Starting phenix.real_space_refine on Sat Jun 7 19:22:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j31_61104/06_2025/9j31_61104.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j31_61104/06_2025/9j31_61104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j31_61104/06_2025/9j31_61104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j31_61104/06_2025/9j31_61104.map" model { file = "/net/cci-nas-00/data/ceres_data/9j31_61104/06_2025/9j31_61104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j31_61104/06_2025/9j31_61104.cif" } resolution = 3.05 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= -0.001 sd= 0.090 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 59 5.16 5 C 5713 2.51 5 N 1556 2.21 5 O 1666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8994 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "D" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1764 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1938 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "R" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2232 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 11, 'TRANS': 268} Chain breaks: 2 Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Time building chain proxies: 5.44, per 1000 atoms: 0.60 Number of scatterers: 8994 At special positions: 0 Unit cell: (84.63, 119.97, 126.48, 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 59 16.00 O 1666 8.00 N 1556 7.00 C 5713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 134 " distance=2.04 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " distance=2.03 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: 2.22 Conformation dependent library (CDL) restraints added in 997.8 milliseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2134 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 38.8% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'D' and resid 91 through 94 removed outlier: 3.800A pdb=" N GLY D 94 " --> pdb=" O SER D 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 91 through 94' Processing helix chain 'D' and resid 100 through 103 removed outlier: 3.860A pdb=" N LYS D 103 " --> pdb=" O ASP D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 103' Processing helix chain 'D' and resid 125 through 129 removed outlier: 3.827A pdb=" N THR D 129 " --> pdb=" O SER D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 removed outlier: 3.725A pdb=" N VAL D 262 " --> pdb=" O ALA D 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.731A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.974A pdb=" N GLN A 229 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN A 232 " --> pdb=" O GLN A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 290 through 295 removed outlier: 4.051A pdb=" N TYR A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 336 removed outlier: 3.849A pdb=" N ILE A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 374 Processing helix chain 'R' and resid 23 through 28 Processing helix chain 'R' and resid 29 through 56 removed outlier: 3.684A pdb=" N ILE R 33 " --> pdb=" O PRO R 29 " (cutoff:3.500A) Proline residue: R 41 - end of helix Processing helix chain 'R' and resid 59 through 88 removed outlier: 3.868A pdb=" N TYR R 63 " --> pdb=" O GLU R 59 " (cutoff:3.500A) Proline residue: R 79 - end of helix Processing helix chain 'R' and resid 100 through 129 removed outlier: 3.607A pdb=" N ILE R 104 " --> pdb=" O LEU R 100 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR R 107 " --> pdb=" O PHE R 103 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE R 113 " --> pdb=" O ILE R 109 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE R 119 " --> pdb=" O PHE R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 157 Processing helix chain 'R' and resid 183 through 196 Processing helix chain 'R' and resid 198 through 218 Processing helix chain 'R' and resid 223 through 245 Processing helix chain 'R' and resid 245 through 262 removed outlier: 3.506A pdb=" N HIS R 249 " --> pdb=" O PHE R 245 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE R 261 " --> pdb=" O VAL R 257 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN R 262 " --> pdb=" O LEU R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 271 removed outlier: 3.592A pdb=" N ASN R 271 " --> pdb=" O GLY R 268 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 284 removed outlier: 3.537A pdb=" N ALA R 281 " --> pdb=" O HIS R 277 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER R 284 " --> pdb=" O LEU