Starting phenix.real_space_refine on Sun Aug 24 04:48:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vdc_64982/08_2025/9vdc_64982.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vdc_64982/08_2025/9vdc_64982.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 { model { file = "/net/cci-nas-00/data/ceres_data/9vdc_64982/08_2025/9vdc_64982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vdc_64982/08_2025/9vdc_64982.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vdc_64982/08_2025/9vdc_64982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vdc_64982/08_2025/9vdc_64982.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.020 sd= 0.080 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: 5 Type Number sf(0) Gaussians S 34 5.16 5 C 5303 2.51 5 N 1289 2.21 5 O 1471 1.98 5 H 8443 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16540 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 8257 Classifications: {'peptide': 544} Modifications used: {'COO': 1, 'NH3': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 525} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 8255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 8255 Classifications: {'peptide': 545} Modifications used: {'COO': 1, 'NH3': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 526} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Time building chain proxies: 3.35, per 1000 atoms: 0.20 Number of scatterers: 16540 At special positions: 0 Unit cell: (81.965, 107.315, 111.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 O 1471 8.00 N 1289 7.00 C 5303 6.00 H 8443 1.00 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: 1.36 Conformation dependent library (CDL) restraints added in 519.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1974 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 8 sheets defined 68.0% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.747A pdb=" N ASN A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 19 Processing helix chain 'A' and resid 20 through 29 removed outlier: 3.696A pdb=" N TYR A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 50 Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 58 through 88 removed outlier: 3.862A pdb=" N GLY A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Proline residue: A 79 - end of helix removed outlier: 3.813A pdb=" N ILE A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER A 83 " --> pdb=" O PRO A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 115 Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 133 through 145 removed outlier: 4.032A pdb=" N SER A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 180 removed outlier: 3.672A pdb=" N ILE A 159 " --> pdb=" O TYR A 155 " (cutoff:3.500A) Proline residue: A 160 - end of helix removed outlier: 3.794A pdb=" N VAL A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N VAL A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU A 175 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N PHE A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 189 through 201 Processing helix chain 'A' and resid 228 through 236 removed outlier: 3.618A pdb=" N VAL A 232 " --> pdb=" O THR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 302 through 312 removed outlier: 4.496A pdb=" N GLN A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASP A 310 " --> pdb=" O LYS A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.686A pdb=" N PHE A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 330' Processing helix chain 'A' and resid 344 through 353 Processing helix chain 'A' and resid 364 through 381 removed outlier: 3.607A pdb=" N PHE A 368 " --> pdb=" O ASN A 364 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 408 Processing helix chain 'A' and resid 422 through 442 removed outlier: 5.037A pdb=" N LEU A 431 " --> pdb=" O GLN A 427 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASN A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 454 through 478 removed outlier: 3.829A pdb=" N LEU A 458 " --> pdb=" O GLY A 454 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Proline residue: A 468 - end of helix Processing helix chain 'A' and resid 483 through 490 removed outlier: 3.753A pdb=" N ILE A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE A 488 " --> pdb=" O PRO A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 509 removed outlier: 3.762A pdb=" N LEU A 501 " --> pdb=" O LEU A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 543 Proline residue: A 522 - end of helix removed outlier: 4.198A pdb=" N ALA A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE A 526 " --> pdb=" O PRO A 522 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Proline residue: A 536 - end of helix Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.736A pdb=" N ASN B 6 " --> pdb=" O ASN B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 19 Processing helix chain 'B' and resid 20 through 29 removed outlier: 3.708A pdb=" N TYR B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 