Starting phenix.real_space_refine on Thu Jun 5 12:11:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vq5_32086/06_2025/7vq5_32086.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vq5_32086/06_2025/7vq5_32086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vq5_32086/06_2025/7vq5_32086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vq5_32086/06_2025/7vq5_32086.map" model { file = "/net/cci-nas-00/data/ceres_data/7vq5_32086/06_2025/7vq5_32086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vq5_32086/06_2025/7vq5_32086.cif" } resolution = 3.1 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= -0.000 sd= 0.005 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 34 5.16 5 C 4074 2.51 5 N 1052 2.21 5 O 1155 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 6315 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3153 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 12, 'TRANS': 387} Chain breaks: 1 Chain: "B" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3153 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 12, 'TRANS': 387} Chain breaks: 1 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'LMR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.39, per 1000 atoms: 0.70 Number of scatterers: 6315 At special positions: 0 Unit cell: (83.148, 90.246, 112.554, 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 34 16.00 O 1155 8.00 N 1052 7.00 C 4074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 945.5 milliseconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 0 sheets defined 86.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 1 through 18 removed outlier: 3.609A pdb=" N ASP A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.942A pdb=" N GLY A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 66 Processing helix chain 'A' and resid 69 through 102 removed outlier: 3.819A pdb=" N THR A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 125 removed outlier: 4.587A pdb=" N ILE A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 134 through 151 removed outlier: 3.716A pdb=" N ILE A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 183 Processing helix chain 'A' and resid 187 through 214 Processing helix chain 'A' and resid 223 through 241 removed outlier: 5.024A pdb=" N ARG A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP A 241 " --> pdb=" O LYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 256 removed outlier: 3.855A pdb=" N GLU A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 256 " --> pdb=" O TYR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 293 removed outlier: 3.541A pdb=" N TYR A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 305 removed outlier: 3.819A pdb=" N LYS A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 330 Processing helix chain 'A' and resid 335 through 357 removed outlier: 4.400A pdb=" N ILE A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER A 344 " --> pdb=" O HIS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 removed outlier: 4.332A pdb=" N ASP A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 363 " --> pdb=" O LEU A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 359 through 363' Processing helix chain 'A' and resid 364 through 398 Processing helix chain 'B' and resid 2 through 18 removed outlier: 3.518A pdb=" N ILE B 7 " --> pdb=" O LYS B 3 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 10 " --> pdb=" O GLU B 6 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 39 removed outlier: 3.543A pdb=" N ILE B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 66 removed outlier: 3.523A pdb=" N VAL B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 64 " --> pdb=" O MET B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 102 removed outlier: 3.893A pdb=" N THR B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG B 99 " --> pdb=" O HIS B 95 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 125 removed outlier: 4.046A pdb=" N VAL B 111 " --> pdb=" O PRO B 107 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 