R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 294 removed outlier: 3.946A pdb=" N VAL R 288 " --> pdb=" O SER R 284 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing helix chain 'R' and resid 298 through 315 Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.583A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.381A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.629A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.995A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.582A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.690A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.901A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.510A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 41 through 45 removed outlier: 3.559A pdb=" N PHE D 118 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER D 109 " --> pdb=" O PHE D 118 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 48 through 50 removed outlier: 5.976A pdb=" N ARG D 76 " --> pdb=" O TRP D 85 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N TRP D 85 " --> pdb=" O ARG D 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 194 through 197 Processing sheet with id=AB2, first strand: chain 'D' and resid 223 through 227 removed outlier: 6.503A pdb=" N TRP D 214 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 57 through 58 removed outlier: 4.189A pdb=" N VAL A 217 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLY A 40 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 236 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE A 237 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N PHE A 273 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE A 239 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASN A 275 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL A 241 " --> pdb=" O ASN A 275 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1293 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: 2.97 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2934 1.34 - 1.46: 2176 1.46 - 1.58: 3994 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 9188 Sorted by residual: bond pdb=" C LEU R 78 " pdb=" N PRO R 79 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.28e-02 6.10e+03 3.06e+00 bond pdb=" CG LYS B 301 " pdb=" CD LYS B 301 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.33e+00 bond pdb=" CB LYS B 301 " pdb=" CG LYS B 301 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.16e+00 bond pdb=" CB PRO G 53 " pdb=" CG PRO G 53 " ideal model delta sigma weight residual 1.492 1.562 -0.070 5.00e-02 4.00e+02 1.94e+00 bond pdb=" CA MET R 182 " pdb=" C MET R 182 " ideal model delta sigma weight residual 1.521 1.536 -0.015 1.14e-02 7.69e+03 1.65e+00 ... (remaining 9183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 12236 2.18 - 4.36: 189 4.36 - 6.55: 19 6.55 - 8.73: 2 8.73 - 10.91: 3 Bond angle restraints: 12449 Sorted by residual: angle pdb=" CB LYS B 301 " pdb=" CG LYS B 301 " pdb=" CD LYS B 301 " ideal model delta sigma weight residual 111.30 121.49 -10.19 2.30e+00 1.89e-01 1.96e+01 angle pdb=" CB MET D 131 " pdb=" CG MET D 131 " pdb=" SD MET D 131 " ideal model delta sigma weight residual 112.70 123.61 -10.91 3.00e+00 1.11e-01 1.32e+01 angle pdb=" N ASN R 22 " pdb=" CA ASN R 22 " pdb=" C ASN R 22 " ideal model delta sigma weight residual 114.75 110.43 4.32 1.26e+00 6.30e-01 1.18e+01 angle pdb=" N MET R 182 " pdb=" CA MET R 182 " pdb=" C MET R 182 " ideal model delta sigma weight residual 114.16 109.18 4.98 1.48e+00 4.57e-01 1.13e+01 angle pdb=" N PHE R 162 " pdb=" CA PHE R 162 " pdb=" C PHE R 162 " ideal model delta sigma weight residual 112.72 108.89 3.83 1.28e+00 6.10e-01 8.94e+00 ... (remaining 12444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 4535 16.91 - 33.82: 690 33.82 - 50.72: 181 50.72 - 67.63: 25 67.63 - 84.54: 14 Dihedral angle restraints: 5445 sinusoidal: 2130 harmonic: 3315 Sorted by residual: dihedral pdb=" CB CYS R 98 " pdb=" SG CYS R 98 " pdb=" SG CYS R 176 " pdb=" CB CYS R 176 " ideal model delta sinusoidal sigma weight residual 93.00 161.18 -68.18 1 1.00e+01 1.00e-02 6.03e+01 dihedral pdb=" CB CYS D 60 " pdb=" SG CYS D 60 " pdb=" SG CYS D 134 " pdb=" CB CYS D 134 " ideal model delta sinusoidal sigma weight residual 93.00 34.99 58.01 1 1.00e+01 1.00e-02 4.51e+01 dihedral pdb=" CA GLN R 28 " pdb=" C GLN R 28 " pdb=" N PRO R 29 " pdb=" CA PRO R 29 " ideal model delta harmonic sigma weight residual 180.00 158.28 21.72 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 5442 