tp) REVERT: D 323 PHE cc_start: 0.8614 (m-80) cc_final: 0.8108 (m-80) REVERT: D 329 ILE cc_start: 0.8433 (tp) cc_final: 0.8217 (tt) REVERT: D 336 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7943 (ttt180) REVERT: H 30 SER cc_start: 0.8391 (OUTLIER) cc_final: 0.8174 (t) REVERT: H 67 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7775 (ttp80) REVERT: H 215 THR cc_start: 0.8240 (p) cc_final: 0.8029 (p) outliers start: 38 outliers final: 26 residues processed: 264 average time/residue: 1.1280 time to fit residues: 318.8578 Evaluate side-chains 272 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 242 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 241 LYS Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 12 optimal weight: 0.0030 chunk 53 optimal weight: 0.8980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.129136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115096 restraints weight = 12183.869| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.90 r_work: 0.3335 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9196 Z= 0.226 Angle : 0.595 10.688 12484 Z= 0.301 Chirality : 0.044 0.215 1437 Planarity : 0.004 0.040 1576 Dihedral : 5.143 70.248 1262 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.34 % Allowed : 22.34 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.81 (0.25), residues: 1150 helix: 1.96 (0.26), residues: 410 sheet: -0.20 (0.30), residues: 279 loop : -0.18 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.003 0.001 HIS D 210 PHE 0.019 0.002 PHE A 339 TYR 0.016 0.002 TYR D 179 ARG 0.008 0.001 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 252 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 6 SER cc_start: 0.8522 (p) cc_final: 0.8250 (p) REVERT: A 9 ASP cc_start: 0.7888 (m-30) cc_final: 0.7633 (m-30) REVERT: A 10 LYS cc_start: 0.8390 (mtmm) cc_final: 0.8140 (mtmm) REVERT: A 39 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7237 (mt-10) REVERT: A 201 PHE cc_start: 0.8498 (m-80) cc_final: 0.7669 (m-80) REVERT: A 290 ASP cc_start: 0.7725 (m-30) cc_final: 0.7396 (m-30) REVERT: A 307 GLU cc_start: 0.7991 (tp30) cc_final: 0.7663 (tp30) REVERT: A 322 LYS cc_start: 0.8060 (ttmt) cc_final: 0.7782 (ttmp) REVERT: B 52 ARG cc_start: 0.8074 (ptp90) cc_final: 0.7790 (ptp90) REVERT: B 98 SER cc_start: 0.8192 (p) cc_final: 0.7865 (t) REVERT: B 212 ASP cc_start: 0.7688 (t70) cc_final: 0.7425 (t0) REVERT: B 221 THR cc_start: 0.8251 (t) cc_final: 0.8046 (m) REVERT: B 227 SER cc_start: 0.8558 (m) cc_final: 0.8037 (t) REVERT: B 271 CYS cc_start: 0.8050 (m) cc_final: 0.7763 (p) REVERT: B 289 TYR cc_start: 0.7688 (m-10) cc_final: 0.7224 (m-80) REVERT: D 74 THR cc_start: 0.8047 (t) cc_final: 0.7771 (p) REVERT: D 75 VAL cc_start: 0.8214 (OUTLIER) cc_final: 0.7781 (t) REVERT: D 115 LYS cc_start: 0.8469 (mmmt) cc_final: 0.7671 (mmpt) REVERT: D 126 SER cc_start: 0.8636 (t) cc_final: 0.8418 (m) REVERT: D 296 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7251 (tp) REVERT: D 323 PHE cc_start: 0.8591 (m-80) cc_final: 0.8144 (m-80) REVERT: D 329 ILE cc_start: 0.8419 (tp) cc_final: 0.8204 (tt) REVERT: D 336 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7945 (ttt180) REVERT: H 30 SER cc_start: 0.8386 (OUTLIER) cc_final: 0.8170 (t) REVERT: H 67 ARG cc_start: 0.8248 (ttp80) cc_final: 0.7937 (ttp80) REVERT: H 199 VAL cc_start: 0.8386 (OUTLIER) cc_final: 0.8104 (m) REVERT: H 215 THR cc_start: 0.8248 (p) cc_final: 0.8033 (p) outliers start: 32 outliers final: 22 residues processed: 264 average time/residue: 1.1270 time to fit residues: 319.0411 Evaluate side-chains 271 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 244 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 241 LYS Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 199 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 9 optimal weight: 0.8980 chunk 57 optimal weight: 0.0980 chunk 86 optimal weight: 0.7980 chunk 65 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.134820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.120701 restraints weight = 12192.219| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.92 r_work: 0.3361 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9196 Z= 0.196 Angle : 0.578 10.323 12484 Z= 0.293 Chirality : 0.043 0.197 1437 Planarity : 0.004 0.041 1576 Dihedral : 5.018 69.924 1262 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.82 % Allowed : 23.59 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.86 (0.26), residues: 1150 helix: 1.99 (0.26), residues: 410 sheet: -0.20 (0.30), residues: 284 loop : -0.13 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.003 0.001 HIS H 35 PHE 0.019 0.002 PHE A 339 TYR 0.016 0.001 TYR D 179 ARG 0.008 0.001 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8362.55 seconds wall clock time: 145 minutes 14.49 seconds (8714.49 seconds total)