Starting phenix.real_space_refine on Wed Sep 25 13:04:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npw_12524/09_2024/7npw_12524.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npw_12524/09_2024/7npw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npw_12524/09_2024/7npw_12524.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npw_12524/09_2024/7npw_12524.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npw_12524/09_2024/7npw_12524.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npw_12524/09_2024/7npw_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 6.80, per 1000 atoms: 0.70 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: 2.67 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: 1.00 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: 2.80 Time building geometry restraints manager: 3.08 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 9.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 25.360 Find NCS groups from input model: 0.300 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.610 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 0.999 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: 0.1679 time to fit residues: 64.3608 Evaluate side-chains 203 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 fitting. rotamer outliers: 26 poor density : 218 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8696 (m-10) cc_final: 0.8198 (t80) REVERT: A 168 ASP cc_start: 0.8824 (m-30) cc_final: 0.8603 (m-30) REVERT: A 177 MET cc_start: 0.8826 (ttp) cc_final: 0.8303 (ttm) REVERT: A 288 TYR cc_start: 0.9080 (t80) cc_final: 0.8696 (t80) REVERT: A 336 LEU cc_start: 0.8547 (tt) cc_final: 0.8219 (pp) REVERT: A 451 MET cc_start: 0.9141 (mmp) cc_final: 0.8694 (mmp) REVERT: B 80 TYR cc_start: 0.8648 (m-10) cc_final: 0.8137 (t80) REVERT: B 251 MET cc_start: 0.7686 (tmm) cc_final: 0.7417 (tmm) REVERT: B 288 TYR cc_start: 0.9171 (t80) cc_final: 0.8750 (t80) REVERT: B 405 TYR cc_start: 0.8821 (t80) cc_final: 0.8491 (t80) REVERT: B 451 MET cc_start: 0.9042 (mmp) cc_final: 0.8414 (mmp) REVERT: C 80 TYR cc_start: 0.8690 (m-10) cc_final: 0.8089 (t80) REVERT: C 108 MET cc_start: 0.9045 (mmm) cc_final: 0.8546 (tpp) REVERT: C 177 MET cc_start: 0.8731 (mtt) cc_final: 0.8258 (ttp) REVERT: C 251 MET cc_start: 0.8348 (mtp) cc_final: 0.8100 (tmm) REVERT: C 286 MET cc_start: 0.9270 (mmp) cc_final: 0.8899 (tpp) REVERT: C 288 TYR cc_start: 0.8892 (t80) cc_final: 0.8622 (t80) REVERT: C 307 MET cc_start: 0.6098 (tmm) cc_final: 0.5676 (tmm) REVERT: C 336 LEU cc_start: 0.8490 (tt) cc_final: 0.8243 (pp) REVERT: C 451 MET cc_start: 0.9126 (mmp) cc_final: 0.8636 (mmp) outliers start: 26 outliers final: 20 residues processed: 228 average time/residue: 0.1739 time to fit residues: 58.8719 Evaluate side-chains 222 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 202 time to evaluate : 1.290 ------------------------------------------------------------------------------- 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 63 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 chunk 123 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 39 optimal weight: 0.0050 chunk 91 optimal weight: 0.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9885 Z= 0.180 Angle : 0.604 10.373 13428 Z= 0.305 Chirality : 0.040 0.181 1689 Planarity : 0.004 0.031 1641 Dihedral : 3.760 16.898 1344 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.84 % Allowed : 17.61 % Favored : 79.55 % 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: 1.09 (0.24), residues: 1254 helix: 1.49 (0.16), residues: 978 sheet: -1.43 (0.83), residues: 48 loop : -2.10 (0.36), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 473 HIS 0.001 0.000 HIS A 328 PHE 0.021 0.001 PHE B 170 TYR 0.018 0.001 TYR C 75 ARG 0.004 0.001 ARG C 388 *********************** 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 246 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 216 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8701 (m-10) cc_final: 0.8191 (t80) REVERT: A 251 MET cc_start: 0.7922 (tmm) cc_final: 0.7694 (tmm) REVERT: A 288 TYR cc_start: 0.9066 (t80) cc_final: 0.8850 (t80) REVERT: A 317 TYR cc_start: 0.9342 (t80) cc_final: 0.9136 (t80) REVERT: A 451 MET cc_start: 0.9167 (mmp) cc_final: 0.8677 (mmp) REVERT: B 80 TYR cc_start: 0.8619 (m-10) cc_final: 0.8099 (t80) REVERT: B 288 TYR cc_start: 0.9114 (t80) cc_final: 0.8762 (t80) REVERT: B 451 MET cc_start: 0.9063 (mmp) cc_final: 0.8514 (mmp) REVERT: B 468 ILE cc_start: 0.9522 (OUTLIER) cc_final: 0.9055 (tp) REVERT: C 80 TYR cc_start: 0.8769 (m-10) cc_final: 0.8176 (t80) REVERT: C 108 MET cc_start: 0.9060 (mmm) cc_final: 0.8510 (tpp) REVERT: C 251 MET cc_start: 0.8356 (mtp) cc_final: 0.8117 (tmm) REVERT: C 286 MET cc_start: 0.9346 (mmp) cc_final: 0.8986 (tpp) REVERT: C 307 MET cc_start: 0.5974 (tmm) cc_final: 0.5719 (tmm) REVERT: C 316 MET cc_start: 0.9364 (mmm) cc_final: 0.9124 (mtm) REVERT: C 336 LEU cc_start: 0.8648 (tt) cc_final: 0.8434 (pp) REVERT: C 405 TYR cc_start: 0.8813 (t80) cc_final: 0.8301 (t80) REVERT: C 451 MET cc_start: 0.9153 (mmp) cc_final: 0.8397 (mmp) outliers start: 30 outliers final: 23 residues processed: 228 average time/residue: 0.1731 time to fit residues: 58.6584 Evaluate side-chains 209 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 185 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 94 MET 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 B residue 468 ILE 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 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 113 optimal weight: 30.0000 chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 chunk 121 optimal weight: 3.9990 chunk 60 optimal weight: 0.3980 chunk 109 optimal weight: 7.9990 chunk 32 optimal weight: 0.2980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9885 Z= 0.186 Angle : 0.616 11.000 13428 Z= 0.309 Chirality : 0.040 0.183 1689 Planarity : 0.004 0.034 1641 Dihedral : 3.749 17.690 1344 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.69 % Allowed : 20.17 % Favored : 76.14 % 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: 1.11 (0.24), residues: 1254 helix: 1.50 (0.16), residues: 981 sheet: -1.53 (0.80), residues: 48 loop : -2.07 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 473 HIS 0.001 0.000 HIS B 328 PHE 0.018 0.001 PHE B 83 TYR 0.024 0.001 TYR C 288 ARG 0.003 0.000 ARG A 90 *********************** 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 fitting. rotamer outliers: 39 poor density : 203 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8721 (m-10) cc_final: 0.8217 (t80) REVERT: A 177 MET cc_start: 0.8894 (ttp) cc_final: 0.8343 (ttm) REVERT: A 242 ASN cc_start: 0.9109 (t0) cc_final: 0.8853 (t0) REVERT: A 288 TYR cc_start: 0.9041 (t80) cc_final: 0.8673 (t80) REVERT: A 405 TYR cc_start: 0.8894 (t80) cc_final: 0.8441 (t80) REVERT: A 451 MET cc_start: 0.9179 (mmp) cc_final: 0.8387 (mmp) REVERT: B 80 TYR cc_start: 0.8652 (m-10) cc_final: 0.8179 (t80) REVERT: B 242 ASN cc_start: 0.9281 (t0) cc_final: 0.8982 (t0) REVERT: B 288 TYR cc_start: 0.9082 (t80) cc_final: 0.8772 (t80) REVERT: B 316 MET cc_start: 0.9485 (mmm) cc_final: 0.9255 (mtm) REVERT: B 451 MET cc_start: 0.9075 (mmp) cc_final: 0.8579 (mmp) REVERT: B 476 ASP cc_start: 0.7681 (m-30) cc_final: 0.7028 (p0) REVERT: C 80 TYR cc_start: 0.8744 (m-10) cc_final: 0.8204 (t80) REVERT: C 177 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8408 (ttp) REVERT: C 286 MET cc_start: 0.9375 (mmp) cc_final: 0.9142 (tpt) REVERT: C 288 TYR cc_start: 0.8941 (t80) cc_final: 0.8680 (t80) REVERT: C 336 LEU cc_start: 0.8740 (tt) cc_final: 0.8502 (pp) REVERT: C 405 TYR cc_start: 0.8910 (t80) cc_final: 0.8540 (t80) REVERT: C 451 MET cc_start: 0.9154 (mmp) cc_final: 0.8362 (mmp) outliers start: 39 outliers final: 24 residues processed: 224 average time/residue: 0.1730 time to fit residues: 57.2085 Evaluate side-chains 211 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 186 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 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 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 232 VAL 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 101 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3124 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= 