Starting phenix.real_space_refine on Fri Oct 10 13:13:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tgi_41237/10_2025/8tgi_41237_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tgi_41237/10_2025/8tgi_41237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tgi_41237/10_2025/8tgi_41237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tgi_41237/10_2025/8tgi_41237.map" model { file = "/net/cci-nas-00/data/ceres_data/8tgi_41237/10_2025/8tgi_41237_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tgi_41237/10_2025/8tgi_41237_trim.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.023 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 57 5.16 5 C 3846 2.51 5 N 900 2.21 5 O 983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5786 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2873 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 23, 'TRANS': 361} Chain breaks: 1 Chain: "B" Number of atoms: 2858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2858 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 21, 'TRANS': 360} Chain breaks: 2 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'LDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.81, per 1000 atoms: 0.31 Number of scatterers: 5786 At special positions: 0 Unit cell: (77.688, 57.104, 114.208, 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 57 16.00 O 983 8.00 N 900 7.00 C 3846 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: 0.50 Conformation dependent library (CDL) restraints added in 396.2 milliseconds Enol-peptide restraints added in 1.4 microseconds 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1370 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 0 sheets defined 90.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.574A pdb=" N VAL A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A 39 " --> pdb=" O ASN A 35 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 51 removed outlier: 3.591A pdb=" N TYR A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 144 Processing helix chain 'A' and resid 144 through 165 removed outlier: 3.843A pdb=" N LEU A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Proline residue: A 155 - end of helix Proline residue: A 159 - end of helix removed outlier: 3.936A pdb=" N ASN A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 187 removed outlier: 3.502A pdb=" N PHE A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 219 removed outlier: 4.166A pdb=" N VAL A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 254 removed outlier: 4.055A pdb=" N ARG A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ALA A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Proline residue: A 245 - end of helix Processing helix chain 'A' and resid 256 through 278 removed outlier: 4.344A pdb=" N PHE A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 299 through 318 removed outlier: 3.686A pdb=" N LEU A 303 " --> pdb=" O ASP A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 331 removed outlier: 3.783A pdb=" N THR A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 336 through 342 removed outlier: 3.891A pdb=" N LEU A 340 " --> pdb=" O TRP A 336 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 364 removed outlier: 4.012A pdb=" N VAL A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASN A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 383 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 388 through 391 Processing helix chain 'A' and resid 392 through 421 Proline residue: A 412 - end of helix removed outlier: 4.205A pdb=" N GLY A 415 " --> pdb=" O MET A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 455 removed outlier: 3.566A pdb=" N TYR A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Proline residue: A 445 - end of helix removed outlier: 5.032A pdb=" N GLY A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ALA A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 472 Processing helix chain 'A' and resid 473 through 480 removed outlier: 4.231A pdb=" N SER A 480 " --> pdb=" O TYR A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 54 removed outlier: 4.205A pdb=" N VAL B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Proline residue: B 43 - end of helix Proline residue: B 46 - end of helix removed outlier: 3.564A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 165 removed outlier: 4.423A pdb=" N LYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) Proline residue: B 155 - end of helix removed outlier: 3.899A pdb=" N GLY B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Proline residue: B 159 - end of helix removed outlier: 4.226A pdb=" N ASN B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B 163 " --> pdb=" O PRO B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 187 removed outlier: 3.862A pdb=" N PHE B 174 " --> pdb=" O MET B 170 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 175 " --> pdb=" O PHE B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 219 removed outlier: 3.731A pdb=" N LEU B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 250 removed outlier: 3.935A pdb=" N ARG B 227 " --> pdb=" O HIS B 223 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Proline residue: B 245 - end of helix removed