Starting phenix.real_space_refine on Fri Apr 5 21:57:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgi_41237/04_2024/8tgi_41237_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgi_41237/04_2024/8tgi_41237.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgi_41237/04_2024/8tgi_41237_trim_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgi_41237/04_2024/8tgi_41237_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgi_41237/04_2024/8tgi_41237_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgi_41237/04_2024/8tgi_41237.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgi_41237/04_2024/8tgi_41237.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgi_41237/04_2024/8tgi_41237_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgi_41237/04_2024/8tgi_41237_trim_updated.pdb" } 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 Residue "A TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 3.65, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 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... running ksdssp... Secondary structure from input PDB file: 29 helices and 0 sheets defined 84.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 20 through 40 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) Processing helix chain 'A' and resid 42 through 50 Proline residue: A 46 - end of helix removed outlier: 3.591A pdb=" N TYR A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 145 through 164 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 167 through 186 removed outlier: 3.502A pdb=" N PHE A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 218 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 222 through 253 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 277 removed outlier: 4.344A pdb=" N PHE A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 296 No H-bonds generated for 'chain 'A' and resid 293 through 296' Processing helix chain 'A' and resid 300 through 330 removed outlier: 4.433A pdb=" N LEU A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Proline residue: A 321 - end of helix Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 335 through 341 removed outlier: 3.797A pdb=" N GLY A 339 " --> pdb=" O TRP A 336 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 341 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 363 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 365 through 385 Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 389 through 420 removed outlier: 3.500A pdb=" N ILE A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY A 394 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Proline residue: A 395 - end of helix removed outlier: 3.522A pdb=" N SER A 408 " --> pdb=" O MET A 405 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET A 411 " --> pdb=" O SER A 408 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 427 through 454 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 457 through 479 Proline residue: A 473 - end of helix removed outlier: 4.638A pdb=" N TYR A 476 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N TYR A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG A 479 " --> pdb=" O CYS A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 53 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 136 through 164 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 167 through 186 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 190 through 218 removed outlier: 3.675A pdb=" N LEU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 249 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 258 through 275 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) Processing helix chain 'B' and resid 293 through 298 removed outlier: 3.535A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LYS B 298 " --> pdb=" O PHE B 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 293 through 298' Processing helix chain 'B' and resid 300 through 330 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 340 through 363 removed outlier: 3.546A pdb=" N LEU B 343 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Proline residue: B 344 - end of helix removed outlier: 4.935A pdb=" N SER B 348 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE B 356 " --> pdb=" O THR B 353 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA B 360 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ASN B 361 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS B 362 " --> pdb=" O LEU B 359 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET B 363 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 385 Proline residue: B 384 - end of helix Processing helix chain 'B' and resid 389 through 421 removed outlier: 4.011A pdb=" N GLY B 394 " --> pdb=" O GLY B 391 " (cutoff:3.500A) Proline residue: B 395 - end of helix removed outlier: 4.560A pdb=" N MET B 411 " --> pdb=" O SER B 408 " (cutoff:3.500A) Proline residue: B 412 - end of helix