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 910 0.036 - 0.071: 343 0.071 - 0.107: 102 0.107 - 0.142: 35 0.142 - 0.178: 2 Chirality restraints: 1392 Sorted by residual: chirality pdb=" CB THR R 279 " pdb=" CA THR R 279 " pdb=" OG1 THR R 279 " pdb=" CG2 THR R 279 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA MET B 188 " pdb=" N MET B 188 " pdb=" C MET B 188 " pdb=" CB MET B 188 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 1389 not shown) Planarity restraints: 1587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN R 28 " 0.065 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO R 29 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO R 29 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO R 29 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " -0.065 5.00e-02 4.00e+02 9.74e-02 1.52e+01 pdb=" N PRO G 53 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 215 " 0.011 2.00e-02 2.50e+03 1.88e-02 6.18e+00 pdb=" CG PHE A 215 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 215 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 215 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 215 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE A 215 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 215 " 0.008 2.00e-02 2.50e+03 ... (remaining 1584 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 186 2.67 - 3.23: 8673 3.23 - 3.78: 14477 3.78 - 4.34: 19490 4.34 - 4.90: 32407 Nonbonded interactions: 75233 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.110 3.040 nonbonded pdb=" O LEU R 38 " pdb=" OG1 THR R 42 " model vdw 2.157 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.159 3.040 nonbonded pdb=" O GLU R 153 " pdb=" ND2 ASN R 157 " model vdw 2.221 3.120 nonbonded pdb=" OD1 ASP D 261 " pdb=" OH TYR D 265 " model vdw 2.223 3.040 ... (remaining 75228 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: 1.260 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: 0.080 Process input model: 23.500 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9190 Z= 0.148 Angle : 0.658 10.910 12453 Z= 0.363 Chirality : 0.042 0.178 1392 Planarity : 0.006 0.100 1587 Dihedral : 17.216 84.539 3305 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.21 % Allowed : 28.40 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.26), residues: 1126 helix: 1.41 (0.26), residues: 392 sheet: 0.24 (0.32), residues: 263 loop : -0.68 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 81 HIS 0.005 0.001 HIS R 249 PHE 0.036 0.002 PHE A 215 TYR 0.018 0.002 TYR D 141 ARG 0.007 0.001 ARG A 266 Details of bonding type rmsd hydrogen bonds : bond 0.14020 ( 459) hydrogen bonds : angle 6.15942 ( 1293) SS BOND : bond 0.00509 ( 2) SS BOND : angle 0.65166 ( 4) covalent geometry : bond 0.00322 ( 9188) covalent geometry : angle 0.65841 (12449) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 187 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7023 (mtp-110) cc_final: 0.6742 (mtp180) REVERT: B 127 LYS cc_start: 0.8352 (mttp) cc_final: 0.8060 (mttp) REVERT: B 129 ARG cc_start: 0.7617 (ttt90) cc_final: 0.7293 (mmm160) REVERT: B 212 ASP cc_start: 0.7382 (p0) cc_final: 0.7068 (p0) REVERT: B 259 GLN cc_start: 0.6902 (mt0) cc_final: 0.6518 (mp10) REVERT: D 121 MET cc_start: 0.7100 (mtm) cc_final: 0.6846 (mtm) REVERT: D 228 TYR cc_start: 0.7875 (p90) cc_final: 0.7476 (p90) REVERT: A 213 HIS cc_start: 0.7121 (t-170) cc_final: 0.6880 (t-170) REVERT: A 257 LYS cc_start: 0.7050 (tttt) cc_final: 0.6476 (ttmt) REVERT: A 276 LYS cc_start: 0.7980 (mttm) cc_final: 0.7691 (mttt) REVERT: A 327 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7001 (mm-30) REVERT: A 339 ARG cc_start: 0.7481 (mtm180) cc_final: 0.7174 (mmp-170) REVERT: A 374 TYR cc_start: 0.8420 (m-80) cc_final: 0.8127 (m-80) REVERT: R 196 LEU cc_start: 0.8348 (mt) cc_final: 0.8132 (mt) REVERT: R 205 MET cc_start: 0.8267 (ttm) cc_final: 0.7978 (ttt) REVERT: G 26 ASP cc_start: 0.8390 (m-30) cc_final: 0.7842 (p0) outliers start: 2 outliers final: 0 residues processed: 188 average time/residue: 0.2260 time to fit residues: 57.4910 Evaluate side-chains 141 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 40.0000 chunk 29 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 0.0060 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 GLN A 206 GLN R 53 GLN R 66 ASN R 219 ASN ** R 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.191605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.153760 restraints weight = 9575.478| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.21 r_work: 0.3341 