133 removed outlier: 4.026A pdb=" N THR B 132 " --> pdb=" O PRO B 128 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS B 133 " --> pdb=" O TRP B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 149 removed outlier: 3.549A pdb=" N ILE B 138 " --> pdb=" O PHE B 134 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE B 145 " --> pdb=" O PHE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 183 removed outlier: 3.715A pdb=" N MET B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 163 " --> pdb=" O MET B 159 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 215 removed outlier: 3.812A pdb=" N ASP B 201 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP B 212 " --> pdb=" O GLN B 208 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 241 removed outlier: 4.884A pdb=" N ARG B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP B 241 " --> pdb=" O LYS B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 256 removed outlier: 3.657A pdb=" N GLU B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU B 254 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TRP B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 256 " --> pdb=" O TYR B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 291 removed outlier: 3.512A pdb=" N GLN B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 304 removed outlier: 3.665A pdb=" N LYS B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 330 removed outlier: 3.881A pdb=" N GLU B 323 " --> pdb=" O ASN B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 357 removed outlier: 4.307A pdb=" N ILE B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 343 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER B 344 " --> pdb=" O HIS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 removed outlier: 4.277A pdb=" N ASP B 362 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL B 363 " --> pdb=" O LEU B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 359 through 363' Processing helix chain 'B' and resid 364 through 396 removed outlier: 4.667A pdb=" N SER B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 387 " --> pdb=" O ASN B 383 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1446 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: 1.73 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1586 1.33 - 1.45: 1178 1.45 - 1.57: 3618 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6442 Sorted by residual: bond pdb=" C1 LMR B 601 " pdb=" C2 LMR B 601 " ideal model delta sigma weight residual 1.543 1.495 0.048 2.00e-02 2.50e+03 5.70e+00 bond pdb=" C ILE B 53 " pdb=" O ILE B 53 " ideal model delta sigma weight residual 1.236 1.212 0.025 1.19e-02 7.06e+03 4.27e+00 bond pdb=" C ILE A 53 " pdb=" O ILE A 53 " ideal model delta sigma weight residual 1.236 1.212 0.024 1.19e-02 7.06e+03 4.09e+00 bond pdb=" CB THR A 168 " pdb=" CG2 THR A 168 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.09e+00 bond pdb=" C3 LMR B 601 " pdb=" C4 LMR B 601 " ideal model delta sigma weight residual 1.538 1.503 0.035 2.00e-02 2.50e+03 3.07e+00 ... (remaining 6437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 8187 1.47 - 2.94: 453 2.94 - 4.42: 47 4.42 - 5.89: 7 5.89 - 7.36: 8 Bond angle restraints: 8702 Sorted by residual: angle pdb=" C GLU A 307 " pdb=" N THR A 308 " pdb=" CA THR A 308 " ideal model delta sigma weight residual 119.83 116.03 3.80 1.11e+00 8.12e-01 1.17e+01 angle pdb=" N TYR A 39 " pdb=" CA TYR A 39 " pdb=" C TYR A 39 " ideal model delta sigma weight residual 111.36 114.89 -3.53 1.09e+00 8.42e-01 1.05e+01 angle pdb=" C GLU B 6 " pdb=" N ILE B 7 " pdb=" CA ILE B 7 " ideal model delta sigma weight residual 122.35 118.75 3.60 1.18e+00 7.18e-01 9.31e+00 angle pdb=" C THR A 132 " pdb=" N LYS A 133 " pdb=" CA LYS A 133 " ideal model delta sigma weight residual 122.42 118.05 4.37 1.55e+00 4.16e-01 7.96e+00 angle pdb=" C GLY B 260 " pdb=" N GLN B 261 " pdb=" CA GLN B 261 " ideal model delta sigma weight residual 124.31 128.72 -4.41 1.67e+00 3.59e-01 6.98e+00 ... (remaining 8697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3384 17.98 - 35.95: 405 35.95 - 53.93: 68 53.93 - 71.91: 5 71.91 - 89.89: 1 Dihedral angle restraints: 3863 sinusoidal: 1539 harmonic: 2324 Sorted by residual: dihedral pdb=" CA PRO A 299 " pdb=" C PRO A 299 " pdb=" N VAL A 300 " pdb=" CA VAL A 300 " ideal model delta harmonic sigma weight residual 180.00 -156.85 -23.15 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA TRP A 255 " pdb=" C TRP A 255 " pdb=" N GLU A 256 " pdb=" CA GLU A 256 " ideal model delta harmonic sigma weight residual -180.00 -161.40 -18.60 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA LEU A 233 " pdb=" C LEU A 233 " pdb=" N GLU A 234 " pdb=" CA GLU A 234 " ideal model delta harmonic sigma weight residual 180.00 -163.11 -16.89 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 3860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 783 0.054 - 0.108: 197 0.108 - 0.163: 15 0.163 - 0.217: 1 0.217 - 0.271: 1 Chirality restraints: 997 Sorted by residual: chirality pdb=" CA TYR A 39 " pdb=" N TYR A 39 " pdb=" C TYR A 39 " pdb=" CB TYR A 39 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA TYR A 40 " pdb=" N TYR A 40 " pdb=" C TYR A 40 " pdb=" CB TYR A 40 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CA PRO B 258 " pdb=" N PRO B 258 " pdb=" C PRO B 258 " pdb=" CB PRO B 258 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 994 not shown) Planarity restraints: 1092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 257 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO B 258 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 258 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 258 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 18 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO A 19 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 19 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 19 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 200 " -0.013 2.00e-02 2.50e+03 1.02e-02 1.81e+00 pdb=" CG PHE B 200 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE B 200 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 200 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 200 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 200 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 200 " -0.003 2.00e-02 2.50e+03 ... (remaining 1089 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 97 2.67 - 3.23: 6464 3.23 - 3.78: 9458 3.78 - 4.34: 12794 4.34 - 4.90: 21454 Nonbonded interactions: 50267 Sorted by model distance: nonbonded pdb=" OH TYR B 236 " pdb=" OD1 ASP B 286 " model vdw 2.110 3.040 nonbonded pdb=" OE1 GLU B 246 " pdb=" NH2 ARG B 279 " model vdw 2.185 3.120 nonbonded pdb=" O ILE B 369 " pdb=" OG1 THR B 373 " model vdw 2.210 3.040 nonbonded pdb=" NH2 ARG B 80 " pdb=" O4A LMR B 601 " model vdw 2.242 3.120 nonbonded pdb=" NZ LYS B 133 " pdb=" OE1 GLU B 254 " model vdw 2.247 3.120 ... (remaining 50262 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 405) } 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: 0.400 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.490 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.020 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 : 0.009 0.067 6442 Z= 0.399 Angle : 0.766 7.360 8702 Z= 0.446 Chirality : 0.046 0.271 997 Planarity : 0.004 0.043 1092 Dihedral : 14.845 89.886 2359 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.14 % Allowed : 12.36 % Favored : 87.50 % 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: -3.56 (0.25), residues: 792 helix: -1.79 (0.17), residues: 664 sheet: None (None), residues: 0 loop : -4.38 (0.42), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 255 HIS 0.006 0.002 HIS B 259 PHE 0.023 0.002 PHE B 200 TYR 0.015 0.002 TYR A 271 ARG 0.005 0.001 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.23076 ( 482) hydrogen bonds : angle 8.18318 ( 1446) covalent geometry : bond 0.00932 ( 6442) covalent geometry : angle 0.76622 ( 