removed outlier: 3.611A pdb=" N LEU B 420 " --> pdb=" O LEU B 417 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG B 421 " --> pdb=" O VAL B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 454 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 457 through 478 removed outlier: 3.842A pdb=" N MET B 461 " --> pdb=" O PHE B 457 " (cutoff:3.500A) Proline residue: B 473 - end of helix removed outlier: 4.931A pdb=" N TYR B 476 " --> pdb=" O ALA B 472 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N TYR B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1023 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: 1.53 Time building geometry restraints manager: 2.46 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=" C10 YHR B 601 " pdb=" C11 YHR B 601 " ideal model delta sigma weight residual 1.572 1.433 0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" C13 YHR B 601 " pdb=" C14 YHR B 601 " ideal model delta sigma weight residual 1.567 1.497 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " ideal model delta sigma weight residual 1.531 1.467 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C11 YHR B 601 " pdb=" C12 YHR B 601 " ideal model delta sigma weight residual 1.397 1.337 0.060 2.00e-02 2.50e+03 8.86e+00 bond pdb=" C11 YHR B 601 " pdb=" C23 YHR B 601 " ideal model delta sigma weight residual 1.373 1.429 -0.056 2.00e-02 2.50e+03 7.70e+00 ... (remaining 5925 not shown) Histogram of bond angle deviations from ideal: 98.72 - 106.17: 201 106.17 - 113.61: 3280 113.61 - 121.06: 3291 121.06 - 128.50: 1266 128.50 - 135.95: 39 Bond angle restraints: 8077 Sorted by residual: angle pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C9 YHR B 601 " ideal model delta sigma weight residual 99.45 131.20 -31.75 3.00e+00 1.11e-01 1.12e+02 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=" C25 YHR B 601 " pdb=" C26 YHR B 601 " pdb=" O28 YHR B 601 " ideal model delta sigma weight residual 137.71 119.08 18.63 3.00e+00 1.11e-01 3.86e+01 angle pdb=" C27 YHR B 601 " pdb=" C26 YHR B 601 " pdb=" O28 YHR B 601 " ideal model delta sigma weight residual 101.89 119.37 -17.48 3.00e+00 1.11e-01 3.39e+01 angle pdb=" C12 YHR B 601 " pdb=" C13 YHR B 601 " pdb=" N8 YHR B 601 " ideal model delta sigma weight residual 117.31 101.43 15.88 3.00e+00 1.11e-01 2.80e+01 ... (remaining 8072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.03: 3076 23.03 - 46.05: 304 46.05 - 69.08: 48 69.08 - 92.10: 3 92.10 - 115.13: 1 Dihedral angle restraints: 3432 sinusoidal: 1276 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 53.17 -61.96 115.13 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" C15 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 53.02 -38.98 92.00 1 3.00e+01 1.11e-03 1.10e+01 ... (remaining 3429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 777 0.053 - 0.105: 155 0.105 - 0.158: 27 0.158 - 0.210: 6 0.210 - 0.263: 3 Chirality restraints: 968 Sorted by residual: 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=" C15 YHR B 601 " pdb=" C14 YHR B 601 " pdb=" C16 YHR B 601 " pdb=" C6 YHR B 601 " both_signs ideal model delta sigma weight residual False 2.66 2.41 0.25 2.00e-01 2.50e+01 1.53e+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: 608 2.75 - 3.28: 6063 3.28 - 3.82: 9693 3.82 - 4.36: 10701 4.36 - 4.90: 19150 Nonbonded interactions: 46215 Sorted by model distance: nonbonded pdb=" O TRP B 326 " pdb=" OG1 THR B 330 " model vdw 2.208 2.440 nonbonded pdb=" O ARG A 138 " pdb=" OH TYR A 190 " model vdw 2.227 2.440 nonbonded pdb=" O ILE B 443 " pdb=" OG1 THR B 447 " model vdw 2.250 2.440 nonbonded pdb=" O THR A 464 " pdb=" ND2 ASN A 468 " model vdw 2.298 2.520 nonbonded pdb=" O GLY A 158 " pdb=" OG1 THR A 161 " model vdw 2.302 2.440 ... (remaining 46210 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 3.020 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: 0.000 Extract box with map and model: 12.730 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.460 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.420 ------------------------------------------------------------------------------- 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 0.139 5930 Z= 0.278 Angle : 0.876 31.750 8077 Z= 0.412 Chirality : 0.047 0.263 968 Planarity : 0.007 0.088 985 Dihedral : 17.294 115.127 2062 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 fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 0.525 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: 0.1279 time to fit residues: 23.9072 Evaluate side-chains 133 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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: 0.3980 chunk 31 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 0.0970 chunk 69 optimal weight: 0.0980 overall best weight: 0.3378 ------------------------------------------------------------------------------- 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** B 35 ASN B 396 