Starting phenix.real_space_refine on Tue Feb 11 13:32:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tgi_41237/02_2025/8tgi_41237_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tgi_41237/02_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_41237/02_2025/8tgi_41237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tgi_41237/02_2025/8tgi_41237.map" model { file = "/net/cci-nas-00/data/ceres_data/8tgi_41237/02_2025/8tgi_41237_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tgi_41237/02_2025/8tgi_41237_trim.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.94, per 1000 atoms: 0.85 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: 1.59 Conformation dependent library (CDL) restraints added in 903.5 milliseconds 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: 0.57 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: 1.82 Time building geometry restraints manager: 1.82 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: 4.630 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.480 Find NCS groups from input model: 0.260 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.790 ------------------------------------------------------------------------------- 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= 0.292 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 (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: 0.60 (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 TRP 0.011 0.001 TRP B 326 HIS 0.001 0.001 HIS A 416 PHE 0.020 0.001 PHE A 48 TYR 0.008 0.001 TYR A 430 ARG 0.004 0.000 ARG A 421 *********************** 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 : 0.609 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: 0.1328 time to fit residues: 24.8213 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 : 0.589 ------------------------------------------------------------------------------- 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 64 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 0.0770 chunk 19 optimal weight: 0.0060 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 0.0970 chunk 36 optimal weight: 0.5980 chunk 44 optimal weight: 0.0070 chunk 69 optimal weight: 0.7980 overall best weight: 0.1570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN B 35 ASN B 396 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.140965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.129763 restraints weight = 8165.720| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.07 r_work: 0.3618 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.1068 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= 0.191 Angle : 0.642 7.520 8077 Z= 0.310 Chirality : 0.043 0.144 968 Planarity : 0.005 0.048 985 Dihedral : 8.504 73.248 878 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.38 % Allowed : 28.73 % 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 (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: 1.60 (0.31), residues: 757 helix: 1.66 (0.22), residues: 595 sheet: None (None), residues: 0 loop : -1.15 (0.43), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 326 HIS 0.002 0.001 HIS B 422 PHE 0.012 0.001 PHE A 356 TYR 0.008 0.001 TYR A 430 ARG 0.002 0.000 ARG A 421 *********************** 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 164 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 192 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7617 (mm) REVERT: B 170 MET cc_start: 0.6646 (tpt) cc_final: 0.6417 (tpt) REVERT: B 410 MET cc_start: 0.7743 (mmt) cc_final: 0.7501 (mmm) outliers start: 27 outliers final: 10 residues processed: 153 average time/residue: 0.1244 time to fit residues: 27.6922 Evaluate side-chains 140 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 363 MET 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 174 PHE Chi-restraints excluded: chain B residue 289 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 16 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 42 optimal weight: 0.0070 chunk 67 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 = 0.3814 r_free = 0.3814 target = 0.136972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.125774 restraints weight = 8263.017| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.08 r_work: 0.3559 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 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 : 0.004 0.048 5930 Z= 0.275 Angle : 0.656 10.640 8077 Z= 0.318 Chirality : 0.045 0.189 968 Planarity : 0.005 0.044 985 Dihedral : 7.068 55.912 875 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 5.03 % Allowed : 27.60 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.31), residues: 757 helix: 1.82 (0.22), residues: 590 sheet: None (None), residues: 0 loop : -1.14 (0.43), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 336 HIS 0.002 0.001 HIS A 167 PHE 0.011 0.001 PHE B 356 TYR 0.013 0.002 TYR A 349 ARG 0.002 0.000 ARG A 421 *********************** 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 167 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 192 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7729 (mm) REVERT: A 250 MET cc_start: 0.4981 (mmm) cc_final: 0.4722 (mmm) REVERT: A 374 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8193 (mt) REVERT: B 367 LEU cc_start: 0.8090 (tp) cc_final: 0.7761 (tt) REVERT: B 457 PHE cc_start: 0.7220 (t80) cc_final: 0.6757 (t80) REVERT: B 477 TYR cc_start: 0.7403 (m-10) cc_final: 0.6894 (m-80) outliers start: 31 outliers final: 13 residues processed: 149 average time/residue: 0.1161 time to fit residues: 25.1171 Evaluate side-chains 148 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR 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 134 GLU Chi-restraints excluded: chain B residue 174 PHE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 15 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 60 optimal weight: 0.0970 chunk 47 optimal weight: 0.9990 chunk 2 optimal weight: 0.0980 chunk 72 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3816 r_free = 0.3816 target = 0.136831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.125329 restraints weight = 8481.531| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.12 r_work: 0.3555 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1682 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= 0.252 Angle : 0.656 12.159 8077 Z= 0.314 Chirality : 0.045 0.149 968 Planarity : 0.005 0.046 985 Dihedral : 6.112 50.466 875 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 5.19 % Allowed : 27.92 % 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 (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: 1.88 (0.31), residues: 757 helix: 1.88 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -1.11 (0.43), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 336 HIS 0.002 0.001 HIS A 167 PHE 0.013 0.001 PHE A 437 TYR 0.011 0.001 TYR A 166 ARG 0.003 0.000 ARG A 421 *********************** 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 168 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.598 Fit side-chains REVERT: A 192 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7743 (mm) REVERT: A 250 MET cc_start: 0.4877 (mmm) cc_final: 0.4584 (mmm) REVERT: B 21 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: B 367 LEU cc_start: 0.8011 (tp) cc_final: 0.7701 (tt) REVERT: B 389 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7747 (tt) REVERT: B 474 LEU cc_start: 0.8672 (mt) cc_final: 0.8453 (mp) REVERT: B 477 TYR cc_start: 0.7448 (m-10) cc_final: 0.6920 (m-80) outliers start: 32 outliers final: 16 residues processed: 147 average time/residue: 0.1219 time to fit residues: 25.9515 Evaluate side-chains 153 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 21 GLN Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 174 PHE 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 37 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 0.0060 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 0.0980 chunk 35 optimal weight: 0.0770 chunk 45 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 overall best weight: 0.3154 ------------------------------------------------------------------------------- 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 = 0.137440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.126684 restraints weight = 8231.777| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.01 r_work: 0.3590 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1775 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= 0.201 Angle : 0.646 11.850 8077 Z= 0.303 Chirality : 0.043 0.137 968 Planarity : 0.005 0.043 985 Dihedral : 5.558 50.392 875 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 4.22 % Allowed : 29.71 % Favored : 66.07 % 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: 2.03 (0.31), residues: 757 helix: 2.00 (0.22), residues: 590 sheet: None (None), residues: 0 loop : -1.05 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 326 HIS 0.001 0.001 HIS A 167 PHE 0.013 0.001 PHE B 457 TYR 0.009 0.001 TYR A 430 ARG 0.003 0.000 ARG A 421 *********************** 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 158 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.627 Fit side-chains REVERT: A 192 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7738 (mm) REVERT: A 250 MET cc_start: 0.4929 (mmm) cc_final: 0.4691 (mmm) REVERT: B 149 MET cc_start: 0.8112 (tpp) cc_final: 0.7714 (mmm) REVERT: B 229 MET cc_start: 0.5752 (tpt) cc_final: 0.5445 (mmm) REVERT: B 367 LEU cc_start: 0.8050 (tp) cc_final: 0.7758 (tt) REVERT: B 474 LEU cc_start: 0.8715 (mt) cc_final: 0.8485 (mp) REVERT: B 480 SER cc_start: 0.7856 (t) cc_final: 0.7602 (p) outliers start: 26 outliers final: 8 residues processed: 141 average time/residue: 0.1454 time to fit residues: 29.5732 Evaluate side-chains 139 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 443 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 331 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 52 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 73 optimal weight: 0.0980 chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 72 optimal weight: 0.9980 chunk 32 optimal weight: 0.0270 chunk 57 optimal weight: 0.0670 chunk 21 optimal weight: 0.7980 overall best weight: 0.2576 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.137825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.127319 restraints weight = 8270.339| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.94 r_work: 0.3600 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5930 Z= 0.189 Angle : 0.632 11.747 8077 