50 Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 58 through 88 removed outlier: 3.858A pdb=" N GLY B 62 " --> pdb=" O ASP B 58 " (cutoff:3.500A) Proline residue: B 79 - end of helix removed outlier: 3.812A pdb=" N ILE B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 115 Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 133 through 145 removed outlier: 4.037A pdb=" N SER B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 180 removed outlier: 3.675A pdb=" N ILE B 159 " --> pdb=" O TYR B 155 " (cutoff:3.500A) Proline residue: B 160 - end of helix removed outlier: 3.798A pdb=" N VAL B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N VAL B 174 " --> pdb=" O GLY B 170 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU B 175 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE B 176 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 187 Processing helix chain 'B' and resid 189 through 201 Processing helix chain 'B' and resid 228 through 236 removed outlier: 3.621A pdb=" N VAL B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 302 through 312 removed outlier: 4.499A pdb=" N GLN B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ASP B 310 " --> pdb=" O LYS B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 removed outlier: 3.597A pdb=" N PHE B 328 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER B 329 " --> pdb=" O PRO B 325 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 324 through 330' Processing helix chain 'B' and resid 344 through 353 Processing helix chain 'B' and resid 364 through 381 removed outlier: 3.603A pdb=" N PHE B 368 " --> pdb=" O ASN B 364 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 408 Processing helix chain 'B' and resid 422 through 442 removed outlier: 5.042A pdb=" N LEU B 431 " --> pdb=" O GLN B 427 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ASN B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 453 Processing helix chain 'B' and resid 454 through 478 removed outlier: 3.839A pdb=" N LEU B 458 " --> pdb=" O GLY B 454 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) Proline residue: B 468 - end of helix Processing helix chain 'B' and resid 483 through 490 removed outlier: 3.761A pdb=" N ILE B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE B 488 " --> pdb=" O PRO B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 509 Processing helix chain 'B' and resid 512 through 543 Proline residue: B 522 - end of helix removed outlier: 4.198A pdb=" N ALA B 525 " --> pdb=" O ALA B 521 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE B 526 " --> pdb=" O PRO B 522 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY B 535 " --> pdb=" O LEU B 531 " (cutoff:3.500A) Proline residue: B 536 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 212 through 214 Processing sheet with id=AA2, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AA3, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 385 Processing sheet with id=AA5, first strand: chain 'B' and resid 212 through 214 Processing sheet with id=AA6, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AA7, first strand: chain 'B' and resid 292 through 295 Processing sheet with id=AA8, first strand: chain 'B' and resid 382 through 385 487 hydrogen bonds defined for protein. 1428 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: 3.73 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8437 1.03 - 1.23: 7 1.23 - 1.42: 3263 1.42 - 1.61: 4915 1.61 - 1.81: 62 Bond restraints: 16684 Sorted by residual: bond pdb=" N PRO B 333 " pdb=" CA PRO B 333 " ideal model delta sigma weight residual 1.479 1.468 0.012 1.71e-02 3.42e+03 4.68e-01 bond pdb=" CA PRO B 333 " pdb=" C PRO B 333 " ideal model delta sigma weight residual 1.527 1.520 0.007 1.07e-02 8.73e+03 3.84e-01 bond pdb=" CG PRO A 389 " pdb=" CD PRO A 389 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.65e-01 bond pdb=" CB LEU B 331 " pdb=" CG LEU B 331 " ideal model delta sigma weight residual 1.530 1.542 -0.012 2.00e-02 2.50e+03 3.50e-01 bond pdb=" CG PRO B 389 " pdb=" CD PRO B 389 " ideal model delta sigma weight residual 1.503 1.484 0.019 3.40e-02 8.65e+02 3.23e-01 ... (remaining 16679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 28302 1.03 - 2.06: 1935 2.06 - 3.08: 69 3.08 - 4.11: 28 4.11 - 5.14: 3 Bond angle restraints: 30337 Sorted by residual: angle pdb=" N LEU B 129 " pdb=" CA LEU B 129 " pdb=" C LEU B 129 " ideal model delta sigma weight residual 110.80 105.66 5.14 2.13e+00 2.20e-01 5.82e+00 angle pdb=" N THR B 330 " pdb=" CA THR B 330 " pdb=" C THR B 330 " ideal model delta sigma weight residual 112.12 109.53 2.59 1.34e+00 5.57e-01 3.74e+00 angle pdb=" CA PRO B 333 " pdb=" C PRO B 333 " pdb=" O PRO B 333 " ideal model delta sigma weight residual 123.16 120.41 2.75 1.49e+00 4.50e-01 3.42e+00 angle pdb=" C GLY B 128 " pdb=" N LEU B 129 " pdb=" CA LEU B 129 " ideal model delta sigma weight residual 121.54 118.31 3.23 1.91e+00 2.74e-01 2.85e+00 angle pdb=" N GLY A 173 " pdb=" CA GLY A 173 " pdb=" C GLY A 