Starting phenix.real_space_refine on Fri Feb 14 16:17:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7npw_12524/02_2025/7npw_12524.cif Found real_map, /net/cci-nas-00/data/ceres_data/7npw_12524/02_2025/7npw_12524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7npw_12524/02_2025/7npw_12524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7npw_12524/02_2025/7npw_12524.map" model { file = "/net/cci-nas-00/data/ceres_data/7npw_12524/02_2025/7npw_12524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7npw_12524/02_2025/7npw_12524.cif" } resolution = 3.99 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 732 atoms to isotropic. 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 60 5.16 5 C 6381 2.51 5 N 1569 2.21 5 O 1713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9723 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3241 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 410} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Restraints were copied for chains: C, B Time building chain proxies: 6.47, per 1000 atoms: 0.67 Number of scatterers: 9723 At special positions: 0 Unit cell: (126.17, 121.286, 83.842, 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 60 16.00 O 1713 8.00 N 1569 7.00 C 6381 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.2 seconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 3 sheets defined 81.3% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 29 through 36 removed outlier: 3.556A pdb=" N VAL A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 48 Processing helix chain 'A' and resid 48 through 69 removed outlier: 3.767A pdb=" N LEU A 52 " --> pdb=" O ASN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 115 Proline residue: A 84 - end of helix removed outlier: 4.932A pdb=" N LEU A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Proline residue: A 98 - end of helix removed outlier: 3.723A pdb=" N ASP A 112 " --> pdb=" O MET A 108 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 146 removed outlier: 3.762A pdb=" N MET A 121 " --> pdb=" O GLY A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 181 through 187 removed outlier: 3.864A pdb=" N PHE A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 259 removed outlier: 3.555A pdb=" N LEU A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 286 removed outlier: 3.650A pdb=" N PHE A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 304 removed outlier: 3.670A pdb=" N VAL A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 303 " --> pdb=" O GLY A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 331 removed outlier: 3.747A pdb=" N ILE A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 341 removed outlier: 3.550A pdb=" N VAL A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 363 removed outlier: 3.820A pdb=" N PHE A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLN A 354 " --> pdb=" O GLY A 350 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ALA A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 386 through 397 removed outlier: 3.547A pdb=" N VAL A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 391 " --> pdb=" O THR A 387 " (cutoff:3.500A) Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 402 through 417 removed outlier: 3.720A pdb=" N ASN A 417 " --> pdb=" O ILE A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 437 removed outlier: 3.896A pdb=" N THR A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 459 Processing helix chain 'A' and resid 464 through 470 removed outlier: 4.027A pdb=" N ILE A 468 " --> pdb=" O ASP A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 497 removed outlier: 3.521A pdb=" N LEU A 475 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 477 " --> pdb=" O TRP A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 Processing helix chain 'B' and resid 41 through 48 Processing helix chain 'B' and resid 48 through 69 removed outlier: 3.768A pdb=" N LEU B 52 " --> pdb=" O ASN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 115 Proline residue: B 84 - end of helix removed outlier: 4.931A pdb=" N LEU B 97 " --> pdb=" O GLN B 93 " (cutoff:3.500A) Proline residue: B 98 - end of helix removed outlier: 3.724A pdb=" N ASP B 112 " --> pdb=" O MET B 108 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 146 removed outlier: 3.762A pdb=" N MET B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 177 Processing helix chain 'B' and resid 181 through 187 removed outlier: 3.865A pdb=" N PHE B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 259 removed outlier: 3.556A pdb=" N LEU B 246 " --> pdb=" O ASN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 286 removed outlier: 3.651A pdb=" N PHE B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 304 removed outlier: 3.669A pdb=" N VAL B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 303 " --> pdb=" O GLY B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 331 removed outlier: 3.747A pdb=" N ILE B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 341 removed outlier: 3.550A