Starting phenix.real_space_refine on Thu Feb 13 11:35:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j31_61104/02_2025/9j31_61104.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j31_61104/02_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_61104/02_2025/9j31_61104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j31_61104/02_2025/9j31_61104.map" model { file = "/net/cci-nas-00/data/ceres_data/9j31_61104/02_2025/9j31_61104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j31_61104/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.00, per 1000 atoms: 0.56 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: 2.29 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.97 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: 2.58 Time building geometry restraints manager: 2.63 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: 0.990 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.980 Find NCS groups from input model: 0.090 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.490 ------------------------------------------------------------------------------- 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 9188 Z= 0.203 Angle : 0.658 10.910 12449 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 *********************** 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 : 0.890 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: 0.2407 time to fit residues: 61.7862 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 : 0.927 ------------------------------------------------------------------------------- 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: 0.3342 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- 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 9188 Z= 0.227 Angle : 0.582 6.169 12449 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 *********************** 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 : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7793 (mtp-110) cc_final: 0.7382 (mmm160) REVERT: B 74 SER cc_start: 0.8555 (p) cc_final: 0.8303 (p) REVERT: B 127 LYS cc_start: 0.8863 (mttp) cc_final: 0.8618 (mttp) REVERT: B 129 ARG cc_start: 0.7986 (ttt90) cc_final: 0.7716 (mmm160) REVERT: B 212 ASP cc_start: 0.8093 (p0) cc_final: 0.7716 (p0) REVERT: B 259 GLN cc_start: 0.7753 (mt0) cc_final: 0.7432 (mp10) REVERT: D 121 MET cc_start: 0.7579 (mtm) cc_final: 0.7227 (mtm) REVERT: D 228 TYR cc_start: 0.8173 (p90) cc_final: 0.7911 (p90) REVERT: A 257 LYS cc_start: 0.8223 (tttt) cc_final: 0.7721 (ttmt) REVERT: R 196 LEU cc_start: 0.8500 (mt) cc_final: 0.8277 (mt) REVERT: R 205 MET cc_start: 0.8343 (ttm) cc_final: 0.8104 (ttm) outliers start: 37 outliers final: 23 residues processed: 173 average time/residue: 0.2316 time to fit residues: 54.8238 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 : 0.935 ------------------------------------------------------------------------------- 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: 0.2980 chunk 9 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.4149 r_free = 0.4149 target = 0.194593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.136732 restraints weight = 9648.583| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.14 r_work: 0.3204 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9188 Z= 0.200 Angle : 0.532 5.904 12449 Z= 0.283 Chirality : 0.042 0.140 1392 Planarity : 0.004 0.060 1587 Dihedral : 4.278 25.111 1250 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % 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: 0.72 (0.26), residues: 1126 helix: 1.82 (0.26), residues: 399 sheet: 0.37 (0.32), residues: 259 loop : -0.60 (0.30), residues: 468 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 0.015 0.001 PHE R 105 TYR 0.016 0.002 TYR A 322 ARG 0.002 0.000 ARG R 193 *********************** 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 163 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7790 (mtp-110) cc_final: 0.7252 (mmm160) REVERT: B 96 ARG cc_start: 0.8388 (mmm-85) cc_final: 0.8011 (mpt180) REVERT: B 127 LYS cc_start: 0.8909 (mttp) cc_final: 0.8554 (mttp) REVERT: B 