173 " ideal model delta sigma weight residual 112.60 110.16 2.44 1.53e+00 4.27e-01 2.54e+00 ... (remaining 30332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6858 17.97 - 35.93: 612 35.93 - 53.90: 254 53.90 - 71.86: 74 71.86 - 89.83: 4 Dihedral angle restraints: 7802 sinusoidal: 4219 harmonic: 3583 Sorted by residual: dihedral pdb=" CA LEU B 129 " pdb=" C LEU B 129 " pdb=" N THR B 130 " pdb=" CA THR B 130 " ideal model delta harmonic sigma weight residual 180.00 -158.67 -21.33 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA PHE A 17 " pdb=" C PHE A 17 " pdb=" N ILE A 18 " pdb=" CA ILE A 18 " ideal model delta harmonic sigma weight residual 180.00 162.73 17.27 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA PHE B 17 " pdb=" C PHE B 17 " pdb=" N ILE B 18 " pdb=" CA ILE B 18 " ideal model delta harmonic sigma weight residual 180.00 162.73 17.27 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 7799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 852 0.027 - 0.054: 320 0.054 - 0.080: 129 0.080 - 0.107: 72 0.107 - 0.134: 16 Chirality restraints: 1389 Sorted by residual: chirality pdb=" CA ILE A 204 " pdb=" N ILE A 204 " pdb=" C ILE A 204 " pdb=" CB ILE A 204 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA ILE B 204 " pdb=" N ILE B 204 " pdb=" C ILE B 204 " pdb=" CB ILE B 204 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA VAL A 388 " pdb=" N VAL A 388 " pdb=" C VAL A 388 " pdb=" CB VAL A 388 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 1386 not shown) Planarity restraints: 2431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 388 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO A 389 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 389 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 389 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 388 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO B 389 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 389 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 389 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 355 " -0.117 9.50e-02 1.11e+02 3.90e-02 1.84e+00 pdb=" NE ARG A 355 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 355 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 355 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 355 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 355 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 355 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 355 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 355 " -0.000 2.00e-02 2.50e+03 ... (remaining 2428 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.39: 6650 2.39 - 2.94: 38347 2.94 - 3.49: 41397 3.49 - 4.05: 53766 4.05 - 4.60: 80802 Nonbonded interactions: 220962 Sorted by model distance: nonbonded pdb="HD22 ASN A 278 " pdb="HD22 ASN B 278 " model vdw 1.833 2.100 nonbonded pdb=" HG3 ARG B 355 " pdb="HH11 ARG B 355 " model vdw 1.857 2.270 nonbonded pdb=" HG3 ARG A 355 " pdb="HH11 ARG A 355 " model vdw 1.858 2.270 nonbonded pdb=" HA LEU A 296 " pdb=" H GLY A 354 " model vdw 1.897 2.270 nonbonded pdb=" H ILE A 270 " pdb="HG12 ILE A 270 " model vdw 1.906 2.270 ... (remaining 220957 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 1 through 332 or (resid 333 and (name N or name CA or name \ C or name O or name CB or name CG or name CD )) or resid 334 through 601)) selection = (chain 'B' and (resid 1 through 331A or resid 332 through 601)) } 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: 1.570 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: 0.100 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.120 Find NCS groups from input model: 0.250 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8241 Z= 0.134 Angle : 0.468 5.139 11191 Z= 0.256 Chirality : 0.038 0.134 1389 Planarity : 0.004 0.051 1385 Dihedral : 16.385 89.825 2879 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.38 % Allowed : 27.07 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.27), residues: 1081 helix: 2.01 (0.21), residues: 698 sheet: -1.00 (0.87), residues: 24 loop : -1.86 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 355 TYR 0.006 0.001 TYR B 163 PHE 0.010 0.001 PHE A 368 TRP 0.002 0.001 TRP A 367 HIS 0.001 0.000 HIS A 469 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8241) covalent geometry : angle 0.46760 (11191) hydrogen bonds : bond 0.05100 ( 487) hydrogen bonds : angle 4.06479 ( 1428) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ASN cc_start: 0.8102 (p0) cc_final: 0.7765 (m-40) REVERT: A 280 LEU cc_start: 0.6935 (mm) cc_final: 0.6568 (mt) REVERT: A 309 GLN cc_start: 0.9058 (mt0) cc_final: 0.8425 (mp10) REVERT: B 25 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8143 (mp) REVERT: B 49 ILE cc_start: 0.9055 (tt) cc_final: 0.8770 (tt) REVERT: B 183 PRO cc_start: 0.8705 (Cg_exo) cc_final: 0.8499 (Cg_endo) REVERT: B 542 LEU cc_start: 0.8533 (mp) cc_final: 0.8151 (mp) outliers start: 12 outliers final: 10 residues processed: 161 average time/residue: 0.1404 