8702) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.662 Fit side-chains REVERT: A 95 HIS cc_start: 0.8017 (OUTLIER) cc_final: 0.6907 (t-90) REVERT: A 228 LYS cc_start: 0.7209 (pttt) cc_final: 0.6790 (pttt) REVERT: A 368 MET cc_start: 0.7920 (mmm) cc_final: 0.7591 (mmm) REVERT: A 372 MET cc_start: 0.8479 (mmm) cc_final: 0.8169 (mmm) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.2101 time to fit residues: 25.5599 Evaluate side-chains 77 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 266 HIS A 293 ASN A 340 HIS A 383 ASN B 266 HIS B 289 ASN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.139104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.101434 restraints weight = 8333.103| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.24 r_work: 0.3120 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6442 Z= 0.139 Angle : 0.506 5.599 8702 Z= 0.282 Chirality : 0.038 0.143 997 Planarity : 0.004 0.035 1092 Dihedral : 4.795 53.246 867 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.44 % Allowed : 13.65 % Favored : 84.91 % 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: -0.40 (0.29), residues: 792 helix: 0.41 (0.19), residues: 674 sheet: None (None), residues: 0 loop : -3.94 (0.47), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 255 HIS 0.004 0.001 HIS B 193 PHE 0.015 0.001 PHE A 206 TYR 0.017 0.002 TYR A 39 ARG 0.003 0.000 ARG A 400 Details of bonding type rmsd hydrogen bonds : bond 0.05668 ( 482) hydrogen bonds : angle 3.99873 ( 1446) covalent geometry : bond 0.00285 ( 6442) covalent geometry : angle 0.50562 ( 8702) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.699 Fit side-chains REVERT: A 95 HIS cc_start: 0.8053 (OUTLIER) cc_final: 0.7049 (t-90) REVERT: A 228 LYS cc_start: 0.6772 (pttt) cc_final: 0.6449 (pttt) REVERT: A 331 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.7619 (mpp) REVERT: A 372 MET cc_start: 0.8822 (mmm) cc_final: 0.8373 (mmm) REVERT: B 10 GLU cc_start: 0.8198 (tp30) cc_final: 0.7972 (tp30) REVERT: B 17 GLU cc_start: 0.8157 (tt0) cc_final: 0.7937 (tt0) REVERT: B 209 ASP cc_start: 0.7959 (m-30) cc_final: 0.7696 (m-30) REVERT: B 228 LYS cc_start: 0.7360 (mttm) cc_final: 0.6755 (pttt) REVERT: B 312 ARG cc_start: 0.8640 (tpp-160) cc_final: 0.8313 (tpp80) outliers start: 10 outliers final: 4 residues processed: 101 average time/residue: 0.1839 time to fit residues: 25.2531 Evaluate side-chains 92 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 331 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 47 optimal weight: 0.0470 chunk 31 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 393 HIS B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.141167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.103876 restraints weight = 8386.579| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.25 r_work: 0.3144 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6442 Z= 0.123 Angle : 0.459 5.144 8702 Z= 0.250 Chirality : 0.037 0.147 997 Planarity : 0.003 0.037 1092 Dihedral : 4.493 54.200 867 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.44 % Allowed : 16.24 % Favored : 82.33 % 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: 1.01 (0.30), residues: 792 helix: 1.33 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -3.47 (0.52), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 255 HIS 0.007 0.001 HIS A 393 PHE 0.015 0.001 PHE A 206 TYR 0.016 0.002 TYR A 39 ARG 0.003 0.000 ARG B 229 Details of bonding type rmsd hydrogen bonds : bond 0.04801 ( 482) hydrogen bonds : angle 3.62323 ( 1446) covalent geometry : bond 0.00261 ( 6442) covalent geometry : angle 0.45856 ( 8702) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.750 Fit side-chains REVERT: A 95 HIS cc_start: 0.8074 (OUTLIER) cc_final: 0.7072 (t-90) REVERT: A 228 LYS cc_start: 0.6707 (pttt) cc_final: 0.6433 (pttt) REVERT: A 331 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.7719 (mpp) REVERT: A 368 MET cc_start: 0.8071 (mmm) cc_final: 0.7794 (mmm) REVERT: A 372 MET cc_start: 0.8745 (mmm) cc_final: 0.8303 (mmm) REVERT: B 40 