pdb=" N VAL B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 363 removed outlier: 3.819A pdb=" N PHE B 348 " --> pdb=" O ASN B 344 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLN B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ALA B 355 " --> pdb=" O GLY B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 379 Processing helix chain 'B' and resid 386 through 397 removed outlier: 3.546A pdb=" N VAL B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU B 391 " --> pdb=" O THR B 387 " (cutoff:3.500A) Proline residue: B 392 - end of helix Processing helix chain 'B' and resid 402 through 417 removed outlier: 3.719A pdb=" N ASN B 417 " --> pdb=" O ILE B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 437 removed outlier: 3.897A pdb=" N THR B 428 " --> pdb=" O GLY B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 459 Processing helix chain 'B' and resid 464 through 470 removed outlier: 4.026A pdb=" N ILE B 468 " --> pdb=" O ASP B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 497 removed outlier: 3.520A pdb=" N LEU B 475 " --> pdb=" O VAL B 471 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 477 " --> pdb=" O TRP B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 36 Processing helix chain 'C' and resid 41 through 48 Processing helix chain 'C' and resid 48 through 69 removed outlier: 3.767A pdb=" N LEU C 52 " --> pdb=" O ASN C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 115 Proline residue: C 84 - end of helix removed outlier: 4.931A pdb=" N LEU C 97 " --> pdb=" O GLN C 93 " (cutoff:3.500A) Proline residue: C 98 - end of helix removed outlier: 3.723A pdb=" N ASP C 112 " --> pdb=" O MET C 108 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER C 113 " --> pdb=" O ALA C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 146 removed outlier: 3.762A pdb=" N MET C 121 " --> pdb=" O GLY C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 177 Processing helix chain 'C' and resid 181 through 187 removed outlier: 3.865A pdb=" N PHE C 187 " --> pdb=" O VAL C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 259 removed outlier: 3.555A pdb=" N LEU C 246 " --> pdb=" O ASN C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 286 removed outlier: 3.651A pdb=" N PHE C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 304 removed outlier: 3.669A pdb=" N VAL C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 303 " --> pdb=" O GLY C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 331 removed outlier: 3.747A pdb=" N ILE C 310 " --> pdb=" O ASP C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 341 removed outlier: 3.550A pdb=" N VAL C 340 " --> pdb=" O LEU C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 363 removed outlier: 3.820A pdb=" N PHE C 348 " --> pdb=" O ASN C 344 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLN C 354 " --> pdb=" O GLY C 350 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ALA C 355 " --> pdb=" O GLY C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 379 Processing helix chain 'C' and resid 386 through 397 removed outlier: 3.547A pdb=" N VAL C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU C 391 " --> pdb=" O THR C 387 " (cutoff:3.500A) Proline residue: C 392 - end of helix Processing helix chain 'C' and resid 402 through 417 removed outlier: 3.720A pdb=" N ASN C 417 " --> pdb=" O ILE C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 437 removed outlier: 3.897A pdb=" N THR C 428 " --> pdb=" O GLY C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 459 Processing helix chain 'C' and resid 464 through 470 removed outlier: 4.025A pdb=" N ILE C 468 " --> pdb=" O ASP C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 497 removed outlier: 3.520A pdb=" N LEU C 475 " --> pdb=" O VAL C 471 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG C 477 " --> pdb=" O TRP C 473 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 190 removed outlier: 3.516A pdb=" N VAL A 238 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 188 through 190 removed outlier: 3.517A pdb=" N VAL B 238 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 188 through 190 removed outlier: 3.517A pdb=" N VAL C 238 " --> pdb=" O GLN C 189 " (cutoff:3.500A) 708 hydrogen bonds defined for protein. 2124 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: 2.92 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3018 1.34 - 1.46: 1839 1.46 - 1.58: 4917 1.58 - 1.70: 0 1.70 - 1.81: 111 Bond restraints: 9885 Sorted by residual: bond pdb=" C ALA C 289 " pdb=" N PRO C 290 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.64e-01 bond pdb=" C ALA B 289 " pdb=" N PRO B 290 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.39e-01 bond pdb=" C ALA A 289 " pdb=" N PRO A 290 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.19e-01 bond pdb=" CA GLN B 93 " pdb=" CB GLN B 93 " ideal model delta sigma weight residual 1.530 1.546 -0.015 1.75e-02 3.27e+03 7.81e-01 bond pdb=" CA GLN A 93 " pdb=" CB GLN A 93 " ideal model delta sigma weight residual 1.530 1.546 -0.015 