outlier: 3.660A pdb=" N SER B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.544A pdb=" N ILE B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 removed outlier: 3.535A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 331 removed outlier: 4.207A pdb=" N GLY B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Proline residue: B 321 - end of helix Proline residue: B 324 - end of helix Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 342 through 364 removed outlier: 3.840A pdb=" N SER B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASN B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LYS B 362 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 388 through 391 Processing helix chain 'B' and resid 392 through 422 Proline residue: B 412 - end of helix Processing helix chain 'B' and resid 427 through 455 removed outlier: 3.634A pdb=" N ALA B 431 " --> pdb=" O GLY B 427 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Proline residue: B 445 - end of helix removed outlier: 3.919A pdb=" N ALA B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 472 removed outlier: 4.083A pdb=" N LEU B 460 " --> pdb=" O GLY B 456 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET B 461 " --> pdb=" O PHE B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 479 removed outlier: 3.571A pdb=" N ARG B 479 " --> pdb=" O TYR B 476 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1296 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: 1.02 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 865 1.31 - 1.43: 1566 1.43 - 1.56: 3398 1.56 - 1.68: 1 1.68 - 1.81: 100 Bond restraints: 5930 Sorted by residual: bond pdb=" C31 YHR B 601 " pdb=" O30 YHR B 601 " ideal model delta sigma weight residual 1.326 1.401 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C17 YHR B 601 " pdb=" O19 YHR B 601 " ideal model delta sigma weight residual 1.325 1.397 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C35 YHR B 601 " pdb=" O43 YHR B 601 " ideal model delta sigma weight residual 1.343 1.403 -0.060 2.00e-02 2.50e+03 9.03e+00 bond pdb=" C10 YHR B 601 " pdb=" C11 YHR B 601 " ideal model delta sigma weight residual 1.492 1.433 0.059 2.00e-02 2.50e+03 8.79e+00 bond pdb=" C13 YHR B 601 " pdb=" N8 YHR B 601 " ideal model delta sigma weight residual 1.459 1.518 -0.059 2.00e-02 2.50e+03 8.73e+00 ... (remaining 5925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 8032 3.86 - 7.72: 40 7.72 - 11.59: 4 11.59 - 15.45: 0 15.45 - 19.31: 1 Bond angle restraints: 8077 Sorted by residual: angle pdb=" N LEU B 359 " pdb=" CA LEU B 359 " pdb=" C LEU B 359 " ideal model delta sigma weight residual 112.41 120.86 -8.45 1.30e+00 5.92e-01 4.22e+01 angle pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C9 YHR B 601 " ideal model delta sigma weight residual 111.89 131.20 -19.31 3.00e+00 1.11e-01 4.14e+01 angle pdb=" C VAL A 41 " pdb=" N VAL A 42 " pdb=" CA VAL A 42 " ideal model delta sigma weight residual 120.33 123.60 -3.27 8.00e-01 1.56e+00 1.67e+01 angle pdb=" C10 YHR B 601 " pdb=" C11 YHR B 601 " pdb=" C23 YHR B 601 " ideal model delta sigma weight residual 130.82 120.88 9.94 3.00e+00 1.11e-01 1.10e+01 angle pdb=" CA GLU A 320 " pdb=" C GLU A 320 " pdb=" N PRO A 321 " ideal model delta sigma weight residual 118.44 123.66 -5.22 1.59e+00 3.96e-01 1.08e+01 ... (remaining 8072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.92: 3127 23.92 - 47.85: 302 47.85 - 71.77: 43 71.77 - 95.69: 5 95.69 - 119.62: 3 Dihedral angle restraints: 3480 sinusoidal: 1324 harmonic: 2156 Sorted by residual: dihedral pdb=" CA PRO B 43 " pdb=" C PRO B 43 " pdb=" N ILE B 44 " pdb=" CA ILE B 44 " ideal model delta harmonic sigma weight residual -180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" C13 YHR B 601 " pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C6 YHR B 601 " ideal model delta sinusoidal sigma weight residual 57.66 -61.96 119.62 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" C5 YHR B 601 " pdb=" C6 YHR B 601 " pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " ideal model delta sinusoidal sigma weight residual -67.41 -170.02 102.61 1 3.00e+01 1.11e-03 1.30e+01 ... (remaining 3477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 859 0.070 - 0.140: 99 0.140 - 0.210: 7 0.210 - 0.280: 2 0.280 - 0.350: 1 Chirality restraints: 968 Sorted by residual: chirality pdb=" C13 YHR B 601 " pdb=" C12 YHR B 601 " pdb=" C14 YHR B 601 " pdb=" N8 YHR B 601 " both_signs ideal model delta sigma weight residual False -2.29 -2.64 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CB VAL B 425 " pdb=" CA VAL B 425 " pdb=" CG1 VAL B 425 " pdb=" CG2 VAL B 425 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA LEU B 359 " pdb=" N LEU B 359 " pdb=" C LEU B 359 " pdb=" CB LEU B 359 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 965 not shown) Planarity restraints: 985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 42 " 0.058 5.00e-02 4.00e+02 8.79e-02 1.24e+01 pdb=" N PRO B 43 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO B 43 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 43 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 319 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" C LEU A 319 