time to fit residues: 34.9920 Evaluate side-chains 145 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 342 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.102216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.072194 restraints weight = 50621.901| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.67 r_work: 0.2922 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8241 Z= 0.172 Angle : 0.498 5.435 11191 Z= 0.270 Chirality : 0.039 0.144 1389 Planarity : 0.004 0.038 1385 Dihedral : 6.802 57.831 1161 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 3.34 % Allowed : 25.46 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.27), residues: 1081 helix: 1.77 (0.20), residues: 699 sheet: -1.45 (0.76), residues: 44 loop : -2.00 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 355 TYR 0.013 0.001 TYR B 365 PHE 0.016 0.001 PHE A 368 TRP 0.003 0.001 TRP A 367 HIS 0.002 0.001 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8241) covalent geometry : angle 0.49842 (11191) hydrogen bonds : bond 0.03953 ( 487) hydrogen bonds : angle 4.21912 ( 1428) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ASN cc_start: 0.8142 (p0) cc_final: 0.7915 (p0) REVERT: A 309 GLN cc_start: 0.9122 (mt0) cc_final: 0.8512 (mp10) REVERT: B 542 LEU cc_start: 0.8728 (mp) cc_final: 0.8491 (mp) outliers start: 29 outliers final: 22 residues processed: 153 average time/residue: 0.1600 time to fit residues: 37.0719 Evaluate side-chains 150 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 498 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** 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 = 0.3583 r_free = 0.3583 target = 0.102725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.072823 restraints weight = 51042.986| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.70 r_work: 0.2928 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8241 Z= 0.126 Angle : 0.461 5.185 11191 Z= 0.249 Chirality : 0.038 0.142 1389 Planarity : 0.003 0.040 1385 Dihedral : 6.372 57.549 1155 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.65 % Allowed : 25.69 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.27), residues: 1081 helix: 1.85 (0.21), residues: 700 sheet: -1.35 (0.82), residues: 34 loop : -2.00 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 355 TYR 0.007 0.001 TYR B 163 PHE 0.013 0.001 PHE A 368 TRP 0.004 0.001 TRP A 367 HIS 0.001 0.000 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8241) covalent geometry : angle 0.46071 (11191) hydrogen bonds : bond 0.03556 ( 487) hydrogen bonds : angle 4.13117 ( 1428) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ASN cc_start: 0.8140 (p0) cc_final: 0.7921 (p0) REVERT: A 309 GLN cc_start: 0.9106 (mt0) cc_final: 0.8484 (mp10) outliers start: 23 outliers final: 20 residues processed: 148 average time/residue: 0.1506 time to fit residues: 33.9129 Evaluate side-chains 145 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 396 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 5 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** 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 = 0.3584 r_free = 0.3584 target = 0.102706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.072894 restraints weight = 50699.756| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.68 r_work: 0.2932 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8241 Z= 0.128 Angle : 0.461 5.216 11191 Z= 0.250 Chirality : 0.039 0.143 1389 Planarity : 0.003 0.040 1385 Dihedral : 6.275 58.182 1153 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.46 % Allowed : 24.88 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.27), residues: 1081 helix: 1.90 (0.21), residues: 696 sheet: -0.95 (0.86), residues: 32 loop : -2.00 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 355 TYR 0.007 0.001 TYR B 163 PHE 0.012 0.001 PHE A 368 TRP 0.004 0.001 TRP A 367 HIS 0.001 0.000 HIS A 469 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8241) covalent geometry : angle 0.46084 (11191) hydrogen bonds : bond 0.03535 ( 487) hydrogen bonds : angle 4.11433 ( 1428) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ASN cc_start: 0.8115 (p0) cc_final: 0.7885 (p0) REVERT: A 309 GLN cc_start: 0.9091 (mt0) cc_final: 0.8493 (mp10) REVERT: B 25 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8170 (mp) outliers start: 30 outliers final: 29 residues processed: 153 average time/residue: 0.1509 time to fit residues: 34.9458 Evaluate side-chains 156 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 465 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** 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 = 0.3592 r_free = 0.3592 target = 0.102307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.072699 restraints weight = 50857.501| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.64 r_work: 0.2961 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8241 Z= 0.187 Angle : 0.494 5.632 11191 Z= 0.273 Chirality : 0.039 0.143 1389 Planarity : 0.004 0.043 1385 Dihedral : 6.395 58.682 1153 