1.75e-02 3.27e+03 7.66e-01 ... (remaining 9880 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 12920 1.50 - 3.00: 392 3.00 - 4.50: 74 4.50 - 6.00: 33 6.00 - 7.51: 9 Bond angle restraints: 13428 Sorted by residual: angle pdb=" C ILE A 469 " pdb=" CA ILE A 469 " pdb=" CB ILE A 469 " ideal model delta sigma weight residual 111.37 107.02 4.35 1.68e+00 3.54e-01 6.71e+00 angle pdb=" C ILE C 469 " pdb=" CA ILE C 469 " pdb=" CB ILE C 469 " ideal model delta sigma weight residual 111.37 107.06 4.31 1.68e+00 3.54e-01 6.57e+00 angle pdb=" C ILE B 469 " pdb=" CA ILE B 469 " pdb=" CB ILE B 469 " ideal model delta sigma weight residual 111.37 107.09 4.28 1.68e+00 3.54e-01 6.50e+00 angle pdb=" CB MET B 89 " pdb=" CG MET B 89 " pdb=" SD MET B 89 " ideal model delta sigma weight residual 112.70 120.21 -7.51 3.00e+00 1.11e-01 6.26e+00 angle pdb=" CB MET A 89 " pdb=" CG MET A 89 " pdb=" SD MET A 89 " ideal model delta sigma weight residual 112.70 120.19 -7.49 3.00e+00 1.11e-01 6.23e+00 ... (remaining 13423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 5373 18.00 - 35.99: 411 35.99 - 53.99: 72 53.99 - 71.99: 12 71.99 - 89.98: 9 Dihedral angle restraints: 5877 sinusoidal: 2226 harmonic: 3651 Sorted by residual: dihedral pdb=" CA GLN B 93 " pdb=" C GLN B 93 " pdb=" N MET B 94 " pdb=" CA MET B 94 " ideal model delta harmonic sigma weight residual 180.00 157.70 22.30 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA GLN C 93 " pdb=" C GLN C 93 " pdb=" N MET C 94 " pdb=" CA MET C 94 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA GLN A 93 " pdb=" C GLN A 93 " pdb=" N MET A 94 " pdb=" CA MET A 94 " ideal model delta harmonic sigma weight residual 180.00 157.81 22.19 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 5874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 960 0.028 - 0.056: 445 0.056 - 0.085: 191 0.085 - 0.113: 81 0.113 - 0.141: 12 Chirality restraints: 1689 Sorted by residual: chirality pdb=" CB VAL A 471 " pdb=" CA VAL A 471 " pdb=" CG1 VAL A 471 " pdb=" CG2 VAL A 471 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CB VAL B 471 " pdb=" CA VAL B 471 " pdb=" CG1 VAL B 471 " pdb=" CG2 VAL B 471 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CB VAL C 471 " pdb=" CA VAL C 471 " pdb=" CG1 VAL C 471 " pdb=" CG2 VAL C 471 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 1686 not shown) Planarity restraints: 1641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 373 " -0.010 2.00e-02 2.50e+03 9.92e-03 1.72e+00 pdb=" CG PHE A 373 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 373 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 373 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 373 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 373 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 373 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 373 " -0.010 2.00e-02 2.50e+03 9.91e-03 1.72e+00 pdb=" CG PHE B 373 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE B 373 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 373 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 373 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 373 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 373 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 373 " -0.010 2.00e-02 2.50e+03 9.70e-03 1.65e+00 pdb=" CG PHE C 373 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE C 373 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE C 373 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 373 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 373 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 373 " -0.001 2.00e-02 2.50e+03 ... (remaining 1638 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2577 2.81 - 3.33: 10837 3.33 - 3.86: 16117 3.86 - 4.38: 17040 4.38 - 4.90: 29648 Nonbonded interactions: 76219 Sorted by model distance: nonbonded pdb=" O LYS A 384 " pdb=" NH1 ARG A 388 " model vdw 2.290 3.120 nonbonded pdb=" O LYS B 384 " pdb=" NH1 ARG B 388 " model vdw 2.290 3.120 nonbonded pdb=" O LYS C 384 " pdb=" NH1 ARG C 388 " model vdw 2.290 3.120 nonbonded pdb=" O LEU B 369 " pdb=" OG1 THR B 372 " model vdw 2.295 3.040 nonbonded pdb=" O LEU A 369 " pdb=" OG1 THR A 372 " model vdw 2.295 3.040 ... (remaining 76214 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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 group one per residue 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: 3.