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU A 319 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU A 320 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 168 " -0.038 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO A 169 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 169 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 169 " -0.032 5.00e-02 4.00e+02 ... (remaining 982 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 607 2.75 - 3.28: 5992 3.28 - 3.82: 9656 3.82 - 4.36: 10628 4.36 - 4.90: 19132 Nonbonded interactions: 46015 Sorted by model distance: nonbonded pdb=" O TRP B 326 " pdb=" OG1 THR B 330 " model vdw 2.208 3.040 nonbonded pdb=" O ARG A 138 " pdb=" OH TYR A 190 " model vdw 2.227 3.040 nonbonded pdb=" O ILE B 443 " pdb=" OG1 THR B 447 " model vdw 2.250 3.040 nonbonded pdb=" O THR A 464 " pdb=" ND2 ASN A 468 " model vdw 2.298 3.120 nonbonded pdb=" O GLY A 158 " pdb=" OG1 THR A 161 " model vdw 2.302 3.040 ... (remaining 46010 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' and (resid 20 through 278 or resid 288 through 482)) selection = (chain 'B' and (resid 20 through 51 or resid 134 through 482)) } 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: 6.190 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.120 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 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 : 0.004 0.075 5930 Z= 0.222 Angle : 0.758 19.310 8077 Z= 0.385 Chirality : 0.047 0.350 968 Planarity : 0.007 0.088 985 Dihedral : 18.038 119.617 2110 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 22.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.81 % Allowed : 32.14 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.29), residues: 757 helix: 0.99 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -1.65 (0.40), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 421 TYR 0.008 0.001 TYR A 430 PHE 0.020 0.001 PHE A 48 TRP 0.011 0.001 TRP B 326 HIS 0.001 0.001 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 5930) covalent geometry : angle 0.75779 ( 8077) hydrogen bonds : bond 0.16125 ( 443) hydrogen bonds : angle 5.38597 ( 1296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 0.141 Fit side-chains REVERT: A 373 MET cc_start: 0.7791 (mmt) cc_final: 0.5397 (mmt) outliers start: 5 outliers final: 3 residues processed: 133 average time/residue: 0.0571 time to fit residues: 10.8791 Evaluate side-chains 133 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 130 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 289 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 162 ASN ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN B 35 ASN ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.137328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.126105 restraints weight = 8334.222| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.10 r_work: 0.3564 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5930 Z= 0.184 Angle : 0.679 9.482 8077 Z= 0.333 Chirality : 0.046 0.152 968 Planarity : 0.006 0.049 985 Dihedral : 8.244 65.532 878 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 5.03 % Allowed : 28.08 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.31), residues: 757 helix: 1.61 (0.22), residues: 590 sheet: None (None), residues: 0 loop : -1.16 (0.43), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 421 TYR 0.014 0.002 TYR A 166 PHE 0.011 0.001 PHE A 356 TRP 0.007 0.001 TRP A 336 HIS 0.003 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 5930) covalent geometry : angle 0.67918 ( 8077) hydrogen bonds : bond 0.05043 ( 443) hydrogen bonds : angle 4.37424 ( 1296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 192 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7677 (mm) REVERT: A 250 MET cc_start: 0.4954 (mmm) cc_final: 0.4727 (mmm) REVERT: A 421 ARG cc_start: 0.7282 (mtp85) cc_final: 0.7077 (mtp180) REVERT: B 168 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8362 (mp) REVERT: B 457 PHE cc_start: 0.7200 (t80) cc_final: 0.6651 (t80) REVERT: B 477 TYR cc_start: 0.7361 (m-10) cc_final: 0.6856 (m-80) outliers start: 31 outliers final: 11 residues processed: 155 average time/residue: 0.0526 time to fit residues: 11.8371 Evaluate side-chains 145 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 410 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 67 optimal weight: 0.2980 chunk 25 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 31 optimal weight: 0.0170 chunk 3 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.137895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.126514 restraints weight = 8405.924| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.12 r_work: 0.3572 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5930 Z= 0.143 Angle : 0.639 10.768 8077 Z= 0.306 Chirality : 0.044 0.139 968 Planarity : 0.005 0.044 985 Dihedral : 6.792 52.961 875 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 5.68 % Allowed : 28.08 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.31), residues: 757 helix: 1.81 (0.22), residues: 590 sheet: None (None), residues: 0 loop : -1.21 (0.43), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 421 TYR 0.011 0.001 TYR B 166 PHE 0.011 0.001 PHE B 356 TRP 0.007 0.001 TRP A 