Z= 0.298 Chirality : 0.042 0.135 968 Planarity : 0.005 0.042 985 Dihedral : 5.385 50.203 875 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.41 % Allowed : 30.84 % 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 (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: 2.15 (0.32), residues: 757 helix: 2.08 (0.22), residues: 590 sheet: None (None), residues: 0 loop : -1.00 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.001 0.000 HIS A 167 PHE 0.013 0.001 PHE A 356 TYR 0.009 0.001 TYR A 430 ARG 0.002 0.000 ARG A 421 *********************** 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 154 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.554 Fit side-chains REVERT: A 192 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7764 (mm) REVERT: B 149 MET cc_start: 0.8124 (tpp) cc_final: 0.7718 (mmm) REVERT: B 261 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7899 (mm) REVERT: B 367 LEU cc_start: 0.8045 (tp) cc_final: 0.7740 (tt) REVERT: B 411 MET cc_start: 0.8025 (mmt) cc_final: 0.7811 (mpp) REVERT: B 474 LEU cc_start: 0.8724 (mt) cc_final: 0.8483 (mp) REVERT: B 480 SER cc_start: 0.7825 (t) cc_final: 0.7567 (p) outliers start: 21 outliers final: 13 residues processed: 139 average time/residue: 0.1251 time to fit residues: 25.3151 Evaluate side-chains 146 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 401 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 261 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 428 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 44 optimal weight: 0.4980 chunk 75 optimal weight: 0.6980 chunk 35 optimal weight: 0.1980 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.0370 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 overall best weight: 0.4258 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.136891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.126445 restraints weight = 8247.899| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.93 r_work: 0.3588 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1932 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= 0.229 Angle : 0.654 12.291 8077 Z= 0.308 Chirality : 0.043 0.137 968 Planarity : 0.005 0.041 985 Dihedral : 5.338 49.819 875 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.57 % Allowed : 30.68 % 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 (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: 2.01 (0.32), residues: 757 helix: 1.99 (0.22), residues: 600 sheet: None (None), residues: 0 loop : -1.30 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 326 HIS 0.002 0.001 HIS A 167 PHE 0.012 0.001 PHE B 356 TYR 0.009 0.001 TYR A 430 ARG 0.003 0.000 ARG A 421 *********************** 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 153 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.592 Fit side-chains REVERT: A 192 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7804 (mm) REVERT: B 149 MET cc_start: 0.8127 (tpp) cc_final: 0.7669 (mmm) REVERT: B 367 LEU cc_start: 0.8069 (tp) cc_final: 0.7794 (tt) REVERT: B 474 LEU cc_start: 0.8731 (mt) cc_final: 0.8503 (mp) outliers start: 22 outliers final: 14 residues processed: 138 average time/residue: 0.1249 time to fit residues: 25.0609 Evaluate side-chains 144 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET 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 328 MET Chi-restraints excluded: chain A residue 363 MET 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 22 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 428 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.135209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.124958 restraints weight = 8206.772| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.89 r_work: 0.3570 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2086 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= 0.282 Angle : 0.683 13.207 8077 Z= 0.325 Chirality : 0.045 0.143 968 Planarity : 0.005 0.044 985 Dihedral : 5.399 49.489 875 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.22 % Allowed : 29.87 % Favored : 65.91 % 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: 1.90 (0.31), residues: 757 helix: 1.87 (0.22), residues: 605 sheet: None (None), residues: 0 loop : -1.22 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 336 HIS 0.003 0.001 HIS A 167 PHE 0.013 0.001 PHE B 457 TYR 0.013 0.002 TYR A 349 ARG 0.003 0.000 ARG A 421 *********************** 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 158 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.620 Fit side-chains REVERT: A 192 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7873 (mm) REVERT: B 367 LEU cc_start: 0.8093 (tp) cc_final: 0.7804 (tt) REVERT: B 373 MET cc_start: 0.7797 (tpp) cc_final: 0.7546 (mtp) REVERT: B 410 MET cc_start: 0.7767 (mmp) cc_final: 0.7496 (mmm) REVERT: B 474 LEU cc_start: 0.8719 (mt) cc_final: 0.8490 (mp) REVERT: B 480 SER cc_start: 0.7899 (t) cc_final: 0.7603 (p) outliers start: 26 outliers final: 16 residues processed: 141 average time/residue: 0.1189 time to fit residues: 24.3883 Evaluate side-chains 148 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 328 MET Chi-restraints excluded: chain A residue 363 MET 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 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 