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9190 Z= 0.152 Angle : 0.582 6.169 12453 Z= 0.308 Chirality : 0.044 0.148 1392 Planarity : 0.005 0.068 1587 Dihedral : 4.404 24.851 1250 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.53 % Favored : 95.38 % Rotamer: Outliers : 3.81 % Allowed : 25.31 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.63 (0.26), residues: 1126 helix: 1.69 (0.26), residues: 399 sheet: 0.40 (0.32), residues: 259 loop : -0.64 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.007 0.001 HIS R 249 PHE 0.018 0.002 PHE R 105 TYR 0.019 0.002 TYR A 322 ARG 0.004 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03684 ( 459) hydrogen bonds : angle 4.86437 ( 1293) SS BOND : bond 0.00348 ( 2) SS BOND : angle 0.58381 ( 4) covalent geometry : bond 0.00348 ( 9188) covalent geometry : angle 0.58202 (12449) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7788 (mtp-110) cc_final: 0.7378 (mmm160) REVERT: B 74 SER cc_start: 0.8553 (p) cc_final: 0.8301 (p) REVERT: B 127 LYS cc_start: 0.8861 (mttp) cc_final: 0.8615 (mttp) REVERT: B 129 ARG cc_start: 0.7988 (ttt90) cc_final: 0.7718 (mmm160) REVERT: B 212 ASP cc_start: 0.8091 (p0) cc_final: 0.7714 (p0) REVERT: B 259 GLN cc_start: 0.7754 (mt0) cc_final: 0.7430 (mp10) REVERT: D 121 MET cc_start: 0.7572 (mtm) cc_final: 0.7220 (mtm) REVERT: D 228 TYR cc_start: 0.8169 (p90) cc_final: 0.7907 (p90) REVERT: A 257 LYS cc_start: 0.8223 (tttt) cc_final: 0.7719 (ttmt) REVERT: R 196 LEU cc_start: 0.8502 (mt) cc_final: 0.8278 (mt) REVERT: R 205 MET cc_start: 0.8345 (ttm) cc_final: 0.8105 (ttm) outliers start: 37 outliers final: 23 residues processed: 173 average time/residue: 0.2287 time to fit residues: 54.3065 Evaluate side-chains 150 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain R residue 88 HIS Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.9980 chunk 56 optimal weight: 0.0870 chunk 9 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 1 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.195573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.138013 restraints weight = 9660.464| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.14 r_work: 0.3241 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9190 Z= 0.124 Angle : 0.525 5.846 12453 Z= 0.280 Chirality : 0.042 0.136 1392 Planarity : 0.004 0.060 1587 Dihedral : 4.241 24.112 1250 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.98 % Allowed : 26.13 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.26), residues: 1126 helix: 1.84 (0.26), residues: 400 sheet: 0.38 (0.32), residues: 259 loop : -0.60 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.006 0.001 HIS R 249 PHE 0.016 0.001 PHE R 105 TYR 0.016 0.002 TYR A 322 ARG 0.002 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 459) hydrogen bonds : angle 4.63876 ( 1293) SS BOND : bond 0.00401 ( 2) SS BOND : angle 0.73910 ( 4) covalent geometry : bond 0.00281 ( 9188) covalent geometry : angle 0.52453 (12449) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7702 (mtp-110) cc_final: 0.7214 (mmm160) REVERT: B 96 ARG cc_start: 0.8391 (mmm-85) cc_final: 0.8021 (mpt180) REVERT: B 127 LYS cc_start: 0.8898 (mttp) cc_final: 0.8566 (mttp) REVERT: B 129 ARG cc_start: 0.7937 (ttt90) cc_final: 0.7611 (mmm160) REVERT: B 212 ASP cc_start: 0.8002 (p0) cc_final: 0.7550 (p0) REVERT: B 259 GLN cc_start: 0.7765 (mt0) cc_final: 0.7156 (mp10) REVERT: D 228 TYR cc_start: 0.8027 (p90) cc_final: 0.7765 (p90) REVERT: A 25 LYS cc_start: 0.8524 (mptt) cc_final: 0.7977 (mtmt) REVERT: A 202 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6688 (tp30) REVERT: A 263 ARG cc_start: 0.8340 (ttp-110) cc_final: 0.7657 (ttp-110) REVERT: A 361 ASP cc_start: 0.8276 (m-30) cc_final: 0.7946 (m-30) REVERT: R 196 LEU cc_start: 0.8402 (mt) cc_final: 0.8192 (mt) REVERT: R 205 MET cc_start: 0.8335 (ttm) cc_final: 0.8044 (ttm) outliers start: 29 outliers final: 22 residues processed: 155 average time/residue: 0.2157 time to fit residues: 46.6068 Evaluate side-chains 141 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain R residue 88 HIS Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 102 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 ASN R 129 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.188877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.134465 restraints weight = 9475.524| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.30 r_work: 0.3106 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9190 Z= 0.196 Angle : 0.593 6.485 12453 Z= 0.310 