366 HIS 0.002 0.001 HIS B 422 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 5930) covalent geometry : angle 0.63918 ( 8077) hydrogen bonds : bond 0.04541 ( 443) hydrogen bonds : angle 4.23452 ( 1296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.197 Fit side-chains REVERT: A 192 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7723 (mm) REVERT: A 374 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8136 (mp) REVERT: B 168 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8379 (mp) REVERT: B 170 MET cc_start: 0.6796 (tpt) cc_final: 0.6549 (tpt) REVERT: B 367 LEU cc_start: 0.7967 (tp) cc_final: 0.7645 (tt) REVERT: B 477 TYR cc_start: 0.7390 (m-10) cc_final: 0.6863 (m-80) outliers start: 35 outliers final: 17 residues processed: 149 average time/residue: 0.0499 time to fit residues: 10.9705 Evaluate side-chains 152 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 50 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 chunk 64 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.137235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.126089 restraints weight = 8369.683| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.04 r_work: 0.3567 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5930 Z= 0.154 Angle : 0.657 11.974 8077 Z= 0.313 Chirality : 0.044 0.133 968 Planarity : 0.005 0.045 985 Dihedral : 5.977 50.837 875 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 5.68 % Allowed : 28.08 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.31), residues: 757 helix: 1.87 (0.22), residues: 590 sheet: None (None), residues: 0 loop : -1.13 (0.44), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 421 TYR 0.010 0.001 TYR A 166 PHE 0.014 0.001 PHE B 457 TRP 0.006 0.001 TRP B 326 HIS 0.002 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 5930) covalent geometry : angle 0.65678 ( 8077) hydrogen bonds : bond 0.04527 ( 443) hydrogen bonds : angle 4.24310 ( 1296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.206 Fit side-chains REVERT: A 192 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7738 (mm) REVERT: A 374 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8151 (mp) REVERT: B 21 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7707 (mp10) REVERT: B 168 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8399 (mp) REVERT: B 367 LEU cc_start: 0.8105 (tp) cc_final: 0.7793 (tt) REVERT: B 389 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7781 (tt) REVERT: B 474 LEU cc_start: 0.8687 (mt) cc_final: 0.8471 (mp) REVERT: B 477 TYR cc_start: 0.7438 (m-10) cc_final: 0.6922 (m-80) REVERT: B 480 SER cc_start: 0.7944 (t) cc_final: 0.7719 (p) outliers start: 35 outliers final: 19 residues processed: 145 average time/residue: 0.0501 time to fit residues: 10.8090 Evaluate side-chains 157 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 45 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.135508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.124677 restraints weight = 8374.748| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.03 r_work: 0.3558 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5930 Z= 0.171 Angle : 0.682 12.726 8077 Z= 0.322 Chirality : 0.045 0.137 968 Planarity : 0.005 0.046 985 Dihedral : 5.668 50.601 875 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 5.68 % Allowed : 27.92 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.31), residues: 757 helix: 1.80 (0.22), residues: 598 sheet: None (None), residues: 0 loop : -1.38 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 421 TYR 0.011 0.001 TYR A 166 PHE 0.012 0.001 PHE B 457 TRP 0.007 0.001 TRP A 336 HIS 0.002 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 5930) covalent geometry : angle 0.68152 ( 8077) hydrogen bonds : bond 0.04720 ( 443) hydrogen bonds : angle 4.29151 ( 1296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.201 Fit side-chains REVERT: A 192 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7771 (mm) REVERT: A 250 MET cc_start: 0.4779 (mmm) cc_final: 0.4471 (mmm) REVERT: A 374 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8138 (mp) REVERT: A 421 ARG cc_start: 0.7487 (mtp85) cc_final: 0.7086 (mtp180) REVERT: B 21 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7745 (mp10) REVERT: B 168 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8414 (mp) REVERT: B 367 LEU cc_start: 0.8084 (tp) cc_final: 0.7760 (tt) REVERT: B 474 LEU cc_start: 0.8694 (mt) cc_final: 0.8471 (mp) outliers start: 35 outliers final: 20 residues processed: 145 average time/residue: 0.0526 time to fit residues: 11.0771 Evaluate side-chains 158 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 59 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 61 optimal weight: 0.0980 chunk 56 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.135606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.124806 restraints weight = 8293.215| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.02 r_work: 0.3559 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5930 Z= 0.168 Angle : 0.668 12.855 8077 Z= 0.317 Chirality : 0.045 0.141 968 Planarity : 0.005 0.046 985 Dihedral : 5.592 50.264 875 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 5.19 % Allowed : 28.57 