129 ARG cc_start: 0.7952 (ttt90) cc_final: 0.7625 (mmm160) REVERT: B 212 ASP cc_start: 0.8007 (p0) cc_final: 0.7547 (p0) REVERT: B 259 GLN cc_start: 0.7768 (mt0) cc_final: 0.7142 (mp10) REVERT: D 228 TYR cc_start: 0.8044 (p90) cc_final: 0.7791 (p90) REVERT: A 25 LYS cc_start: 0.8539 (mptt) cc_final: 0.7981 (mtmt) REVERT: A 263 ARG cc_start: 0.8325 (ttp-110) cc_final: 0.7625 (ttp-110) REVERT: R 144 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7752 (mt) REVERT: R 182 MET cc_start: 0.5348 (tpp) cc_final: 0.5021 (mmm) REVERT: R 196 LEU cc_start: 0.8408 (mt) cc_final: 0.8202 (mt) REVERT: R 205 MET cc_start: 0.8365 (ttm) cc_final: 0.8078 (ttm) outliers start: 29 outliers final: 23 residues processed: 157 average time/residue: 0.2074 time to fit residues: 45.7611 Evaluate side-chains 144 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 B residue 318 LEU 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 144 LEU 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: 8.9990 chunk 34 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 chunk 108 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.191804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.138213 restraints weight = 9493.604| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.21 r_work: 0.3184 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9188 Z= 0.220 Angle : 0.541 5.860 12449 Z= 0.284 Chirality : 0.042 0.146 1392 Planarity : 0.004 0.058 1587 Dihedral : 4.257 25.344 1250 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.91 % Allowed : 25.72 % Favored : 70.37 % 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: 0.68 (0.26), residues: 1126 helix: 1.87 (0.26), residues: 399 sheet: 0.25 (0.32), residues: 254 loop : -0.64 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS A 340 PHE 0.023 0.002 PHE R 27 TYR 0.017 0.002 TYR A 322 ARG 0.003 0.000 ARG B 251 *********************** 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 162 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7879 (mtp-110) cc_final: 0.7262 (mmm160) REVERT: B 96 ARG cc_start: 0.8542 (mmm-85) cc_final: 0.7983 (mpt180) REVERT: B 127 LYS cc_start: 0.8905 (mttp) cc_final: 0.8493 (mttp) REVERT: B 129 ARG cc_start: 0.7978 (ttt90) cc_final: 0.7624 (mmm160) REVERT: B 156 GLN cc_start: 0.8348 (mt0) cc_final: 0.8143 (mt0) REVERT: B 212 ASP cc_start: 0.8042 (p0) cc_final: 0.7466 (p0) REVERT: B 262 MET cc_start: 0.7862 (ptp) cc_final: 0.7656 (ptp) REVERT: D 121 MET cc_start: 0.7599 (mtm) cc_final: 0.7383 (mtm) REVERT: A 10 LYS cc_start: 0.7782 (ttmt) cc_final: 0.7258 (mttp) REVERT: A 263 ARG cc_start: 0.8426 (ttp-110) cc_final: 0.7639 (ttp-110) REVERT: A 361 ASP cc_start: 0.8693 (m-30) cc_final: 0.8488 (m-30) REVERT: R 144 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7753 (mt) REVERT: R 243 LEU cc_start: 0.7459 (mt) cc_final: 0.7258 (mt) outliers start: 38 outliers final: 28 residues processed: 156 average time/residue: 0.2201 time to fit residues: 47.5446 Evaluate side-chains 145 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU 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 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 144 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: 0.6980 chunk 70 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.187976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.142896 restraints weight = 9444.197| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.98 r_work: 0.3115 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9188 Z= 0.241 Angle : 0.543 6.019 12449 Z= 0.286 Chirality : 0.043 0.149 1392 Planarity : 0.004 0.057 1587 Dihedral : 4.241 24.143 1250 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.82 % Favored : 96.09 % Rotamer: Outliers : 4.01 % Allowed : 26.34 % Favored : 69.65 % 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: 0.67 (0.25), residues: 1126 helix: 1.95 (0.25), residues: 393 sheet: 0.21 (0.33), residues: 240 loop : -0.65 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS R 87 PHE 0.015 0.002 PHE B 151 TYR 0.015 0.002 TYR A 322 ARG 0.004 0.000 ARG A 330 *********************** 