Chirality : 0.044 0.168 1392 Planarity : 0.005 0.059 1587 Dihedral : 4.499 25.285 1250 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.12 % Allowed : 25.93 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.26), residues: 1126 helix: 1.78 (0.26), residues: 392 sheet: 0.19 (0.31), residues: 270 loop : -0.64 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.004 0.001 HIS A 340 PHE 0.025 0.002 PHE R 27 TYR 0.021 0.002 TYR A 374 ARG 0.004 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 459) hydrogen bonds : angle 4.82794 ( 1293) SS BOND : bond 0.00287 ( 2) SS BOND : angle 0.53290 ( 4) covalent geometry : bond 0.00460 ( 9188) covalent geometry : angle 0.59280 (12449) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7616 (tm-30) REVERT: B 42 ARG cc_start: 0.7322 (mmm160) cc_final: 0.7050 (mmm160) REVERT: B 46 ARG cc_start: 0.7960 (mtp-110) cc_final: 0.7321 (mmm160) REVERT: B 96 ARG cc_start: 0.8577 (mmm-85) cc_final: 0.8021 (mpt180) REVERT: B 127 LYS cc_start: 0.8923 (mttp) cc_final: 0.8436 (mttp) REVERT: B 129 ARG cc_start: 0.8020 (ttt90) cc_final: 0.7650 (mmm160) REVERT: B 212 ASP cc_start: 0.8116 (p0) cc_final: 0.7562 (p0) REVERT: A 10 LYS cc_start: 0.7898 (ttmt) cc_final: 0.7363 (mttp) REVERT: R 182 MET cc_start: 0.4895 (tpt) cc_final: 0.4126 (mmt) REVERT: R 205 MET cc_start: 0.8503 (ttm) cc_final: 0.8215 (ttm) outliers start: 40 outliers final: 30 residues processed: 165 average time/residue: 0.2213 time to fit residues: 50.2901 Evaluate side-chains 147 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 88 HIS Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 7 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 88 ASN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.187215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.133452 restraints weight = 9517.493| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.10 r_work: 0.3174 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9190 Z= 0.160 Angle : 0.550 6.235 12453 Z= 0.289 Chirality : 0.043 0.152 1392 Planarity : 0.004 0.056 1587 Dihedral : 4.350 24.750 1250 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.17 % Favored : 95.74 % Rotamer: Outliers : 3.70 % Allowed : 26.54 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.62 (0.25), residues: 1126 helix: 1.91 (0.26), residues: 393 sheet: 0.12 (0.32), residues: 260 loop : -0.67 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS R 87 PHE 0.028 0.002 PHE D 106 TYR 0.016 0.002 TYR A 374 ARG 0.004 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 459) hydrogen bonds : angle 4.71973 ( 1293) SS BOND : bond 0.00283 ( 2) SS BOND : angle 0.63022 ( 4) covalent geometry : bond 0.00375 ( 9188) covalent geometry : angle 0.54998 (12449) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.961 Fit side-chains REVERT: B 17 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7779 (tm-30) REVERT: B 42 ARG cc_start: 0.7301 (mmm160) cc_final: 0.7023 (mmm160) REVERT: B 46 ARG cc_start: 0.8053 (mtp-110) cc_final: 0.7440 (mmm160) REVERT: B 96 ARG cc_start: 0.8580 (mmm-85) cc_final: 0.8056 (mpt180) REVERT: B 127 LYS cc_start: 0.8941 (mttp) cc_final: 0.8434 (mttp) REVERT: B 129 ARG cc_start: 0.8022 (ttt90) cc_final: 0.7643 (mmm160) REVERT: B 212 ASP cc_start: 0.8161 (p0) cc_final: 0.7590 (p0) REVERT: B 226 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.8022 (mm-30) REVERT: B 303 ASP cc_start: 0.7926 (p0) cc_final: 0.7125 (m-30) REVERT: A 9 ASP cc_start: 0.8250 (m-30) cc_final: 0.7973 (m-30) REVERT: R 66 ASN cc_start: 0.8644 (m110) cc_final: 0.8314 (m110) REVERT: R 135 LYS cc_start: 0.7786 (ttmt) cc_final: 0.6718 (pttp) REVERT: R 182 MET cc_start: 0.4620 (tpt) cc_final: 0.4178 (mmt) outliers start: 36 outliers final: 27 residues processed: 151 average time/residue: 0.2362 time to fit residues: 48.9041 Evaluate side-chains 146 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 14 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.1980 chunk 87 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.191061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.145516 restraints weight = 9497.785| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 3.14 r_work: 0.3240 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9190 Z= 0.123 Angle : 0.520 5.724 12453 Z= 0.274 Chirality : 0.041 0.138 1392 Planarity : 0.004 0.056 1587 Dihedral : 4.170 23.555 1250 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.26 % Favored : 95.65 % Rotamer: Outliers : 3.29 % Allowed : 27.26 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.25), residues: 