TYR cc_start: 0.8792 (t80) cc_final: 0.8546 (t80) REVERT: B 209 ASP cc_start: 0.7901 (m-30) cc_final: 0.7643 (m-30) REVERT: B 228 LYS cc_start: 0.7151 (mttm) cc_final: 0.6625 (pttt) REVERT: B 312 ARG cc_start: 0.8503 (tpp-160) cc_final: 0.8291 (tpp80) REVERT: B 405 MET cc_start: 0.5271 (ttm) cc_final: 0.5011 (ttm) outliers start: 10 outliers final: 6 residues processed: 107 average time/residue: 0.1807 time to fit residues: 26.0883 Evaluate side-chains 98 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 371 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.140081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.102189 restraints weight = 8701.505| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.26 r_work: 0.3149 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6442 Z= 0.163 Angle : 0.486 5.862 8702 Z= 0.264 Chirality : 0.038 0.141 997 Planarity : 0.003 0.039 1092 Dihedral : 4.633 57.160 867 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.44 % Allowed : 17.24 % Favored : 80.32 % 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: 1.40 (0.31), residues: 792 helix: 1.62 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -3.35 (0.50), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 255 HIS 0.004 0.001 HIS A 193 PHE 0.013 0.001 PHE B 264 TYR 0.016 0.001 TYR A 39 ARG 0.004 0.000 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.05339 ( 482) hydrogen bonds : angle 3.68272 ( 1446) covalent geometry : bond 0.00375 ( 6442) covalent geometry : angle 0.48635 ( 8702) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.671 Fit side-chains REVERT: A 95 HIS cc_start: 0.8304 (OUTLIER) cc_final: 0.7228 (t-90) REVERT: A 228 LYS cc_start: 0.6907 (pttt) cc_final: 0.6582 (pttt) REVERT: A 246 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8158 (mt-10) REVERT: A 331 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.7706 (mpp) REVERT: A 368 MET cc_start: 0.8177 (mmm) cc_final: 0.7965 (mmm) REVERT: A 372 MET cc_start: 0.8832 (mmm) cc_final: 0.8400 (mmm) REVERT: B 209 ASP cc_start: 0.7926 (m-30) cc_final: 0.7675 (m-30) REVERT: B 228 LYS cc_start: 0.7370 (mttm) cc_final: 0.6831 (pttt) REVERT: B 288 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8170 (tt) REVERT: B 312 ARG cc_start: 0.8704 (tpp-160) cc_final: 0.8422 (tpp80) REVERT: B 405 MET cc_start: 0.5310 (ttm) cc_final: 0.5098 (ttm) outliers start: 17 outliers final: 8 residues processed: 99 average time/residue: 0.2153 time to fit residues: 29.9293 Evaluate side-chains 97 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 348 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.143069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105523 restraints weight = 8644.912| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.27 r_work: 0.3191 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6442 Z= 0.116 Angle : 0.441 5.108 8702 Z= 0.240 Chirality : 0.036 0.144 997 Planarity : 0.003 0.039 1092 Dihedral : 4.425 57.010 867 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.44 % Allowed : 19.25 % Favored : 79.31 % 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: 1.90 (0.31), residues: 792 helix: 1.91 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -2.90 (0.54), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 255 HIS 0.003 0.001 HIS B 193 PHE 0.014 0.001 PHE A 206 TYR 0.014 0.001 TYR B 41 ARG 0.005 0.000 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04490 ( 482) hydrogen bonds : angle 3.48567 ( 1446) covalent geometry : bond 0.00243 ( 6442) covalent geometry : angle 0.44065 ( 8702) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.754 Fit side-chains REVERT: A 95 HIS cc_start: 0.8219 (OUTLIER) cc_final: 0.7083 (t-90) REVERT: A 228 LYS cc_start: 0.6798 (pttt) cc_final: 0.6495 (pttt) REVERT: A 246 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8213 (mt-10) REVERT: A 331 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.7726 (mpp) REVERT: A 368 MET cc_start: 0.8113 (mmm) cc_final: 0.7855 (mmm) REVERT: A 372 MET cc_start: 0.8701 (mmm) cc_final: 0.8295 (mmm) REVERT: B 154 ARG cc_start: 0.7174 (mtp85) cc_final: 0.6400 (mmm160) REVERT: B 209 ASP cc_start: 0.7868 (m-30) cc_final: 0.7580 (m-30) REVERT: B 228 LYS cc_start: 0.7312 (mttm) cc_final: 0.6829 (pttt) REVERT: B 312 ARG cc_start: 0.8636 (tpp-160) cc_final: 0.8389 (tpp80) REVERT: B 368 MET cc_start: 0.7858 (tpp) cc_final: 0.7600 (tpp) REVERT: B 405 MET cc_start: 0.5298 (ttm) cc_final: 0.5091 (ttm) outliers start: 10 outliers final: 6 residues processed: 103 average time/residue: 0.1825 time to fit residues: 25.6926 Evaluate side-chains 99 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 371 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 35 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.139113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.101307 restraints weight = 8668.218| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.25 r_work: 0.3129 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6442 Z= 0.179 Angle : 0.500 5.160 8702 Z= 0.270 Chirality : 0.038 0.139 997 Planarity : 0.003 0.039 1092 Dihedral : 4.627 59.776 867 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.59 % Allowed : 19.83 % Favored : 77.59 % 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: 1.86 (0.30), residues: 792 helix: 1.88 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -2.87 (0.54), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 255 HIS 0.004 0.001 HIS A 193 PHE 0.022 0.001 PHE A 206 TYR 0.016 0.002 TYR B 41 ARG 0.003 0.000 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.05372 ( 482) hydrogen bonds : angle 3.65679 ( 1446) covalent geometry : bond 0.00418 ( 6442) covalent geometry : angle 0.50043 ( 8702) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.665 Fit side-chains REVERT: A 95 HIS cc_start: 0.8379 (OUTLIER) cc_final: 0.7333 (t-90) REVERT: A 228 LYS cc_start: 0.6889 (pttt) cc_final: 0.6567 (pttt) REVERT: A 246 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8178 (mt-10) REVERT: A 331 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.7679 (mpp) REVERT: A 372 MET cc_start: 0.8782 (mmm) cc_final: 0.8364 (mmm) REVERT: B 95 HIS cc_start: 0.8275 (OUTLIER) cc_final: 0.7720 (t70) REVERT: B 154 ARG cc_start: 0.7201 (mtp85) cc_final: 0.6414 (mmm160) REVERT: B 228 LYS cc_start: 0.7402 (mttm) cc_final: 0.6879 (pttt) REVERT: B 312 ARG cc_start: 0.8673 (tpp-160) cc_final: 0.8449 (tpt170) REVERT: B 368 MET cc_start: 0.7913 (tpp) cc_final: 0.7693 (tpp) outliers start: 18 outliers final: 10 residues processed: 100 average time/residue: 0.1741 time to fit residues: 24.1303 Evaluate side-chains 102 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 381 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 20 optimal weight: 6.9990 chunk 46 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.144189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.106718 restraints weight = 8616.410| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.28 r_work: 0.3213 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6442 Z= 0.111 Angle : 0.444 5.131 8702 Z= 0.240 Chirality : 0.036 0.146 997 Planarity : 0.003 0.039 1092 Dihedral : 4.380 59.110 867 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.29 % Allowed : 20.98 % Favored : 77.73 % 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: 2.19 (0.31), residues: 792 helix: 2.11 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -2.86 (0.55), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 129 HIS 0.003 0.001 HIS B 193 PHE 0.013 0.001 PHE A 206 TYR 0.018 0.002 TYR B 41 ARG 0.003 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 482) hydrogen bonds : angle 3.42641 ( 1446) covalent geometry : bond 0.00227 ( 6442) covalent geometry : angle 0.44433 ( 8702) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.794 Fit side-chains REVERT: A 95 HIS cc_start: 0.8324 (OUTLIER) cc_final: 0.7175 (t-90) REVERT: A 228 LYS cc_start: 0.6724 (pttt) cc_final: 0.6453 (pttt) REVERT: A 246 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8163 (mt-10) REVERT: A 