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.570 Find NCS groups from input model: 0.170 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 0.022 9885 Z= 0.158 Angle : 0.673 7.505 13428 Z= 0.354 Chirality : 0.041 0.141 1689 Planarity : 0.004 0.030 1641 Dihedral : 13.765 89.984 3525 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.24), residues: 1254 helix: 1.46 (0.17), residues: 945 sheet: -1.52 (0.79), residues: 48 loop : -2.10 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 346 HIS 0.001 0.000 HIS C 328 PHE 0.023 0.001 PHE A 373 TYR 0.017 0.001 TYR C 405 ARG 0.011 0.001 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8711 (m-10) cc_final: 0.8231 (t80) REVERT: A 288 TYR cc_start: 0.9215 (t80) cc_final: 0.8787 (t80) REVERT: A 451 MET cc_start: 0.9204 (mmp) cc_final: 0.8754 (mmp) REVERT: A 476 ASP cc_start: 0.7474 (m-30) cc_final: 0.7077 (t0) REVERT: B 80 TYR cc_start: 0.8565 (m-10) cc_final: 0.8080 (t80) REVERT: B 189 GLN cc_start: 0.7050 (mp-120) cc_final: 0.6827 (mp10) REVERT: B 288 TYR cc_start: 0.9303 (t80) cc_final: 0.9002 (t80) REVERT: B 451 MET cc_start: 0.9069 (mmp) cc_final: 0.8611 (mmp) REVERT: C 80 TYR cc_start: 0.8669 (m-10) cc_final: 0.8027 (t80) REVERT: C 108 MET cc_start: 0.9013 (mmm) cc_final: 0.8619 (tpp) REVERT: C 251 MET cc_start: 0.8225 (mtp) cc_final: 0.7982 (tmm) REVERT: C 307 MET cc_start: 0.6234 (tmm) cc_final: 0.6021 (tmm) REVERT: C 451 MET cc_start: 0.9136 (mmp) cc_final: 0.8645 (mmp) REVERT: C 476 ASP cc_start: 0.7366 (m-30) cc_final: 0.7049 (t0) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.1706 time to fit residues: 65.2615 Evaluate side-chains 203 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 73 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 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 = 0.3871 r_free = 0.3871 target = 0.104305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.076088 restraints weight = 35123.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.078566 restraints weight = 17558.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.080212 restraints weight = 11271.858| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9885 Z= 0.164 Angle : 0.616 10.348 13428 Z= 0.309 Chirality : 0.040 0.137 1689 Planarity : 0.004 0.028 1641 Dihedral : 3.830 19.070 1344 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.46 % Allowed : 14.20 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.24), residues: 1254 helix: 1.45 (0.16), residues: 975 sheet: -1.44 (0.82), residues: 48 loop : -2.25 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 473 HIS 0.000 0.000 HIS C 328 PHE 0.016 0.001 PHE B 83 TYR 0.019 0.001 TYR B 75 ARG 0.006 0.001 ARG C 388 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 218 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8662 (m-10) cc_final: 0.8231 (t80) REVERT: A 177 MET cc_start: 0.8689 (ttp) cc_final: 0.8165 (ttm) REVERT: A 316 MET cc_start: 0.9294 (mmm) cc_final: 0.9077 (mmm) REVERT: A 336 LEU cc_start: 0.8561 (tt) cc_final: 0.8203 (pp) REVERT: A 451 MET cc_start: 0.8995 (mmp) cc_final: 0.8557 (mmp) REVERT: B 80 TYR cc_start: 0.8630 (m-10) cc_final: 0.8180 (t80) REVERT: B 251 MET cc_start: 0.7765 (tmm) cc_final: 0.7435 (tmm) REVERT: B 288 TYR cc_start: 0.9156 (t80) cc_final: 0.8893 (t80) REVERT: B 316 MET cc_start: 0.9334 (mmm) cc_final: 0.9119 (mmm) REVERT: B 336 LEU cc_start: 0.8665 (tt) cc_final: 0.8461 (pp) REVERT: B 405 TYR cc_start: 0.8937 (t80) cc_final: 0.8575 (t80) REVERT: B 451 MET cc_start: 0.8913 (mmp) cc_final: 0.8284 (mmp) REVERT: C 80 TYR cc_start: 0.8707 (m-10) cc_final: 0.8152 (t80) REVERT: C 89 MET cc_start: 0.9024 (mmm) cc_final: 0.8773 (tpp) REVERT: C 108 MET cc_start: 0.9008 (mmm) cc_final: 0.8655 (tpp) REVERT: C 177 MET cc_start: 0.8632 (mtt) cc_final: 0.8287 (ttp) REVERT: C 286 MET cc_start: 0.9095 (mmp) cc_final: 0.8700 (tpp) REVERT: C 307 MET cc_start: 0.6480 (tmm) cc_final: 0.5961 (tmm) REVERT: C 316 MET cc_start: 0.9213 (mmm) cc_final: 0.8993 (mmm) REVERT: C 336 LEU cc_start: 0.8497 (tt) cc_final: 0.8229 (pp) REVERT: C 451 MET cc_start: 0.8998 (mmp) cc_final: 0.8501 (mmp) outliers start: 26 outliers final: 20 residues processed: 228 average time/residue: 0.1794 time to fit residues: 60.8442 Evaluate side-chains 222 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 448 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 64 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 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 = 0.3859 r_free = 0.3859 target = 0.102246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.074479 restraints weight = 34842.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.076629 restraints weight = 18447.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.078016 restraints weight = 12338.273| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9885 Z= 0.216 Angle : 0.622 10.625 13428 Z= 0.320 Chirality : 0.041 0.153 1689 Planarity : 0.004 0.035 1641 Dihedral : 3.882 17.234 1344 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.03 % Allowed : 17.80 % Favored : 79.17 % 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: 1.02 (0.24), residues: 1254 helix: 1.42 (0.16), residues: 981 sheet: -1.42 (0.82), residues: 48 loop : -2.10 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 287 HIS 0.002 0.000 HIS A 328 PHE 0.021 0.002 PHE B 170 TYR 0.025 0.002 TYR C 288 ARG 0.006 0.001 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8672 (m-10) cc_final: 0.8328 (t80) REVERT: A 288 TYR cc_start: 0.8990 (t80) cc_final: 0.8747 (t80) REVERT: A 317 TYR cc_start: 0.9317 (t80) cc_final: 0.9043 (t80) REVERT: A 336 LEU cc_start: 0.8741 (tt) cc_final: 