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.38 % Allowed : 23.73 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.27), residues: 1081 helix: 1.71 (0.21), residues: 695 sheet: -1.38 (0.77), residues: 42 loop : -2.05 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 355 TYR 0.009 0.001 TYR B 365 PHE 0.015 0.001 PHE A 368 TRP 0.002 0.001 TRP B 367 HIS 0.001 0.000 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 8241) covalent geometry : angle 0.49415 (11191) hydrogen bonds : bond 0.04212 ( 487) hydrogen bonds : angle 4.27415 ( 1428) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 130 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ASN cc_start: 0.8180 (p0) cc_final: 0.7925 (p0) REVERT: A 309 GLN cc_start: 0.9114 (mt0) cc_final: 0.8527 (mp10) REVERT: B 25 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8262 (mp) REVERT: B 70 MET cc_start: 0.8804 (mmt) cc_final: 0.8403 (mmt) outliers start: 38 outliers final: 33 residues processed: 164 average time/residue: 0.1345 time to fit residues: 33.9762 Evaluate side-chains 160 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 498 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 77 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 55 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** 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 = 0.3614 r_free = 0.3614 target = 0.103729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.074159 restraints weight = 50516.484| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.65 r_work: 0.2984 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8241 Z= 0.120 Angle : 0.464 5.263 11191 Z= 0.251 Chirality : 0.039 0.142 1389 Planarity : 0.003 0.043 1385 Dihedral : 6.023 59.909 1150 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.92 % Allowed : 24.88 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.27), residues: 1081 helix: 1.85 (0.21), residues: 694 sheet: -1.29 (0.79), residues: 42 loop : -1.97 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 355 TYR 0.007 0.001 TYR B 163 PHE 0.012 0.001 PHE B 368 TRP 0.005 0.001 TRP B 367 HIS 0.001 0.000 HIS B 469 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8241) covalent geometry : angle 0.46404 (11191) hydrogen bonds : bond 0.03573 ( 487) hydrogen bonds : angle 4.14964 ( 1428) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ASN cc_start: 0.8096 (p0) cc_final: 0.7860 (p0) REVERT: A 309 GLN cc_start: 0.9115 (mt0) cc_final: 0.8529 (mp10) REVERT: B 25 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8227 (mp) outliers start: 34 outliers final: 31 residues processed: 157 average time/residue: 0.1573 time to fit residues: 37.6249 Evaluate side-chains 155 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 465 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 1 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** 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 = 0.3593 r_free = 0.3593 target = 0.102459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.072807 restraints weight = 50960.208| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.64 r_work: 0.2964 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8241 Z= 0.178 Angle : 0.487 5.522 11191 Z= 0.267 Chirality : 0.039 0.143 1389 Planarity : 0.004 0.044 1385 Dihedral : 6.063 59.651 1150 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.84 % Allowed : 23.73 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.27), residues: 1081 helix: 1.74 (0.21), residues: 695 sheet: -1.41 (0.78), residues: 42 loop : -2.04 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 355 TYR 0.008 0.001 TYR B 163 PHE 0.013 0.001 PHE B 368 TRP 0.003 0.001 TRP A 367 HIS 0.001 0.000 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 8241) covalent geometry : angle 0.48658 (11191) hydrogen bonds : bond 0.03982 ( 487) hydrogen bonds : angle 4.23199 ( 1428) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ASN cc_start: 0.8117 (p0) cc_final: 0.7883 (p0) REVERT: A 309 GLN cc_start: 0.9129 (mt0) cc_final: 0.8567 (mp10) REVERT: B 25 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8243 (mp) outliers start: 42 outliers final: 40 residues processed: 164 average time/residue: 0.1592 time to fit residues: 39.9018 Evaluate side-chains 169 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 128 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 498 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** 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 = 0.3599 r_free = 0.3599 target = 0.102829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.073164 restraints weight = 51062.795| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.66 r_work: 0.2969 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8241 Z= 0.149 Angle : 0.476 5.451 11191 Z= 0.260 Chirality : 0.039 0.143 1389 Planarity : 0.003 0.047 1385 Dihedral : 6.044 58.755 1150 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.84 % Allowed : 23.73 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.27), residues: 