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.0929 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= 0.212 Angle : 0.637 7.219 8077 Z= 0.312 Chirality : 0.044 0.218 968 Planarity : 0.006 0.047 985 Dihedral : 6.183 60.910 830 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.38 % Allowed : 29.06 % 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: 1.01 (0.31), residues: 757 helix: 1.23 (0.22), residues: 587 sheet: None (None), residues: 0 loop : -1.19 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 326 HIS 0.002 0.001 HIS A 416 PHE 0.014 0.001 PHE B 356 TYR 0.010 0.001 TYR A 430 ARG 0.001 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 161 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 0.627 Fit side-chains REVERT: A 192 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7473 (mm) REVERT: B 410 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7208 (mmm) outliers start: 27 outliers final: 11 residues processed: 146 average time/residue: 0.1295 time to fit residues: 26.8587 Evaluate side-chains 139 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 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 174 PHE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 330 THR 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 38 optimal weight: 0.0970 chunk 21 optimal weight: 0.7980 chunk 57 optimal weight: 0.0870 chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 61 optimal weight: 0.0270 chunk 68 optimal weight: 0.5980 chunk 23 optimal weight: 0.0570 chunk 55 optimal weight: 0.5980 overall best weight: 0.1732 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5930 Z= 0.168 Angle : 0.592 7.828 8077 Z= 0.286 Chirality : 0.042 0.278 968 Planarity : 0.005 0.037 985 Dihedral : 5.733 52.481 827 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.71 % Allowed : 29.38 % 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: 1.12 (0.31), residues: 757 helix: 1.32 (0.22), residues: 583 sheet: None (None), residues: 0 loop : -1.11 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.001 0.000 HIS B 416 PHE 0.017 0.001 PHE B 457 TYR 0.010 0.001 TYR A 430 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 159 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 0.533 Fit side-chains REVERT: A 192 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7465 (mm) REVERT: A 310 CYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7555 (t) REVERT: A 314 MET cc_start: 0.7519 (mtm) cc_final: 0.7277 (mtt) REVERT: A 374 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7825 (mt) REVERT: B 367 LEU cc_start: 0.7975 (tp) cc_final: 0.7720 (tt) outliers start: 29 outliers final: 12 residues processed: 144 average time/residue: 0.1385 time to fit residues: 28.0447 Evaluate side-chains 144 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 310 CYS 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 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 174 PHE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 289 LYS 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 68 optimal weight: 0.6980 chunk 51 optimal weight: 0.0980 chunk 35 optimal weight: 0.0770 chunk 7 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 65 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 overall best weight: 0.3538 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5930 Z= 0.197 Angle : 0.597 8.098 8077 Z= 0.290 Chirality : 0.043 0.153 968 Planarity : 0.005 0.038 985 Dihedral : 5.735 56.930 827 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 5.52 % Allowed : 29.22 % Favored : 65.26 % 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: 1.18 (0.31), residues: 757 helix: 1.36 (0.22), residues: 582 sheet: None (None), residues: 0 loop : -1.10 (0.45), residues: 175 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 0.012 0.001 PHE B 356 TYR 0.010 0.001 TYR A 430 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 167 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 0.639 Fit side-chains REVERT: A 192 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7524 (mm) REVERT: A 250 MET cc_start: 0.4600 (mmm) cc_final: 0.4398 (mmm) REVERT: B 367 LEU cc_start: 0.7989 (tp) cc_final: 0.7722 (tt) REVERT: B 411 MET cc_start: 0.8051 (mmt) cc_final: 0.7849 (mpp) outliers start: 34 outliers final: 15 residues processed: 145 average time/residue: 0.1396 time to fit residues: 28.7196 Evaluate side-chains 150 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 275 LEU Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 215 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.0770 chunk 41 optimal weight: 0.0470 chunk 1 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 0.0270 chunk 50 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 18 optimal weight: 0.0170 overall best weight: 0.1532 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5930 Z= 0.158 Angle : 0.588 8.671 8077 Z= 0.281 Chirality : 0.041 0.125 968 