331 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.7682 (mpp) REVERT: A 368 MET cc_start: 0.8112 (mmm) cc_final: 0.7504 (mmm) REVERT: A 372 MET cc_start: 0.8651 (mmm) cc_final: 0.8078 (mmm) REVERT: A 405 MET cc_start: 0.5490 (mmt) cc_final: 0.4872 (mmm) REVERT: B 154 ARG cc_start: 0.7309 (mtp85) cc_final: 0.6474 (mmm160) REVERT: B 228 LYS cc_start: 0.7216 (mttm) cc_final: 0.6761 (pttt) REVERT: B 312 ARG cc_start: 0.8594 (tpp-160) cc_final: 0.8339 (tpt170) REVERT: B 313 MET cc_start: 0.8016 (mtt) cc_final: 0.7772 (mtp) outliers start: 9 outliers final: 4 residues processed: 104 average time/residue: 0.1683 time to fit residues: 24.0235 Evaluate side-chains 98 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 348 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 33 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.143006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105553 restraints weight = 8555.127| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.25 r_work: 0.3189 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6442 Z= 0.126 Angle : 0.450 5.271 8702 Z= 0.244 Chirality : 0.037 0.143 997 Planarity : 0.003 0.039 1092 Dihedral : 4.394 59.655 867 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.72 % Allowed : 21.55 % Favored : 76.72 % 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: 2.31 (0.30), residues: 792 helix: 2.18 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -2.69 (0.55), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 255 HIS 0.003 0.001 HIS A 193 PHE 0.018 0.001 PHE A 153 TYR 0.018 0.001 TYR A 41 ARG 0.002 0.000 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04517 ( 482) hydrogen bonds : angle 3.44167 ( 1446) covalent geometry : bond 0.00278 ( 6442) covalent geometry : angle 0.44994 ( 8702) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.716 Fit side-chains REVERT: A 95 HIS cc_start: 0.8372 (OUTLIER) cc_final: 0.7281 (t-90) REVERT: A 228 LYS cc_start: 0.6831 (pttt) cc_final: 0.6537 (pttt) REVERT: A 246 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8129 (mt-10) REVERT: A 331 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.7705 (mpp) REVERT: A 372 MET cc_start: 0.8688 (mmm) cc_final: 0.8277 (mmm) REVERT: A 405 MET cc_start: 0.5560 (mmt) cc_final: 0.5007 (mmm) REVERT: B 95 HIS cc_start: 0.8121 (OUTLIER) cc_final: 0.7556 (t70) REVERT: B 154 ARG cc_start: 0.7331 (mtp85) cc_final: 0.6459 (mmm160) REVERT: B 228 LYS cc_start: 0.7183 (mttm) cc_final: 0.6728 (pttt) REVERT: B 312 ARG cc_start: 0.8536 (tpp-160) cc_final: 0.8291 (tpt170) outliers start: 12 outliers final: 8 residues processed: 98 average time/residue: 0.1625 time to fit residues: 21.8680 Evaluate side-chains 102 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 371 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 33 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.143856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.106506 restraints weight = 8662.456| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.27 r_work: 0.3202 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6442 Z= 0.118 Angle : 0.444 5.044 8702 Z= 0.240 Chirality : 0.036 0.144 997 Planarity : 0.003 0.039 1092 Dihedral : 4.351 58.928 867 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.58 % Allowed : 21.55 % Favored : 76.87 % 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: 2.38 (0.30), residues: 792 helix: 2.23 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -2.92 (0.52), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 255 HIS 0.003 0.001 HIS B 193 PHE 0.018 0.001 PHE A 153 TYR 0.016 0.001 TYR A 41 ARG 0.002 0.000 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04364 ( 482) hydrogen bonds : angle 3.40458 ( 1446) covalent geometry : bond 0.00256 ( 6442) covalent geometry : angle 0.44380 ( 8702) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.750 Fit side-chains REVERT: A 95 HIS cc_start: 0.8432 (OUTLIER) cc_final: 0.7380 (t-90) REVERT: A 228 LYS cc_start: 0.6868 (pttt) cc_final: 0.6584 (pttt) REVERT: A 246 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8099 (mt-10) REVERT: A 331 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.7731 (mpp) REVERT: A 368 MET cc_start: 0.8111 (mmm) cc_final: 0.7685 (mmm) REVERT: A 372 MET cc_start: 0.8654 (mmm) cc_final: 0.8136 (mmm) REVERT: A 405 MET cc_start: 0.5632 (mmt) cc_final: 0.4976 (mmm) REVERT: B 95 HIS cc_start: 0.8104 (OUTLIER) cc_final: 0.7543 (t70) REVERT: B 154 ARG cc_start: 0.7335 (mtp85) cc_final: 0.6467 (mmm160) REVERT: B 228 LYS cc_start: 0.7167 (mttm) cc_final: 0.6712 (pttt) REVERT: B 312 ARG cc_start: 0.8502 (tpp-160) cc_final: 0.8300 (tpt170) REVERT: B 368 MET cc_start: 0.7863 (tpp) cc_final: 0.7648 (tpp) outliers start: 11 outliers final: 6 residues processed: 100 average time/residue: 0.1631 time to fit residues: 22.5257 Evaluate side-chains 100 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 331 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 55 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.142476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.104879 restraints weight = 8449.484| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.25 r_work: 0.3156 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6442 Z= 0.118 Angle : 0.443 5.058 8702 Z= 0.240 Chirality : 0.036 0.144 997 Planarity : 0.003 0.039 1092 Dihedral : 4.343 58.188 867 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.44 % Allowed : 21.84 % Favored : 76.72 % 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: 2.46 (0.30), residues: 792 helix: 2.30 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -2.84 (0.52), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 255 HIS 0.003 0.001 HIS B 193 PHE 0.019 0.001 PHE A 153 TYR 0.014 0.001 TYR A 50 ARG 0.002 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 482) hydrogen bonds : angle 3.39377 ( 1446) covalent geometry : bond 0.00256 ( 6442) covalent geometry : angle 0.44283 ( 8702) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.715 Fit side-chains REVERT: A 95 HIS cc_start: 0.8357 (OUTLIER) cc_final: 0.7352 (t-90) REVERT: A 228 LYS cc_start: 0.6789 (pttt) cc_final: 0.6518 (pttt) REVERT: A 246 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8094 (mt-10) REVERT: A 331 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.7795 (mpp) REVERT: A 368 MET cc_start: 0.8085 (mmm) cc_final: 0.7367 (mmm) REVERT: A 372 MET cc_start: 0.8580 (mmm) cc_final: 0.7968 (mmm) REVERT: A 405 MET cc_start: 0.5607 (mmt) cc_final: 0.4988 (mmm) REVERT: B 95 HIS cc_start: 0.8028 (OUTLIER) cc_final: 0.7482 (t70) REVERT: B 154 ARG cc_start: 0.7169 (mtp85) cc_final: 0.6297 (mmm160) REVERT: B 228 LYS cc_start: 0.7093 (mttm) cc_final: 0.6659 (pttt) outliers start: 10 outliers final: 6 residues processed: 96 average time/residue: 0.1667 time to fit residues: 22.2496 Evaluate side-chains 98 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 331 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.135963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.098221 restraints weight = 8893.968| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.25 r_work: 0.3078 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 6442 Z= 0.290 Angle : 0.606 5.809 8702 Z= 0.325 Chirality : 0.042 0.136 997 Planarity : 0.004 0.038 1092 Dihedral : 4.779 53.682 867 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.72 % Allowed : 21.98 % Favored : 76.29 % 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: 1.90 (0.30), residues: 792 helix: 1.90 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -2.48 (0.53), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 255 HIS 0.006 0.001 HIS A 193 PHE 0.029 0.002 PHE A 206 TYR 0.013 0.002 TYR B 41 ARG 0.005 0.001 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.06411 ( 482) hydrogen bonds : angle 3.91840 ( 1446) covalent geometry : bond 0.00701 ( 6442) covalent geometry : angle 0.60560 ( 8702) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3782.76 seconds wall clock time: 66 minutes 55.33 seconds (4015.33 seconds total)