0.8529 (pp) REVERT: A 451 MET cc_start: 0.8871 (mmp) cc_final: 0.8390 (mmp) REVERT: A 476 ASP cc_start: 0.7896 (m-30) cc_final: 0.7287 (p0) REVERT: B 80 TYR cc_start: 0.8560 (m-10) cc_final: 0.8246 (t80) REVERT: B 88 LEU cc_start: 0.9786 (tt) cc_final: 0.9453 (tt) REVERT: B 336 LEU cc_start: 0.8869 (tt) cc_final: 0.8598 (pp) REVERT: B 451 MET cc_start: 0.8784 (mmp) cc_final: 0.8294 (mmp) REVERT: C 80 TYR cc_start: 0.8724 (m-10) cc_final: 0.8300 (t80) REVERT: C 108 MET cc_start: 0.8919 (mmm) cc_final: 0.8637 (tpp) REVERT: C 286 MET cc_start: 0.9067 (mmp) cc_final: 0.8795 (tpt) REVERT: C 307 MET cc_start: 0.6503 (tmm) cc_final: 0.6095 (tmm) REVERT: C 316 MET cc_start: 0.9321 (mmm) cc_final: 0.9103 (mmm) REVERT: C 336 LEU cc_start: 0.8751 (tt) cc_final: 0.8492 (pp) REVERT: C 405 TYR cc_start: 0.9080 (t80) cc_final: 0.8627 (t80) REVERT: C 451 MET cc_start: 0.8858 (mmp) cc_final: 0.8115 (mmp) REVERT: C 476 ASP cc_start: 0.7779 (m-30) cc_final: 0.7189 (p0) outliers start: 32 outliers final: 23 residues processed: 220 average time/residue: 0.1839 time to fit residues: 59.8248 Evaluate side-chains 203 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 448 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 93 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 119 optimal weight: 0.0970 chunk 52 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 18 optimal weight: 0.0980 chunk 47 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 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 = 0.3892 r_free = 0.3892 target = 0.104167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.076656 restraints weight = 34448.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.078853 restraints weight = 18470.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.080264 restraints weight = 12305.815| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9885 Z= 0.154 Angle : 0.621 11.232 13428 Z= 0.312 Chirality : 0.041 0.183 1689 Planarity : 0.004 0.032 1641 Dihedral : 3.789 19.651 1344 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.69 % Allowed : 19.98 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.24), residues: 1254 helix: 1.45 (0.16), residues: 981 sheet: -1.63 (0.80), residues: 48 loop : -2.13 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 346 HIS 0.001 0.000 HIS B 328 PHE 0.021 0.001 PHE B 83 TYR 0.018 0.001 TYR B 75 ARG 0.002 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8628 (m-10) cc_final: 0.8307 (t80) REVERT: A 177 MET cc_start: 0.8536 (ttp) cc_final: 0.8133 (ttm) REVERT: A 251 MET cc_start: 0.8128 (tmm) cc_final: 0.7925 (tmm) REVERT: A 336 LEU cc_start: 0.8738 (tt) cc_final: 0.8445 (pp) REVERT: A 451 MET cc_start: 0.8782 (mmp) cc_final: 0.8324 (mmp) REVERT: B 80 TYR cc_start: 0.8542 (m-10) cc_final: 0.8250 (t80) REVERT: B 336 LEU cc_start: 0.8882 (tt) cc_final: 0.8607 (pp) REVERT: B 405 TYR cc_start: 0.9056 (t80) cc_final: 0.8586 (t80) REVERT: B 451 MET cc_start: 0.8668 (mmp) cc_final: 0.7905 (mmp) REVERT: C 80 TYR cc_start: 0.8710 (m-10) cc_final: 0.8305 (t80) REVERT: C 177 MET cc_start: 0.8526 (mtt) cc_final: 0.8290 (ttp) REVERT: C 251 MET cc_start: 0.7892 (tmm) cc_final: 0.7536 (tmm) REVERT: C 286 MET cc_start: 0.9004 (mmp) cc_final: 0.8725 (tpt) REVERT: C 316 MET cc_start: 0.9307 (mmm) cc_final: 0.9096 (mmm) REVERT: C 336 LEU cc_start: 0.8794 (tt) cc_final: 0.8526 (pp) REVERT: C 405 TYR cc_start: 0.9065 (t80) cc_final: 0.8630 (t80) REVERT: C 451 MET cc_start: 0.8796 (mmp) cc_final: 0.7997 (mmp) outliers start: 39 outliers final: 27 residues processed: 226 average time/residue: 0.1781 time to fit residues: 59.7761 Evaluate side-chains 211 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 448 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 60 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 114 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 97 optimal weight: 0.0670 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.103367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.075716 restraints weight = 34849.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.077892 restraints weight = 18547.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.079256 restraints weight = 12411.209| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9885 Z= 0.164 Angle : 0.613 11.635 13428 Z= 0.308 Chirality : 0.041 0.185 1689 Planarity : 0.004 0.035 1641 Dihedral : 3.774 19.398 1344 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.79 % Allowed : 20.74 % Favored : 75.47 % 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: 1.16 (0.24), residues: 1254 helix: 1.55 (0.16), residues: 975 sheet: -1.66 (0.80), residues: 48 loop : -2.06 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 287 HIS 0.001 0.000 HIS C 328 PHE 0.020 0.001 PHE B 83 TYR 0.026 0.002 TYR A 288 ARG 0.001 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8588 (m-10) cc_final: 0.8345 (t80) REVERT: A 177 MET cc_start: 0.8626 (ttp) cc_final: 0.8184 (ttm) REVERT: A 336 LEU cc_start: 0.8774 (tt) cc_final: 0.8494 (pp) REVERT: A 451 MET cc_start: 