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 57 optimal weight: 0.0070 chunk 56 optimal weight: 0.0770 chunk 12 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 0.1980 chunk 42 optimal weight: 0.2980 overall best weight: 0.2356 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.138658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.127146 restraints weight = 8262.860| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.11 r_work: 0.3582 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5930 Z= 0.190 Angle : 0.665 12.067 8077 Z= 0.311 Chirality : 0.043 0.230 968 Planarity : 0.005 0.042 985 Dihedral : 5.175 49.237 875 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.08 % Allowed : 30.36 % Favored : 66.56 % 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: 2.01 (0.32), residues: 757 helix: 1.99 (0.22), residues: 601 sheet: None (None), residues: 0 loop : -1.31 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.001 0.000 HIS A 416 PHE 0.014 0.001 PHE A 437 TYR 0.009 0.001 TYR A 430 ARG 0.002 0.000 ARG A 421 *********************** 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 150 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.580 Fit side-chains REVERT: A 151 LEU cc_start: 0.8450 (tt) cc_final: 0.8216 (mp) REVERT: A 192 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7845 (mm) REVERT: A 250 MET cc_start: 0.4454 (mmm) cc_final: 0.4208 (mmm) REVERT: B 149 MET cc_start: 0.8108 (tpp) cc_final: 0.7609 (mmm) REVERT: B 367 LEU cc_start: 0.8004 (tp) cc_final: 0.7733 (tt) REVERT: B 410 MET cc_start: 0.7814 (mmp) cc_final: 0.7547 (mmm) REVERT: B 428 SER cc_start: 0.7255 (OUTLIER) cc_final: 0.6636 (p) REVERT: B 474 LEU cc_start: 0.8721 (mt) cc_final: 0.8474 (mp) outliers start: 19 outliers final: 13 residues processed: 136 average time/residue: 0.1187 time to fit residues: 23.5498 Evaluate side-chains 145 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 328 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 52 MET 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 428 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 71 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 73 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 0.0980 chunk 57 optimal weight: 5.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 = 0.3832 r_free = 0.3832 target = 0.137967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.126828 restraints weight = 8283.715| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.03 r_work: 0.3582 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5930 Z= 0.226 Angle : 0.682 12.310 8077 Z= 0.319 Chirality : 0.044 0.187 968 Planarity : 0.005 0.042 985 Dihedral : 5.156 48.625 875 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.76 % Allowed : 31.01 % 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 (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: 1.98 (0.32), residues: 757 helix: 1.96 (0.22), residues: 600 sheet: None (None), residues: 0 loop : -1.27 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 326 HIS 0.002 0.001 HIS A 416 PHE 0.013 0.001 PHE A 437 TYR 0.009 0.001 TYR A 430 ARG 0.003 0.000 ARG A 421 ********************** 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 146 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.603 Fit side-chains REVERT: A 151 LEU cc_start: 0.8461 (tt) cc_final: 0.8222 (mp) REVERT: A 192 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7867 (mm) REVERT: A 250 MET cc_start: 0.4470 (mmm) cc_final: 0.4183 (mmm) REVERT: B 367 LEU cc_start: 0.8048 (tp) cc_final: 0.7773 (tt) REVERT: B 410 MET cc_start: 0.7811 (mmp) cc_final: 0.7573 (mmm) REVERT: B 474 LEU cc_start: 0.8729 (mt) cc_final: 0.8485 (mp) outliers start: 17 outliers final: 13 residues processed: 133 average time/residue: 0.1206 time to fit residues: 23.1927 Evaluate side-chains 142 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 328 MET Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 52 MET 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 428 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 11 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 0.1980 chunk 18 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 57 optimal weight: 0.0000 chunk 15 optimal weight: 0.1980 chunk 47 optimal weight: 0.6980 overall best weight: 0.3184 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.138556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.126957 restraints weight = 8434.569| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.15 r_work: 0.3581 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 5930 Z= 0.214 Angle : 0.674 12.160 8077 Z= 0.317 Chirality : 0.044 0.191 968 Planarity : 0.005 0.042 985 Dihedral : 5.119 48.123 875 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.60 % Allowed : 31.33 % Favored : 66.07 % 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: 1.95 (0.32), residues: 757 helix: 1.93 (0.22), residues: 601 sheet: None (None), residues: 0 loop : -1.26 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 326 HIS 0.001 0.000 HIS A 416 PHE 0.014 0.001 PHE B 356 TYR 0.009 0.001 TYR A 430 ARG 0.003 0.000 ARG A 421 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3018.49 seconds wall clock time: 54 minutes 25.20 seconds (3265.20 seconds total)