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 161 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 0.984 Fit side-chains REVERT: B 17 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7680 (tm-30) REVERT: B 42 ARG cc_start: 0.7282 (mmm160) cc_final: 0.7055 (mmm160) REVERT: B 46 ARG cc_start: 0.7937 (mtp-110) cc_final: 0.7257 (mmm160) REVERT: B 96 ARG cc_start: 0.8582 (mmm-85) cc_final: 0.8009 (mpt180) REVERT: B 127 LYS cc_start: 0.8876 (mttp) cc_final: 0.8324 (mttp) REVERT: B 129 ARG cc_start: 0.7921 (ttt90) cc_final: 0.7549 (mmm160) REVERT: B 212 ASP cc_start: 0.8024 (p0) cc_final: 0.7375 (p0) REVERT: B 303 ASP cc_start: 0.7818 (p0) cc_final: 0.6947 (m-30) REVERT: A 10 LYS cc_start: 0.7745 (ttmt) cc_final: 0.7219 (mttp) REVERT: A 25 LYS cc_start: 0.8408 (mptt) cc_final: 0.7798 (mtmt) REVERT: A 361 ASP cc_start: 0.8758 (m-30) cc_final: 0.8489 (m-30) REVERT: R 135 LYS cc_start: 0.7684 (ttmt) cc_final: 0.6559 (pttp) REVERT: R 144 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7615 (mt) outliers start: 39 outliers final: 29 residues processed: 154 average time/residue: 0.2309 time to fit residues: 48.9992 Evaluate side-chains 149 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR 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 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 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 144 LEU 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: 1.9990 chunk 66 optimal weight: 0.3980 chunk 106 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 87 optimal weight: 0.0030 chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.192647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.147423 restraints weight = 9480.456| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.77 r_work: 0.3223 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9188 Z= 0.167 Angle : 0.507 6.711 12449 Z= 0.267 Chirality : 0.041 0.135 1392 Planarity : 0.004 0.056 1587 Dihedral : 4.052 22.873 1250 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.00 % Favored : 95.91 % Rotamer: Outliers : 4.01 % Allowed : 26.75 % 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: 0.80 (0.25), residues: 1126 helix: 1.99 (0.25), residues: 400 sheet: 0.25 (0.33), residues: 252 loop : -0.54 (0.30), residues: 474 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 0.020 0.001 PHE R 259 TYR 0.015 0.001 TYR B 264 ARG 0.007 0.000 ARG R 193 *********************** 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 173 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.972 Fit side-chains REVERT: B 17 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7745 (tm-30) REVERT: B 42 ARG cc_start: 0.7261 (mmm160) cc_final: 0.7012 (mmm160) REVERT: B 46 ARG cc_start: 0.7751 (mtp-110) cc_final: 0.7133 (mmm160) REVERT: B 74 SER cc_start: 0.8885 (OUTLIER) cc_final: 0.8434 (p) REVERT: B 96 ARG cc_start: 0.8405 (mmm-85) cc_final: 0.8037 (mpt180) REVERT: B 127 LYS cc_start: 0.8855 (mttp) cc_final: 0.8427 (mttp) REVERT: B 129 ARG cc_start: 0.7813 (ttt90) cc_final: 0.7422 (mmm160) REVERT: B 212 ASP cc_start: 0.7964 (p0) cc_final: 0.7350 (t0) REVERT: B 303 ASP cc_start: 0.7628 (p0) cc_final: 0.6976 (m-30) REVERT: D 90 SER cc_start: 0.8169 (t) cc_final: 0.7774 (p) REVERT: A 25 LYS cc_start: 0.8429 (mptt) cc_final: 0.7836 (mtmt) REVERT: A 263 ARG cc_start: 0.8367 (ttp-110) cc_final: 0.7581 (ttp-110) REVERT: A 361 ASP cc_start: 0.8562 (m-30) cc_final: 0.8220 (m-30) REVERT: R 78 LEU cc_start: 0.8441 (tp) cc_final: 0.7989 (mp) REVERT: R 135 LYS cc_start: 0.7741 (ttmt) cc_final: 0.6710 (pttp) REVERT: R 144 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7696 (mt) REVERT: R 219 ASN cc_start: 0.7434 (t0) cc_final: 0.7110 (t0) REVERT: G 13 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6754 (tpt90) outliers start: 39 outliers final: 24 residues processed: 164 average time/residue: 0.2288 time to fit residues: 51.5112 Evaluate side-chains 154 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 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 294 CYS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 101 THR 