0.8821 (mmp) cc_final: 0.8330 (mmp) REVERT: B 80 TYR cc_start: 0.8557 (m-10) cc_final: 0.8281 (t80) REVERT: B 177 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8261 (ttp) REVERT: B 184 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8156 (mm-30) REVERT: B 303 GLU cc_start: 0.8835 (pp20) cc_final: 0.8603 (pp20) REVERT: B 336 LEU cc_start: 0.8912 (tt) cc_final: 0.8694 (pp) REVERT: B 405 TYR cc_start: 0.9022 (t80) cc_final: 0.8533 (t80) REVERT: B 451 MET cc_start: 0.8784 (mmp) cc_final: 0.7982 (mmp) REVERT: C 80 TYR cc_start: 0.8655 (m-10) cc_final: 0.8351 (t80) REVERT: C 108 MET cc_start: 0.8539 (tpp) cc_final: 0.8053 (tpp) REVERT: C 171 LEU cc_start: 0.9399 (tp) cc_final: 0.9149 (tp) REVERT: C 177 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8329 (ttp) REVERT: C 316 MET cc_start: 0.9358 (mmm) cc_final: 0.9148 (mmm) REVERT: C 336 LEU cc_start: 0.8848 (tt) cc_final: 0.8541 (pp) REVERT: C 405 TYR cc_start: 0.9041 (t80) cc_final: 0.8584 (t80) REVERT: C 451 MET cc_start: 0.8831 (mmp) cc_final: 0.8002 (mmp) outliers start: 40 outliers final: 26 residues processed: 218 average time/residue: 0.1876 time to fit residues: 60.6010 Evaluate side-chains 212 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 448 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 70 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 30.0000 chunk 95 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 31 optimal weight: 0.0270 chunk 71 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 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 = 0.3870 r_free = 0.3870 target = 0.103228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.075532 restraints weight = 35235.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.077691 restraints weight = 18689.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.079063 restraints weight = 12507.230| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9885 Z= 0.165 Angle : 0.624 11.555 13428 Z= 0.310 Chirality : 0.041 0.183 1689 Planarity : 0.004 0.035 1641 Dihedral : 3.832 22.319 1344 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.50 % Allowed : 22.35 % Favored : 74.15 % 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: 1.16 (0.24), residues: 1254 helix: 1.55 (0.16), residues: 975 sheet: -1.71 (0.80), residues: 48 loop : -2.04 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 346 HIS 0.001 0.000 HIS A 328 PHE 0.021 0.001 PHE B 83 TYR 0.019 0.001 TYR B 288 ARG 0.002 0.000 ARG C 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8633 (m-10) cc_final: 0.8397 (t80) REVERT: A 177 MET cc_start: 0.8597 (ttp) cc_final: 0.8146 (ttm) REVERT: A 303 GLU cc_start: 0.8896 (pp20) cc_final: 0.8670 (pp20) REVERT: A 336 LEU cc_start: 0.8847 (tt) cc_final: 0.8622 (pp) REVERT: A 451 MET cc_start: 0.8778 (mmp) cc_final: 0.8445 (mmp) REVERT: B 80 TYR cc_start: 0.8551 (m-10) cc_final: 0.8282 (t80) REVERT: B 177 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8359 (ttp) REVERT: B 184 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8174 (mm-30) REVERT: B 336 LEU cc_start: 0.8944 (tt) cc_final: 0.8700 (pp) REVERT: B 405 TYR cc_start: 0.9018 (t80) cc_final: 0.8590 (t80) REVERT: B 451 MET cc_start: 0.8738 (mmp) cc_final: 0.7901 (mmp) REVERT: C 80 TYR cc_start: 0.8652 (m-10) cc_final: 0.8304 (t80) REVERT: C 83 PHE cc_start: 0.8268 (t80) cc_final: 0.7861 (t80) REVERT: C 108 MET cc_start: 0.8605 (tpp) cc_final: 0.8082 (tpp) REVERT: C 171 LEU cc_start: 0.9447 (tp) cc_final: 0.9176 (tp) REVERT: C 177 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8317 (ttp) REVERT: C 187 PHE cc_start: 0.9175 (p90) cc_final: 0.8828 (p90) REVERT: C 251 MET cc_start: 0.7835 (tmm) cc_final: 0.7597 (tmm) REVERT: C 316 MET cc_start: 0.9355 (mmm) cc_final: 0.9147 (mmm) REVERT: C 336 LEU cc_start: 0.8888 (tt) cc_final: 0.8583 (pp) REVERT: C 405 TYR cc_start: 0.9037 (t80) cc_final: 0.8562 (t80) REVERT: C 451 MET cc_start: 0.8789 (mmp) cc_final: 0.7953 (mmp) outliers start: 37 outliers final: 28 residues processed: 219 average time/residue: 0.1851 time to fit residues: 60.9103 Evaluate side-chains 215 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 448 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 117 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 115 optimal weight: 4.9990 chunk 79 optimal weight: 0.0470 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 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 = 0.3876 r_free = 0.3876 target = 0.103633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.075903 restraints weight = 35204.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.078133 restraints weight = 18892.