1126 helix: 1.99 (0.26), residues: 400 sheet: 0.13 (0.32), residues: 253 loop : -0.58 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS R 87 PHE 0.018 0.001 PHE R 259 TYR 0.017 0.001 TYR A 374 ARG 0.009 0.000 ARG R 193 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 459) hydrogen bonds : angle 4.58583 ( 1293) SS BOND : bond 0.00287 ( 2) SS BOND : angle 0.67303 ( 4) covalent geometry : bond 0.00282 ( 9188) covalent geometry : angle 0.52025 (12449) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: B 17 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7667 (tt0) REVERT: B 42 ARG cc_start: 0.7238 (mmm160) cc_final: 0.6984 (mmm160) REVERT: B 46 ARG cc_start: 0.7872 (mtp-110) cc_final: 0.7330 (mmm160) REVERT: B 96 ARG cc_start: 0.8403 (mmm-85) cc_final: 0.8040 (mpt180) REVERT: B 127 LYS cc_start: 0.8894 (mttp) cc_final: 0.8545 (mttp) REVERT: B 129 ARG cc_start: 0.7847 (ttt90) cc_final: 0.7474 (mmm160) REVERT: B 212 ASP cc_start: 0.7995 (p0) cc_final: 0.7427 (p0) REVERT: B 226 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7855 (mm-30) REVERT: B 303 ASP cc_start: 0.7673 (p0) cc_final: 0.7031 (m-30) REVERT: D 90 SER cc_start: 0.8231 (t) cc_final: 0.7855 (p) REVERT: A 263 ARG cc_start: 0.8421 (ttp-110) cc_final: 0.7925 (ttp-110) REVERT: R 78 LEU cc_start: 0.8513 (tp) cc_final: 0.8043 (mp) REVERT: R 135 LYS cc_start: 0.7808 (ttmt) cc_final: 0.6820 (pttp) REVERT: R 219 ASN cc_start: 0.7520 (t0) cc_final: 0.7168 (t0) REVERT: G 13 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6772 (tpt90) outliers start: 32 outliers final: 23 residues processed: 152 average time/residue: 0.2283 time to fit residues: 47.1501 Evaluate side-chains 147 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 88 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 chunk 92 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.189907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.144477 restraints weight = 9641.836| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.93 r_work: 0.3295 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9190 Z= 0.130 Angle : 0.522 6.044 12453 Z= 0.275 Chirality : 0.042 0.159 1392 Planarity : 0.004 0.056 1587 Dihedral : 4.115 23.368 1250 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.91 % Favored : 96.00 % Rotamer: Outliers : 3.81 % Allowed : 26.75 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.26), residues: 1126 helix: 2.05 (0.26), residues: 400 sheet: 0.12 (0.32), residues: 263 loop : -0.59 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS R 87 PHE 0.016 0.001 PHE R 27 TYR 0.018 0.001 TYR A 374 ARG 0.004 0.000 ARG R 193 Details of bonding type rmsd hydrogen bonds : bond 0.03335 ( 459) hydrogen bonds : angle 4.53668 ( 1293) SS BOND : bond 0.00287 ( 2) SS BOND : angle 0.69214 ( 4) covalent geometry : bond 0.00300 ( 9188) covalent geometry : angle 0.52238 (12449) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: B 17 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7633 (tt0) REVERT: B 42 ARG cc_start: 0.7302 (mmm160) cc_final: 0.7072 (mmm160) REVERT: B 46 ARG cc_start: 0.7968 (mtp-110) cc_final: 0.7349 (mmm160) REVERT: B 96 ARG cc_start: 0.8400 (mmm-85) cc_final: 0.8041 (mpt180) REVERT: B 129 ARG cc_start: 0.7972 (ttt90) cc_final: 0.7592 (mmm160) REVERT: B 212 ASP cc_start: 0.7981 (p0) cc_final: 0.7396 (p0) REVERT: B 226 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7792 (mm-30) REVERT: D 90 SER cc_start: 0.8256 (t) cc_final: 0.7878 (p) REVERT: A 9 ASP cc_start: 0.8155 (m-30) cc_final: 0.7820 (m-30) REVERT: A 10 LYS cc_start: 0.7799 (ttmt) cc_final: 0.7291 (mttp) REVERT: A 25 LYS cc_start: 0.8513 (mptt) cc_final: 0.8036 (mtmt) REVERT: A 263 ARG cc_start: 0.8433 (ttp-110) cc_final: 0.7683 (ttp-110) REVERT: R 78 LEU cc_start: 0.8577 (tp) cc_final: 0.8101 (mp) REVERT: R 135 LYS cc_start: 0.7797 (ttmt) cc_final: 0.6817 (pttp) REVERT: R 219 ASN cc_start: 0.7547 (t0) cc_final: 0.7188 (t0) REVERT: G 13 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6817 (tpt90) outliers start: 37 outliers final: 29 residues processed: 156 average time/residue: 0.2508 time to fit residues: 54.4761 Evaluate side-chains 152 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 88 HIS Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 87 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.189886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.144338 restraints weight = 9683.123| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.06 r_work: 0.3164 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9190 