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 144 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: 4.9990 chunk 78 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.190235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.144459 restraints weight = 9686.875| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.89 r_work: 0.3262 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9188 Z= 0.223 Angle : 0.535 6.751 12449 Z= 0.280 Chirality : 0.042 0.162 1392 Planarity : 0.004 0.057 1587 Dihedral : 4.126 23.039 1250 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.83 % Rotamer: Outliers : 3.60 % Allowed : 27.06 % 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: 0.77 (0.25), residues: 1126 helix: 2.03 (0.25), residues: 400 sheet: 0.16 (0.33), residues: 240 loop : -0.57 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS R 87 PHE 0.025 0.002 PHE R 259 TYR 0.020 0.002 TYR A 374 ARG 0.005 0.000 ARG R 193 *********************** 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 164 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.809 Fit side-chains REVERT: B 17 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7648 (tt0) REVERT: B 42 ARG cc_start: 0.7299 (mmm160) cc_final: 0.7071 (mmm160) REVERT: B 46 ARG cc_start: 0.7922 (mtp-110) cc_final: 0.7307 (mmm160) REVERT: B 74 SER cc_start: 0.8928 (OUTLIER) cc_final: 0.8432 (p) REVERT: B 96 ARG cc_start: 0.8410 (mmm-85) cc_final: 0.8026 (mpt180) REVERT: B 127 LYS cc_start: 0.8904 (mttp) cc_final: 0.8437 (mttp) REVERT: B 129 ARG cc_start: 0.7853 (ttt90) cc_final: 0.7480 (mmm160) REVERT: B 212 ASP cc_start: 0.8003 (p0) cc_final: 0.7456 (t0) REVERT: B 303 ASP cc_start: 0.7667 (p0) cc_final: 0.7069 (m-30) REVERT: A 10 LYS cc_start: 0.7789 (ttmt) cc_final: 0.7245 (mttp) REVERT: A 263 ARG cc_start: 0.8380 (ttp-110) cc_final: 0.7638 (ttp-110) REVERT: R 78 LEU cc_start: 0.8543 (tp) cc_final: 0.8085 (mp) REVERT: R 135 LYS cc_start: 0.7827 (ttmt) cc_final: 0.6840 (pttp) REVERT: R 144 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7708 (mt) REVERT: G 13 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6785 (tpt90) outliers start: 35 outliers final: 26 residues processed: 157 average time/residue: 0.2356 time to fit residues: 50.0984 Evaluate side-chains 154 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 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 294 CYS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 232 ASN 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 144 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 99 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.191248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.146052 restraints weight = 9735.556| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.86 r_work: 0.3243 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9188 Z= 0.188 Angle : 0.516 5.949 12449 Z= 0.271 Chirality : 0.042 0.159 1392 Planarity : 0.004 0.056 1587 Dihedral : 4.032 21.997 1250 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.00 % Favored : 95.91 % 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: 0.81 (0.25), residues: 1126 helix: 2.04 (0.25), residues: 406 sheet: 0.16 (0.33), residues: 240 loop : -0.53 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS A 340 PHE 0.024 0.001 PHE R 259 TYR 0.018 0.001 TYR A 374 ARG 0.004 0.000 ARG A 330 *********************** 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 163 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 1.006 Fit side-chains REVERT: B 17 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7572 (tt0) REVERT: B 42 ARG cc_start: 0.7377 (mmm160) cc_final: 0.7151 (mmm160) REVERT: B 46 ARG cc_start: 0.7859 (mtp-110) cc_final: 0.7176 (mmm160) REVERT: B 96 ARG cc_start: 0.8389 (mmm-85) cc_final: 0.7981 (mpt180) REVERT: B 127 LYS cc_start: 0.8865 (mttp) cc_final: 0.8483 (mttp) REVERT: B 129 ARG cc_start: 0.7816 (ttt90) cc_final: 0.7434 (mmm160) REVERT: B 212 ASP cc_start: 0.7961 (p0) cc_final: 0.7454 (t0) REVERT: B 303 ASP cc_start: 0.7733 (p0) cc_final: 0.7077 (m-30) REVERT: D 43 VAL cc_start: 0.7282 (OUTLIER) cc_final: 0.7021 (t) REVERT: D 90 SER cc_start: 0.8135 (t) cc_final: 0.7734 (p) REVERT: A 25 LYS cc_start: 0.8465 (mptt) cc_final: 0.7969 (mtmt) REVERT: A 245 ASP cc_start: 0.8021 (t70) cc_final: 0.7807 (t70) REVERT: A 263 ARG cc_start: 0.8412 (ttp-110) cc_final: 0.7623 (ttp-110) REVERT: A 361 ASP cc_start: 0.8321 (m-30) cc_final: 0.8089 (m-30) REVERT: R 78 LEU cc_start: 0.8526 (tp) cc_final: 0.8064 (mp) REVERT: R 135 LYS cc_start: 0.7792 (ttmt) cc_final: 0.6854 (pttp) REVERT: R 144 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7689 (mt) REVERT: R 219 ASN cc_start: 0.7476 (t0) cc_final: 0.7135 (t0) REVERT: G 13 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6826 (tpt90) outliers start: 32 outliers final: 25 residues processed: 155 average time/residue: 0.2372 time to fit residues: 50.7380 Evaluate side-chains 157 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 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 294 CYS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 50 VAL 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 232 ASN 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 144 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 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: 0.6980 chunk 108 optimal weight: 20.0000 chunk 91 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.188902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.133454 restraints weight = 9557.258| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.36 r_work: 0.3173 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9188 Z= 0.201 Angle : 0.523 5.861 12449 Z= 0.274 Chirality : 0.042 0.167 1392 Planarity : 0.004 0.057 1587 Dihedral : 4.053 22.496 1250 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.00 % Favored : 95.91 % Rotamer: Outliers : 3.19 % Allowed : 27.16 % Favored : 69.65 % 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 (0.25), residues: 1126 helix: 2.06 (0.25), residues: 406 sheet: 0.11 (0.33), residues: 240 loop : -0.55 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS A 340 PHE 0.025 0.001 PHE R 259 TYR 0.020 0.002 TYR A 374 ARG 0.004 0.000 ARG B 197 *********************** 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 162 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.874 Fit side-chains REVERT: B 17 GLN cc_start: 0.8031 (tm-30) cc_final: 0.7588 (tt0) REVERT: B 42 ARG cc_start: 0.7372 (mmm160) cc_final: 0.7156 (mmm160) REVERT: B 46 ARG cc_start: 0.7865 (mtp-110) cc_final: 0.7220 (mmm160) REVERT: B 96 ARG cc_start: 0.8367 (mmm-85) cc_final: 0.8013 (mpt180) REVERT: B 127 LYS cc_start: 0.8911 (mttm) cc_final: 0.8524 (mttp) REVERT: B 129 ARG cc_start: 0.7859 (ttt90) cc_final: 0.7488 (mmm160) REVERT: B 212 ASP cc_start: 0.7977 (p0) cc_final: 0.7510 (t0) REVERT: B 303 ASP cc_start: 0.7736 (p0) cc_final: 0.7181 (m-30) REVERT: D 43 VAL cc_start: 0.7380 (OUTLIER) cc_final: 0.7134 (t) REVERT: D 95 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7888 (p) REVERT: D 131 MET cc_start: 0.8203 (mmt) cc_final: 0.7902 (tpp) REVERT: A 25 LYS cc_start: 0.8497 (mptt) cc_final: 0.7971 (mtmt) REVERT: A 245 ASP cc_start: 0.7985 (t70) cc_final: 0.7776 (t70) REVERT: A 263 ARG cc_start: 0.8418 (ttp-110) cc_final: 0.7674 (ttp-110) REVERT: A 361 ASP cc_start: 0.8292 (m-30) cc_final: 0.8051 (m-30) REVERT: R 78 LEU cc_start: 0.8529 (tp) cc_final: 0.8060 (mp) REVERT: R 135 LYS cc_start: 0.7840 (ttmt) cc_final: 0.6961 (pttp) REVERT: R 144 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7683 (mt) REVERT: R 219 ASN cc_start: 0.7483 (t0) cc_final: 0.7173 (t0) REVERT: G 13 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.6863 (tpt90) outliers start: 31 outliers final: 25 residues processed: 155 average time/residue: 0.2266 time to fit residues: 48.0778 Evaluate side-chains 155 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 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 294 CYS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 50 VAL 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 232 ASN 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 144 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 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: 1.9990 chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 101 optimal weight: 0.4980 chunk 93 optimal weight: 0.0050 chunk 54 optimal weight: 6.