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.31), residues: 757 helix: 1.81 (0.22), residues: 599 sheet: None (None), residues: 0 loop : -1.41 (0.45), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 421 TYR 0.011 0.001 TYR A 166 PHE 0.012 0.001 PHE B 356 TRP 0.007 0.001 TRP A 336 HIS 0.002 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 5930) covalent geometry : angle 0.66847 ( 8077) hydrogen bonds : bond 0.04713 ( 443) hydrogen bonds : angle 4.28323 ( 1296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.212 Fit side-chains REVERT: A 149 MET cc_start: 0.8203 (ptp) cc_final: 0.7992 (ptm) REVERT: A 192 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7797 (mm) REVERT: A 250 MET cc_start: 0.4791 (mmm) cc_final: 0.4575 (mmm) REVERT: A 374 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8148 (mp) REVERT: B 21 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7735 (mp10) REVERT: B 168 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8432 (mp) REVERT: B 367 LEU cc_start: 0.8101 (tp) cc_final: 0.7741 (tt) REVERT: B 474 LEU cc_start: 0.8708 (mt) cc_final: 0.8489 (mp) REVERT: B 480 SER cc_start: 0.7908 (t) cc_final: 0.7621 (p) outliers start: 32 outliers final: 18 residues processed: 149 average time/residue: 0.0526 time to fit residues: 11.4865 Evaluate side-chains 155 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 28 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.134417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.123714 restraints weight = 8284.869| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.00 r_work: 0.3544 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5930 Z= 0.197 Angle : 0.692 13.443 8077 Z= 0.332 Chirality : 0.046 0.143 968 Planarity : 0.005 0.048 985 Dihedral : 5.532 49.805 875 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 5.03 % Allowed : 28.73 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.31), residues: 757 helix: 1.74 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -1.26 (0.47), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 421 TYR 0.013 0.002 TYR A 349 PHE 0.012 0.001 PHE B 356 TRP 0.007 0.001 TRP A 336 HIS 0.003 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 5930) covalent geometry : angle 0.69204 ( 8077) hydrogen bonds : bond 0.05053 ( 443) hydrogen bonds : angle 4.38156 ( 1296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.200 Fit side-chains REVERT: A 192 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7895 (mm) REVERT: A 200 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.7160 (tt0) REVERT: A 374 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8148 (mp) REVERT: B 168 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8441 (mp) REVERT: B 474 LEU cc_start: 0.8707 (mt) cc_final: 0.8484 (mp) REVERT: B 480 SER cc_start: 0.7924 (t) cc_final: 0.7629 (p) outliers start: 31 outliers final: 19 residues processed: 139 average time/residue: 0.0535 time to fit residues: 10.8954 Evaluate side-chains 151 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 51 optimal weight: 0.0170 chunk 53 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** 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 = 0.3803 r_free = 0.3803 target = 0.135332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.124970 restraints weight = 8235.831| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.92 r_work: 0.3562 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5930 Z= 0.173 Angle : 0.694 13.084 8077 Z= 0.328 Chirality : 0.045 0.148 968 Planarity : 0.005 0.048 985 Dihedral : 5.425 49.765 875 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 5.52 % Allowed : 28.73 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.31), residues: 757 helix: 1.76 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -1.24 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 421 TYR 0.011 0.001 TYR A 166 PHE 0.013 0.001 PHE B 356 TRP 0.007 0.001 TRP A 336 HIS 0.002 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 5930) covalent geometry : angle 0.69403 ( 8077) hydrogen bonds : bond 0.04823 ( 443) hydrogen bonds : angle 4.36466 ( 1296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.180 Fit side-chains REVERT: A 192 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7920 (mm) REVERT: A 200 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7164 (tt0) REVERT: A 227 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6954 (mtt-85) REVERT: A 250 MET cc_start: 0.4458 (mmm) cc_final: 0.4140 (mmm) REVERT: A 374 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8099 (mp) REVERT: B 168 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8446 (mp) REVERT: B 474 LEU cc_start: 0.8701 (mt) cc_final: 0.8479 (mp) REVERT: B 480 SER cc_start: 0.7883 (t) cc_final: 0.7584 (p) outliers start: 34 outliers final: 21 residues processed: 143 average time/residue: 0.0543 time to fit residues: 11.1594 Evaluate side-chains 154 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 26 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 51 optimal weight: 0.2980 chunk 7 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** 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 = 0.3806 r_free = 0.3806 target = 0.135733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.124944 