Planarity : 0.005 0.037 985 Dihedral : 5.670 56.594 827 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.90 % Allowed : 31.49 % 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 (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: 1.27 (0.32), residues: 757 helix: 1.42 (0.22), residues: 587 sheet: None (None), residues: 0 loop : -1.11 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.001 0.000 HIS B 416 PHE 0.014 0.001 PHE A 437 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 155 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 0.638 Fit side-chains REVERT: A 192 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7465 (mm) REVERT: A 314 MET cc_start: 0.7581 (mtm) cc_final: 0.7374 (mtm) REVERT: B 367 LEU cc_start: 0.7981 (tp) cc_final: 0.7748 (tt) outliers start: 24 outliers final: 15 residues processed: 141 average time/residue: 0.1209 time to fit residues: 24.5767 Evaluate side-chains 144 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 275 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 401 LEU 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 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 294 PHE 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 24 optimal weight: 1.9990 chunk 66 optimal weight: 0.0170 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 61 optimal weight: 0.0370 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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** A 396 ASN B 468 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5930 Z= 0.198 Angle : 0.617 9.965 8077 Z= 0.296 Chirality : 0.042 0.132 968 Planarity : 0.005 0.038 985 Dihedral : 5.710 59.520 827 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.55 % Allowed : 31.17 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.32), residues: 757 helix: 1.43 (0.23), residues: 588 sheet: None (None), residues: 0 loop : -1.34 (0.44), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 326 HIS 0.002 0.001 HIS A 416 PHE 0.010 0.001 PHE A 28 TYR 0.010 0.001 TYR A 430 ARG 0.004 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 158 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 0.671 Fit side-chains REVERT: A 192 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7553 (mm) REVERT: B 367 LEU cc_start: 0.8027 (tp) cc_final: 0.7785 (tt) outliers start: 28 outliers final: 19 residues processed: 141 average time/residue: 0.1227 time to fit residues: 24.7581 Evaluate side-chains 149 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 256 LYS Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 438 CYS 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 174 PHE Chi-restraints excluded: chain B residue 215 LEU 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 322 THR Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 378 THR 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 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.0170 chunk 53 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5930 Z= 0.229 Angle : 0.622 8.587 8077 Z= 0.301 Chirality : 0.043 0.133 968 Planarity : 0.005 0.040 985 Dihedral : 5.843 65.654 827 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.06 % Allowed : 32.14 % Favored : 63.80 % 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: 1.14 (0.32), residues: 757 helix: 1.38 (0.23), residues: 585 sheet: None (None), residues: 0 loop : -1.35 (0.44), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 366 HIS 0.002 0.001 HIS A 416 PHE 0.010 0.001 PHE A 28 TYR 0.011 0.001 TYR A 349 ARG 0.004 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 155 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 0.606 Fit side-chains REVERT: A 149 MET cc_start: 0.8072 (ptp) cc_final: 0.7838 (ptm) REVERT: A 192 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7613 (mm) REVERT: B 367 LEU cc_start: 0.8011 (tp) cc_final: 0.7760 (tt) outliers start: 25 outliers final: 16 residues processed: 140 average time/residue: 0.1199 time to fit residues: 24.3461 Evaluate side-chains 145 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 328 MET Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 438 CYS 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 322 THR Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 378 THR 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 14 optimal weight: 0.3980 chunk 46 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 57 optimal weight: 0.0670 chunk 66 optimal weight: 0.0070 chunk 70 optimal weight: 0.0030 chunk 64 optimal weight: 0.3980 chunk 68 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 overall best weight: 0.1746 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5930 Z= 0.170 Angle : 0.615 11.388 8077 Z= 0.293 Chirality : 0.041 0.135 968 Planarity : 0.005 0.038 985 Dihedral : 5.701 62.995 827 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.25 % Allowed : 32.47 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.32), residues: 