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.079575 restraints weight = 12550.755| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9885 Z= 0.163 Angle : 0.644 10.665 13428 Z= 0.318 Chirality : 0.041 0.191 1689 Planarity : 0.004 0.033 1641 Dihedral : 3.786 20.076 1344 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.41 % Allowed : 24.53 % Favored : 72.06 % 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 (0.24), residues: 1254 helix: 1.55 (0.16), residues: 972 sheet: -1.72 (0.81), residues: 48 loop : -2.08 (0.34), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 346 HIS 0.001 0.000 HIS A 328 PHE 0.023 0.001 PHE B 83 TYR 0.025 0.001 TYR C 288 ARG 0.002 0.000 ARG C 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8618 (m-10) cc_final: 0.8380 (t80) REVERT: A 93 GLN cc_start: 0.8408 (pp30) cc_final: 0.8105 (pp30) REVERT: A 336 LEU cc_start: 0.8895 (tt) cc_final: 0.8670 (pp) REVERT: A 451 MET cc_start: 0.8815 (mmp) cc_final: 0.8509 (mtp) REVERT: B 80 TYR cc_start: 0.8544 (m-10) cc_final: 0.8274 (t80) REVERT: B 184 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8179 (mm-30) REVERT: B 336 LEU cc_start: 0.8942 (tt) cc_final: 0.8700 (pp) REVERT: B 451 MET cc_start: 0.8771 (mmp) cc_final: 0.8144 (mmp) REVERT: C 80 TYR cc_start: 0.8595 (m-10) cc_final: 0.8279 (t80) REVERT: C 108 MET cc_start: 0.8625 (tpp) cc_final: 0.8112 (tpp) REVERT: C 187 PHE cc_start: 0.9179 (p90) cc_final: 0.8800 (p90) REVERT: C 316 MET cc_start: 0.9379 (mmm) cc_final: 0.9172 (mmm) REVERT: C 336 LEU cc_start: 0.8899 (tt) cc_final: 0.8592 (pp) REVERT: C 405 TYR cc_start: 0.9017 (t80) cc_final: 0.8614 (t80) REVERT: C 451 MET cc_start: 0.8838 (mmp) cc_final: 0.7967 (mmp) outliers start: 36 outliers final: 28 residues processed: 223 average time/residue: 0.1764 time to fit residues: 58.5677 Evaluate side-chains 217 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 448 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 16 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 71 optimal weight: 20.0000 chunk 92 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.097319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.069289 restraints weight = 36046.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.071351 restraints weight = 18779.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.072701 restraints weight = 12412.248| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9885 Z= 0.286 Angle : 0.705 10.449 13428 Z= 0.361 Chirality : 0.043 0.171 1689 Planarity : 0.004 0.039 1641 Dihedral : 4.138 22.041 1344 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.31 % Allowed : 24.91 % Favored : 71.78 % 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: 0.88 (0.23), residues: 1254 helix: 1.30 (0.16), residues: 978 sheet: -1.66 (0.81), residues: 48 loop : -1.91 (0.36), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 287 HIS 0.003 0.001 HIS B 146 PHE 0.019 0.002 PHE C 249 TYR 0.018 0.002 TYR B 288 ARG 0.004 0.001 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8668 (m-10) cc_final: 0.8418 (t80) REVERT: A 93 GLN cc_start: 0.8691 (pp30) cc_final: 0.7978 (pp30) REVERT: A 94 MET cc_start: 0.9015 (ttm) cc_final: 0.8728 (ttm) REVERT: A 336 LEU cc_start: 0.9068 (tt) cc_final: 0.8775 (pp) REVERT: A 451 MET cc_start: 0.8880 (mmp) cc_final: 0.8339 (mmp) REVERT: B 80 TYR cc_start: 0.8647 (m-10) cc_final: 0.8437 (t80) REVERT: B 93 GLN cc_start: 0.8687 (pp30) cc_final: 0.8077 (pp30) REVERT: B 184 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8394 (mm-30) REVERT: B 303 GLU cc_start: 0.8847 (pp20) cc_final: 0.8578 (pp20) REVERT: B 336 LEU cc_start: 0.9105 (tt) cc_final: 0.8890 (pp) REVERT: B 405 TYR cc_start: 0.9146 (t80) cc_final: 0.8744 (t80) REVERT: B 451 MET cc_start: 0.8888 (mmp) cc_final: 0.8140 (mmp) REVERT: C 80 TYR cc_start: 0.8647 (m-10) cc_final: 0.8354 (t80) REVERT: C 93 GLN cc_start: 0.8774 (pp30) cc_final: 0.8393 (pp30) REVERT: C 94 MET cc_start: 0.9096 (ttm) cc_final: 0.8890 (ttm) REVERT: C 251 MET cc_start: 0.7967 (tmm) cc_final: 0.7714 (tmm) REVERT: C 336 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8770 (pp) REVERT: C 405 TYR cc_start: 0.9186 (t80) cc_final: 0.8909 (t80) REVERT: C 451 MET cc_start: 0.8873 (mmp) cc_final: 0.8113 (mmp) REVERT: C 476 ASP cc_start: 0.7803 (m-30) cc_final: 0.7205 (p0) outliers start: 35 outliers final: 27 residues processed: 217 average time/residue: 0.1765 time to fit residues: 56.4116 Evaluate side-chains 205 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 448 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 91 optimal weight: 0.6980 chunk 74 optimal weight: 0.0060 chunk 113 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 29 optimal weight: 30.0000 chunk 62 optimal weight: 0.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 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 = 0.3825 r_free = 0.3825 target = 0.101032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.073321 restraints weight = 35122.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.075472 restraints weight = 18209.