Z= 0.148 Angle : 0.537 5.770 12453 Z= 0.282 Chirality : 0.042 0.154 1392 Planarity : 0.004 0.056 1587 Dihedral : 4.148 23.467 1250 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.44 % Favored : 95.47 % Rotamer: Outliers : 3.70 % Allowed : 27.37 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.26), residues: 1126 helix: 2.07 (0.25), residues: 400 sheet: 0.08 (0.32), residues: 256 loop : -0.58 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS D 73 PHE 0.014 0.001 PHE R 259 TYR 0.021 0.002 TYR A 374 ARG 0.004 0.000 ARG R 193 Details of bonding type rmsd hydrogen bonds : bond 0.03424 ( 459) hydrogen bonds : angle 4.55923 ( 1293) SS BOND : bond 0.00318 ( 2) SS BOND : angle 0.82915 ( 4) covalent geometry : bond 0.00346 ( 9188) covalent geometry : angle 0.53708 (12449) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 1.021 Fit side-chains REVERT: B 17 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7566 (tt0) REVERT: B 42 ARG cc_start: 0.7267 (mmm160) cc_final: 0.7049 (mmm160) REVERT: B 46 ARG cc_start: 0.7876 (mtp-110) cc_final: 0.7213 (mmm160) REVERT: B 96 ARG cc_start: 0.8403 (mmm-85) cc_final: 0.7998 (mpt180) REVERT: B 127 LYS cc_start: 0.8891 (mttm) cc_final: 0.8451 (mttp) REVERT: B 129 ARG cc_start: 0.7913 (ttt90) cc_final: 0.7535 (mmm160) REVERT: B 212 ASP cc_start: 0.7958 (p0) cc_final: 0.7396 (t0) REVERT: B 226 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7761 (mm-30) REVERT: B 303 ASP cc_start: 0.7681 (p0) cc_final: 0.6824 (m-30) REVERT: D 95 THR cc_start: 0.8170 (OUTLIER) cc_final: 0.7776 (p) REVERT: A 9 ASP cc_start: 0.8072 (m-30) cc_final: 0.7748 (m-30) REVERT: A 25 LYS cc_start: 0.8416 (mptt) cc_final: 0.7837 (mtmt) REVERT: A 263 ARG cc_start: 0.8388 (ttp-110) cc_final: 0.7583 (ttp-110) REVERT: R 78 LEU cc_start: 0.8505 (tp) cc_final: 0.8043 (mp) REVERT: R 135 LYS cc_start: 0.7784 (ttmt) cc_final: 0.6846 (pttp) REVERT: R 205 MET cc_start: 0.8297 (ttm) cc_final: 0.7829 (ttt) REVERT: G 13 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6790 (tpt90) outliers start: 36 outliers final: 29 residues processed: 155 average time/residue: 0.2181 time to fit residues: 46.5335 Evaluate side-chains 153 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 88 HIS Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.4980 chunk 108 optimal weight: 10.0000 chunk 91 optimal weight: 0.0980 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.191656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146275 restraints weight = 9519.890| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.99 r_work: 0.3196 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9190 Z= 0.119 Angle : 0.515 5.976 12453 Z= 0.271 Chirality : 0.042 0.164 1392 Planarity : 0.004 0.056 1587 Dihedral : 4.070 22.070 1250 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.83 % Rotamer: Outliers : 3.29 % Allowed : 27.37 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.26), residues: 1126 helix: 2.08 (0.25), residues: 406 sheet: 0.08 (0.32), residues: 259 loop : -0.59 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 340 PHE 0.014 0.001 PHE R 259 TYR 0.018 0.001 TYR A 374 ARG 0.005 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03259 ( 459) hydrogen bonds : angle 4.46838 ( 1293) SS BOND : bond 0.00293 ( 2) SS BOND : angle 0.85451 ( 4) covalent geometry : bond 0.00272 ( 9188) covalent geometry : angle 0.51503 (12449) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.909 Fit side-chains REVERT: B 17 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7574 (tt0) REVERT: B 42 ARG cc_start: 0.7456 (mmm160) cc_final: 0.7053 (mmm160) REVERT: B 46 ARG cc_start: 0.7873 (mtp-110) cc_final: 0.7211 (mmm160) REVERT: B 96 ARG cc_start: 0.8375 (mmm-85) cc_final: 0.8018 (mpt180) REVERT: B 127 LYS cc_start: 0.8894 (mttm) cc_final: 0.8521 (mttp) REVERT: B 129 ARG cc_start: 0.7915 (ttt90) cc_final: 0.7518 (mmm160) REVERT: B 212 ASP cc_start: 0.8029 (p0) cc_final: 0.7500 (t0) REVERT: B 226 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7767 (mm-30) REVERT: B 264 TYR cc_start: 0.8748 (m-80) cc_final: 0.8534 (m-80) REVERT: B 303 ASP cc_start: 0.7712 (p0) cc_final: 0.6871 (m-30) REVERT: D 43 VAL cc_start: 0.7310 (OUTLIER) cc_final: 0.7082 (t) REVERT: D 90 SER cc_start: 0.8112 (t) cc_final: 0.7666 (p) REVERT: D 95 THR cc_start: 0.8230 (OUTLIER) cc_final: 0.7847 (p) REVERT: D 131 MET cc_start: 0.8165 (mmt) cc_final: 0.7856 (tpp) REVERT: A 25 LYS cc_start: 0.8470 (mptt) cc_final: 0.7910 (mtmt) REVERT: A 263 ARG cc_start: 0.8427 (ttp-110) cc_final: 