1081 helix: 1.77 (0.21), residues: 694 sheet: -1.37 (0.79), residues: 42 loop : -2.01 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 355 TYR 0.008 0.001 TYR B 163 PHE 0.013 0.001 PHE B 368 TRP 0.004 0.001 TRP B 367 HIS 0.001 0.000 HIS B 469 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8241) covalent geometry : angle 0.47603 (11191) hydrogen bonds : bond 0.03786 ( 487) hydrogen bonds : angle 4.20247 ( 1428) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ASN cc_start: 0.8104 (p0) cc_final: 0.7872 (p0) REVERT: B 25 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8261 (mp) outliers start: 42 outliers final: 39 residues processed: 162 average time/residue: 0.1563 time to fit residues: 38.5447 Evaluate side-chains 166 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 498 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 85 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** 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 = 0.3591 r_free = 0.3591 target = 0.102315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.072664 restraints weight = 51178.600| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.64 r_work: 0.2959 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8241 Z= 0.172 Angle : 0.493 5.583 11191 Z= 0.270 Chirality : 0.039 0.143 1389 Planarity : 0.004 0.048 1385 Dihedral : 6.078 57.960 1150 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 4.84 % Allowed : 23.62 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.27), residues: 1081 helix: 1.70 (0.21), residues: 695 sheet: -1.38 (0.79), residues: 42 loop : -2.11 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 355 TYR 0.008 0.001 TYR B 163 PHE 0.014 0.001 PHE B 368 TRP 0.003 0.001 TRP A 367 HIS 0.001 0.000 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8241) covalent geometry : angle 0.49265 (11191) hydrogen bonds : bond 0.03999 ( 487) hydrogen bonds : angle 4.25450 ( 1428) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ASN cc_start: 0.8122 (p0) cc_final: 0.7882 (p0) REVERT: B 25 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8293 (mp) outliers start: 42 outliers final: 41 residues processed: 163 average time/residue: 0.1400 time to fit residues: 34.5141 Evaluate side-chains 168 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 498 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** 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 = 0.3610 r_free = 0.3610 target = 0.103539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.073955 restraints weight = 50641.448| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.64 r_work: 0.2981 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8241 Z= 0.117 Angle : 0.468 5.263 11191 Z= 0.253 Chirality : 0.039 0.142 1389 Planarity : 0.003 0.050 1385 Dihedral : 6.001 57.640 1150 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 4.38 % Allowed : 23.85 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.27), residues: 1081 helix: 1.84 (0.21), residues: 695 sheet: -1.30 (0.81), residues: 42 loop : -2.03 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 355 TYR 0.008 0.001 TYR B 163 PHE 0.014 0.001 PHE B 34 TRP 0.005 0.001 TRP A 367 HIS 0.001 0.000 HIS B 469 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8241) covalent geometry : angle 0.46796 (11191) hydrogen bonds : bond 0.03562 ( 487) hydrogen bonds : angle 4.14399 ( 1428) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8257 (mp) REVERT: B 70 MET cc_start: 0.8806 (mmt) cc_final: 0.8420 (mmt) outliers start: 38 outliers final: 35 residues processed: 164 average time/residue: 0.1326 time to fit residues: 33.1567 Evaluate side-chains 165 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 465 SER Chi-restraints excluded: chain B residue 498 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 22 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** 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 = 0.3610 r_free = 0.3610 target = 0.103549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.073996 restraints weight = 50813.861| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.64 r_work: 0.2984 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8241 Z= 0.123 Angle : 0.467 5.191 11191 Z= 0.253 Chirality : 0.039 0.143 1389 Planarity : 0.003 0.051 1385 Dihedral : 5.956 57.571 1150 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 3.92 % Allowed : 24.65 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.27), residues: 1081 helix: 1.86 (0.21), residues: 696 sheet: -1.07 (0.86), residues: 32 loop : -2.08 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 355 TYR 0.007 0.001 TYR B 163 PHE 0.014 0.001 PHE B 34 TRP 0.004 0.001 TRP B 367 HIS 0.001 0.000 HIS B 469 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8241) covalent geometry : angle 0.46653 (11191) hydrogen bonds : bond 0.03542 ( 487) hydrogen bonds : angle 4.11721 ( 1428) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3609.44 seconds wall clock time: 62 minutes 3.26 seconds (3723.26 seconds total)