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.076855 restraints weight = 12055.347| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9885 Z= 0.187 Angle : 0.721 11.826 13428 Z= 0.353 Chirality : 0.044 0.189 1689 Planarity : 0.004 0.036 1641 Dihedral : 4.107 24.575 1344 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.46 % Allowed : 26.52 % Favored : 71.02 % 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: 0.80 (0.23), residues: 1254 helix: 1.21 (0.16), residues: 984 sheet: -1.69 (0.81), residues: 48 loop : -1.85 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 473 HIS 0.002 0.000 HIS C 328 PHE 0.022 0.001 PHE B 170 TYR 0.026 0.001 TYR C 288 ARG 0.002 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8710 (pp30) cc_final: 0.7973 (pp30) REVERT: A 336 LEU cc_start: 0.9046 (tt) cc_final: 0.8739 (pp) REVERT: A 451 MET cc_start: 0.8770 (mmp) cc_final: 0.8201 (mmp) REVERT: B 184 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8161 (mm-30) REVERT: B 405 TYR cc_start: 0.9003 (t80) cc_final: 0.8600 (t80) REVERT: B 451 MET cc_start: 0.8791 (mmp) cc_final: 0.8013 (mmp) REVERT: C 80 TYR cc_start: 0.8628 (m-10) cc_final: 0.8274 (t80) REVERT: C 93 GLN cc_start: 0.8764 (pp30) cc_final: 0.8425 (pp30) REVERT: C 336 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8769 (pp) REVERT: C 405 TYR cc_start: 0.9102 (t80) cc_final: 0.8796 (t80) REVERT: C 451 MET cc_start: 0.8784 (mmp) cc_final: 0.8125 (mmp) outliers start: 26 outliers final: 23 residues processed: 220 average time/residue: 0.1868 time to fit residues: 60.5224 Evaluate side-chains 217 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 7 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 66 optimal weight: 0.0870 chunk 113 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 21 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.0470 chunk 54 optimal weight: 5.9990 overall best weight: 0.8658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 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 = 0.3827 r_free = 0.3827 target = 0.101101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.072934 restraints weight = 35614.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.075118 restraints weight = 18290.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.076595 restraints weight = 12033.641| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9885 Z= 0.199 Angle : 0.754 11.510 13428 Z= 0.368 Chirality : 0.044 0.285 1689 Planarity : 0.004 0.033 1641 Dihedral : 4.209 25.872 1344 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.56 % Allowed : 28.03 % Favored : 69.41 % 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: 0.79 (0.24), residues: 1254 helix: 1.21 (0.16), residues: 975 sheet: -1.66 (0.81), residues: 48 loop : -1.78 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 346 HIS 0.002 0.001 HIS B 328 PHE 0.031 0.001 PHE C 83 TYR 0.018 0.001 TYR B 288 ARG 0.002 0.000 ARG A 479 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8673 (pp30) cc_final: 0.8009 (pp30) REVERT: A 336 LEU cc_start: 0.9028 (tt) cc_final: 0.8778 (pp) REVERT: A 451 MET cc_start: 0.8803 (mmp) cc_final: 0.8229 (mmp) REVERT: B 168 ASP cc_start: 0.8840 (m-30) cc_final: 0.8623 (m-30) REVERT: B 184 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8210 (mm-30) REVERT: B 405 TYR cc_start: 0.8839 (t80) cc_final: 0.8411 (t80) REVERT: B 451 MET cc_start: 0.8772 (mmp) cc_final: 0.7990 (mmp) REVERT: C 80 TYR cc_start: 0.8646 (m-10) cc_final: 0.8283 (t80) REVERT: C 93 GLN cc_start: 0.8778 (pp30) cc_final: 0.8451 (pp30) REVERT: C 170 PHE cc_start: 0.9173 (t80) cc_final: 0.8931 (t80) REVERT: C 336 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8827 (pp) REVERT: C 405 TYR cc_start: 0.9081 (t80) cc_final: 0.8749 (t80) REVERT: C 451 MET cc_start: 0.8855 (mmp) cc_final: 0.8018 (mmp) outliers start: 27 outliers final: 25 residues processed: 217 average time/residue: 0.1732 time to fit residues: 55.6687 Evaluate side-chains 217 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 448 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 62 optimal weight: 0.6980 chunk 113 optimal weight: 30.0000 chunk 35 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 101 optimal weight: 0.3980 chunk 66 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 0.0170 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 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 = 0.3850 r_free = 0.3850 target = 0.102372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.074785 restraints weight = 35149.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.076969 restraints weight = 18394.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.078422 restraints weight = 12206.733| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9885 Z= 0.197 Angle : 0.773 12.356 13428 Z= 0.377 Chirality : 0.045 0.257 1689 Planarity : 0.004 0.034 1641 Dihedral : 4.196 24.952 1344 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.56 % Allowed : 28.69 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.24), residues: 1254 helix: 1.13 (0.16), residues: 975 sheet: -1.63 (0.82), residues: 48 loop : -1.73 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 473 HIS 0.002 0.001 HIS B 328 PHE 0.020 0.001 PHE C 474 TYR 0.025 0.001 TYR C 288 ARG 0.002 0.000 ARG A 479 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3173.90 seconds wall clock time: 57 minutes 52.14 seconds (3472.14 seconds total)