0.7654 (ttp-110) REVERT: R 78 LEU cc_start: 0.8487 (tp) cc_final: 0.8008 (mp) REVERT: R 135 LYS cc_start: 0.7779 (ttmt) cc_final: 0.6849 (pttp) REVERT: R 205 MET cc_start: 0.8293 (ttm) cc_final: 0.7986 (ttm) REVERT: R 219 ASN cc_start: 0.7449 (t0) cc_final: 0.7094 (t0) REVERT: G 13 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6835 (tpt90) outliers start: 32 outliers final: 24 residues processed: 151 average time/residue: 0.2583 time to fit residues: 53.3433 Evaluate side-chains 150 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 75 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 83 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.190150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.144161 restraints weight = 9702.096| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.95 r_work: 0.3204 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9190 Z= 0.138 Angle : 0.530 5.726 12453 Z= 0.278 Chirality : 0.042 0.142 1392 Planarity : 0.004 0.057 1587 Dihedral : 4.091 22.606 1250 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.83 % Rotamer: Outliers : 3.40 % Allowed : 27.37 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.25), residues: 1126 helix: 2.05 (0.25), residues: 406 sheet: 0.07 (0.32), residues: 250 loop : -0.59 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS A 340 PHE 0.031 0.002 PHE R 259 TYR 0.014 0.001 TYR A 322 ARG 0.004 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03387 ( 459) hydrogen bonds : angle 4.52201 ( 1293) SS BOND : bond 0.00274 ( 2) SS BOND : angle 0.83775 ( 4) covalent geometry : bond 0.00321 ( 9188) covalent geometry : angle 0.52966 (12449) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.873 Fit side-chains REVERT: B 17 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7577 (tt0) REVERT: B 42 ARG cc_start: 0.7446 (mmm160) cc_final: 0.7043 (mmm160) REVERT: B 46 ARG cc_start: 0.7915 (mtp-110) cc_final: 0.7274 (mmm160) REVERT: B 96 ARG cc_start: 0.8351 (mmm-85) cc_final: 0.8017 (mpt180) REVERT: B 127 LYS cc_start: 0.8919 (mttm) cc_final: 0.8527 (mttp) REVERT: B 129 ARG cc_start: 0.7947 (ttt90) cc_final: 0.7569 (mmm160) REVERT: B 212 ASP cc_start: 0.8047 (p0) cc_final: 0.7507 (t0) REVERT: B 226 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7765 (mm-30) REVERT: B 303 ASP cc_start: 0.7731 (p0) cc_final: 0.6903 (m-30) REVERT: D 43 VAL cc_start: 0.7344 (OUTLIER) cc_final: 0.7113 (t) REVERT: D 95 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.7858 (p) REVERT: D 131 MET cc_start: 0.8195 (mmt) cc_final: 0.7891 (tpp) REVERT: A 25 LYS cc_start: 0.8464 (mptt) cc_final: 0.7879 (mtmt) REVERT: A 263 ARG cc_start: 0.8413 (ttp-110) cc_final: 0.7652 (ttp-110) REVERT: R 78 LEU cc_start: 0.8502 (tp) cc_final: 0.8021 (mp) REVERT: R 135 LYS cc_start: 0.7771 (ttmt) cc_final: 0.6878 (pttp) REVERT: R 205 MET cc_start: 0.8292 (ttm) cc_final: 0.8000 (ttm) REVERT: R 219 ASN cc_start: 0.7487 (t0) cc_final: 0.7124 (t0) REVERT: G 13 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6869 (tpt90) outliers start: 33 outliers final: 27 residues processed: 150 average time/residue: 0.2319 time to fit residues: 47.0879 Evaluate side-chains 151 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain R residue 19 VAL Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 88 HIS Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 41 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.191189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145638 restraints weight = 9656.042| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.88 r_work: 0.3262 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9190 Z= 0.124 Angle : 0.519 5.989 12453 Z= 0.274 Chirality : 0.042 0.138 1392 Planarity : 0.004 0.056 1587 Dihedral : 4.044 22.224 1250 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.17 % Favored : 95.74 % Rotamer: Outliers : 2.88 % Allowed : 28.19 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.26), residues: 1126 helix: 2.10 (0.25), residues: 406 sheet: 0.09 (0.32), residues: 258 loop : -0.60 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS A 340 PHE 0.034 0.001 PHE R 259 TYR 0.019 0.001 TYR A 374 ARG 0.005 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03275 ( 459) hydrogen bonds : angle 4.44895 ( 1293) SS BOND : bond 0.00294 ( 2) SS BOND : angle 0.88631 ( 4) covalent geometry : bond 0.00285 ( 9188) covalent geometry : angle 0.51869 (12449) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5198.34 seconds wall clock time: 91 minutes 17.55 seconds (5477.55 seconds total)