757 helix: 1.45 (0.23), residues: 583 sheet: None (None), residues: 0 loop : -1.33 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.001 0.000 HIS B 416 PHE 0.013 0.001 PHE A 437 TYR 0.010 0.001 TYR A 430 ARG 0.002 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 148 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 0.620 Fit side-chains REVERT: A 149 MET cc_start: 0.7936 (ptp) cc_final: 0.7728 (ptm) REVERT: A 192 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7588 (mm) REVERT: B 367 LEU cc_start: 0.7985 (tp) cc_final: 0.7784 (tt) outliers start: 20 outliers final: 17 residues processed: 135 average time/residue: 0.1250 time to fit residues: 24.2306 Evaluate side-chains 148 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 256 LYS Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 438 CYS 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 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 378 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 64 optimal weight: 0.1980 chunk 68 optimal weight: 0.5980 chunk 44 optimal weight: 0.1980 chunk 72 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 75 optimal weight: 0.0010 overall best weight: 0.2786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2143 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= 0.182 Angle : 0.616 11.500 8077 Z= 0.294 Chirality : 0.042 0.144 968 Planarity : 0.005 0.038 985 Dihedral : 5.659 63.901 827 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.41 % Allowed : 31.49 % Favored : 65.10 % 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: 1.27 (0.32), residues: 757 helix: 1.47 (0.23), residues: 584 sheet: None (None), residues: 0 loop : -1.29 (0.44), residues: 173 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 0.016 0.001 PHE B 356 TYR 0.010 0.001 TYR A 430 ARG 0.003 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 151 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 0.627 Fit side-chains REVERT: A 192 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7621 (mm) REVERT: B 289 LYS cc_start: 0.6656 (OUTLIER) cc_final: 0.5872 (tmtm) REVERT: B 367 LEU cc_start: 0.8014 (tp) cc_final: 0.7791 (tt) outliers start: 21 outliers final: 16 residues processed: 136 average time/residue: 0.1227 time to fit residues: 24.1421 Evaluate side-chains 149 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 328 MET Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 438 CYS 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 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 378 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** A 416 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5930 Z= 0.279 Angle : 0.676 11.365 8077 Z= 0.325 Chirality : 0.045 0.151 968 Planarity : 0.005 0.041 985 Dihedral : 5.840 71.099 827 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.08 % Allowed : 32.47 % Favored : 64.45 % 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: 1.13 (0.32), residues: 757 helix: 1.29 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -1.16 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 336 HIS 0.003 0.001 HIS A 416 PHE 0.015 0.001 PHE B 356 TYR 0.014 0.002 TYR A 349 ARG 0.006 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 149 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 0.623 Fit side-chains REVERT: A 192 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7691 (mm) REVERT: B 21 GLN cc_start: 0.7818 (mp10) cc_final: 0.7572 (mp10) REVERT: B 289 LYS cc_start: 0.6707 (OUTLIER) cc_final: 0.5957 (tmtm) REVERT: B 367 LEU cc_start: 0.8062 (tp) cc_final: 0.7802 (tt) outliers start: 19 outliers final: 12 residues processed: 136 average time/residue: 0.1180 time to fit residues: 23.1403 Evaluate side-chains 143 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 423 THR Chi-restraints excluded: chain A residue 438 CYS 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 378 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 69 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.135473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.124252 restraints weight = 8241.390| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.06 r_work: 0.3543 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5930 Z= 0.278 Angle : 0.681 10.947 8077 Z= 0.328 Chirality : 0.045 0.153 968 Planarity : 0.005 0.040 985 Dihedral : 5.976 76.262 827 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.60 % Allowed : 33.28 % Favored : 64.12 % 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: 0.92 (0.31), residues: 757 helix: 1.14 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -1.24 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 336 HIS 0.002 0.001 HIS A 387 PHE 0.017 0.001 PHE B 356 TYR 0.014 0.002 TYR A 349 ARG 0.007 0.000 ARG A 421 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1718.21 seconds wall clock time: 31 minutes 38.89 seconds (1898.89 seconds total)