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.191322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.146753 restraints weight = 9702.991| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.85 r_work: 0.3279 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9188 Z= 0.173 Angle : 0.512 5.843 12449 Z= 0.267 Chirality : 0.042 0.152 1392 Planarity : 0.004 0.056 1587 Dihedral : 3.994 21.609 1250 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.73 % Favored : 96.18 % Rotamer: Outliers : 2.88 % Allowed : 27.47 % Favored : 69.65 % 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: 0.81 (0.25), residues: 1126 helix: 2.07 (0.25), residues: 408 sheet: 0.12 (0.33), residues: 240 loop : -0.55 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 340 PHE 0.024 0.001 PHE R 259 TYR 0.017 0.001 TYR A 374 ARG 0.004 0.000 ARG B 197 ********************** 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 158 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.948 Fit side-chains REVERT: B 17 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7558 (tt0) REVERT: B 42 ARG cc_start: 0.7409 (mmm160) cc_final: 0.7180 (mmm160) REVERT: B 46 ARG cc_start: 0.7876 (mtp-110) cc_final: 0.7210 (mmm160) REVERT: B 96 ARG cc_start: 0.8387 (mmm-85) cc_final: 0.8032 (mpt180) REVERT: B 127 LYS cc_start: 0.8894 (mttm) cc_final: 0.8532 (mttp) REVERT: B 129 ARG cc_start: 0.7857 (ttt90) cc_final: 0.7470 (mmm160) REVERT: B 171 ILE cc_start: 0.7240 (mm) cc_final: 0.6999 (mm) REVERT: B 212 ASP cc_start: 0.7976 (p0) cc_final: 0.7543 (t0) REVERT: B 264 TYR cc_start: 0.8583 (m-80) cc_final: 0.8127 (m-80) REVERT: B 303 ASP cc_start: 0.7794 (p0) cc_final: 0.7227 (m-30) REVERT: D 43 VAL cc_start: 0.7373 (OUTLIER) cc_final: 0.7139 (t) REVERT: D 90 SER cc_start: 0.8155 (t) cc_final: 0.7790 (p) REVERT: D 131 MET cc_start: 0.8191 (mmt) cc_final: 0.7905 (tpp) REVERT: A 263 ARG cc_start: 0.8432 (ttp-110) cc_final: 0.7680 (ttp-110) REVERT: R 78 LEU cc_start: 0.8494 (tp) cc_final: 0.8023 (mp) REVERT: R 135 LYS cc_start: 0.7785 (ttmt) cc_final: 0.6922 (pttp) REVERT: R 144 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7696 (mt) REVERT: R 189 MET cc_start: 0.5226 (tpp) cc_final: 0.4822 (tpp) REVERT: R 219 ASN cc_start: 0.7314 (t0) cc_final: 0.6987 (t0) REVERT: G 13 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6872 (tpt90) outliers start: 28 outliers final: 22 residues processed: 152 average time/residue: 0.2227 time to fit residues: 46.3321 Evaluate side-chains 152 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU 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 294 CYS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 232 ASN 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 144 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 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: 1.9990 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 104 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 44 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.190004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.144935 restraints weight = 9655.188| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.79 r_work: 0.3253 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9188 Z= 0.180 Angle : 0.513 5.670 12449 Z= 0.268 Chirality : 0.041 0.137 1392 Planarity : 0.004 0.057 1587 Dihedral : 3.989 21.437 1250 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.91 % Favored : 96.00 % Rotamer: Outliers : 2.57 % Allowed : 28.19 % 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: 0.80 (0.25), residues: 1126 helix: 2.06 (0.25), residues: 408 sheet: 0.12 (0.33), residues: 235 loop : -0.57 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 340 PHE 0.027 0.001 PHE R 259 TYR 0.016 0.001 TYR D 228 ARG 0.005 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4925.04 seconds wall clock time: 88 minutes 14.20 seconds (5294.20 seconds total)