restraints weight = 8397.686| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.04 r_work: 0.3557 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5930 Z= 0.160 Angle : 0.691 12.914 8077 Z= 0.324 Chirality : 0.045 0.151 968 Planarity : 0.005 0.046 985 Dihedral : 5.317 49.180 875 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.55 % Allowed : 30.03 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.31), residues: 757 helix: 1.79 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -1.23 (0.48), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 421 TYR 0.010 0.001 TYR A 349 PHE 0.012 0.001 PHE B 356 TRP 0.007 0.001 TRP A 336 HIS 0.002 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 5930) covalent geometry : angle 0.69134 ( 8077) hydrogen bonds : bond 0.04695 ( 443) hydrogen bonds : angle 4.36068 ( 1296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.203 Fit side-chains REVERT: A 192 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7951 (mm) REVERT: A 200 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7222 (tt0) REVERT: A 227 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6973 (mtt-85) REVERT: A 331 MET cc_start: 0.7365 (mtp) cc_final: 0.7001 (mtp) REVERT: A 374 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8084 (mp) REVERT: B 168 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8445 (mp) REVERT: B 474 LEU cc_start: 0.8711 (mt) cc_final: 0.8485 (mp) REVERT: B 480 SER cc_start: 0.7846 (t) cc_final: 0.7544 (p) outliers start: 28 outliers final: 21 residues processed: 138 average time/residue: 0.0569 time to fit residues: 11.2082 Evaluate side-chains 155 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 60 optimal weight: 0.0870 chunk 50 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 48 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** 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 = 0.3818 r_free = 0.3818 target = 0.136921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.125534 restraints weight = 8329.592| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.09 r_work: 0.3557 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5930 Z= 0.154 Angle : 0.687 12.829 8077 Z= 0.322 Chirality : 0.045 0.151 968 Planarity : 0.005 0.047 985 Dihedral : 5.237 48.912 875 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.55 % Allowed : 29.87 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.31), residues: 757 helix: 1.82 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -1.21 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 421 TYR 0.009 0.001 TYR A 349 PHE 0.014 0.001 PHE A 437 TRP 0.006 0.001 TRP A 336 HIS 0.002 0.001 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 5930) covalent geometry : angle 0.68687 ( 8077) hydrogen bonds : bond 0.04606 ( 443) hydrogen bonds : angle 4.31792 ( 1296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.208 Fit side-chains REVERT: A 192 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7973 (mm) REVERT: A 200 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7286 (tt0) REVERT: A 227 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6997 (mtt-85) REVERT: A 331 MET cc_start: 0.7359 (mtp) cc_final: 0.7060 (mtp) REVERT: A 373 MET cc_start: 0.8042 (mmt) cc_final: 0.6164 (mmt) REVERT: A 374 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8028 (mp) REVERT: B 168 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8437 (mp) REVERT: B 428 SER cc_start: 0.7329 (OUTLIER) cc_final: 0.6664 (p) REVERT: B 474 LEU cc_start: 0.8692 (mt) cc_final: 0.8459 (mp) REVERT: B 480 SER cc_start: 0.7867 (t) cc_final: 0.7569 (p) outliers start: 28 outliers final: 19 residues processed: 137 average time/residue: 0.0542 time to fit residues: 10.5480 Evaluate side-chains 151 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 42 optimal weight: 0.0970 chunk 1 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 45 optimal weight: 0.0670 chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 0.0570 chunk 15 optimal weight: 0.5980 overall best weight: 0.3034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** 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 = 0.3835 r_free = 0.3835 target = 0.138154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.126915 restraints weight = 8155.591| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.06 r_work: 0.3578 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5930 Z= 0.136 Angle : 0.680 12.417 8077 Z= 0.318 Chirality : 0.044 0.153 968 Planarity : 0.005 0.045 985 Dihedral : 5.077 48.359 875 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.57 % Allowed : 31.82 % Favored : 64.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.32), residues: 757 helix: 1.89 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -1.14 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 421 TYR 0.008 0.001 TYR A 430 PHE 0.014 0.001 PHE A 437 TRP 0.007 0.001 TRP B 326 HIS 0.001 0.000 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 5930) covalent geometry : angle 0.68016 ( 8077) hydrogen bonds : bond 0.04318 ( 443) hydrogen bonds : angle 4.25236 ( 1296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1384.97 seconds wall clock time: 24 minutes 29.54 seconds (1469.54 seconds total)