0.213 Angle : 0.634 10.964 13428 Z= 0.322 Chirality : 0.041 0.174 1689 Planarity : 0.004 0.038 1641 Dihedral : 3.907 20.593 1344 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.17 % Allowed : 22.35 % Favored : 73.48 % 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: 1.09 (0.24), residues: 1254 helix: 1.47 (0.16), residues: 978 sheet: -1.68 (0.79), residues: 48 loop : -1.94 (0.36), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 346 HIS 0.001 0.000 HIS A 146 PHE 0.023 0.001 PHE C 83 TYR 0.016 0.001 TYR A 317 ARG 0.003 0.000 ARG C 90 *********************** 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 245 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 201 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8755 (m-10) cc_final: 0.8249 (t80) REVERT: A 242 ASN cc_start: 0.9167 (t0) cc_final: 0.8868 (t0) REVERT: A 288 TYR cc_start: 0.9047 (t80) cc_final: 0.8606 (t80) REVERT: A 405 TYR cc_start: 0.8894 (t80) cc_final: 0.8481 (t80) REVERT: A 451 MET cc_start: 0.9127 (mmp) cc_final: 0.8336 (mmp) REVERT: B 80 TYR cc_start: 0.8633 (m-10) cc_final: 0.8321 (t80) REVERT: B 168 ASP cc_start: 0.8985 (m-30) cc_final: 0.8591 (m-30) REVERT: B 171 LEU cc_start: 0.8856 (tp) cc_final: 0.8579 (tp) REVERT: B 242 ASN cc_start: 0.9285 (t0) cc_final: 0.8986 (t0) REVERT: B 451 MET cc_start: 0.9092 (mmp) cc_final: 0.8419 (mmp) REVERT: B 468 ILE cc_start: 0.9586 (OUTLIER) cc_final: 0.9371 (tp) REVERT: B 476 ASP cc_start: 0.7741 (m-30) cc_final: 0.7060 (p0) REVERT: C 80 TYR cc_start: 0.8693 (m-10) cc_final: 0.8289 (t80) REVERT: C 83 PHE cc_start: 0.8554 (t80) cc_final: 0.8108 (t80) REVERT: C 108 MET cc_start: 0.8816 (tpp) cc_final: 0.8204 (tpp) REVERT: C 177 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8465 (ttp) REVERT: C 242 ASN cc_start: 0.9141 (t0) cc_final: 0.8776 (t0) REVERT: C 286 MET cc_start: 0.9344 (mmp) cc_final: 0.9108 (tpt) REVERT: C 288 TYR cc_start: 0.8943 (t80) cc_final: 0.8668 (t80) REVERT: C 336 LEU cc_start: 0.8840 (tt) cc_final: 0.8559 (pp) REVERT: C 405 TYR cc_start: 0.8924 (t80) cc_final: 0.8523 (t80) REVERT: C 451 MET cc_start: 0.9146 (mmp) cc_final: 0.8333 (mmp) REVERT: C 476 ASP cc_start: 0.7698 (m-30) cc_final: 0.7130 (p0) outliers start: 44 outliers final: 28 residues processed: 229 average time/residue: 0.1707 time to fit residues: 58.2980 Evaluate side-chains 219 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 189 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 177 MET Chi-restraints excluded: chain B residue 183 VAL 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 B residue 468 ILE 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 40 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 30.0000 chunk 30 optimal weight: 7.9990 chunk 121 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 117 optimal weight: 8.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9885 Z= 0.226 Angle : 0.645 11.959 13428 Z= 0.328 Chirality : 0.041 0.164 1689 Planarity : 0.004 0.040 1641 Dihedral : 4.006 21.111 1344 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.50 % Allowed : 23.58 % Favored : 72.92 % 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 (0.23), residues: 1254 helix: 1.42 (0.16), residues: 978 sheet: -1.78 (0.78), residues: 48 loop : -1.84 (0.36), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 346 HIS 0.002 0.001 HIS C 328 PHE 0.017 0.001 PHE B 83 TYR 0.026 0.002 TYR B 288 ARG 0.002 0.000 ARG A 280 *********************** 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 249 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 212 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.7998 (ptm) cc_final: 0.7592 (ptm) REVERT: A 80 TYR cc_start: 0.8718 (m-10) cc_final: 0.8283 (t80) REVERT: A 242 ASN cc_start: 0.9115 (t0) cc_final: 0.8755 (t0) REVERT: A 288 TYR cc_start: 0.9004 (t80) cc_final: 0.8520 (t80) REVERT: A 303 GLU cc_start: 0.9021 (pp20) cc_final: 0.8789 (pp20) REVERT: A 405 TYR cc_start: 0.8883 (t80) cc_final: 0.8418 (t80) REVERT: A 451 MET cc_start: 0.9148 (mmp) cc_final: 0.8471 (mmp) REVERT: A 476 ASP cc_start: 0.7815 (m-30) cc_final: 0.7191 (p0) REVERT: B 80 TYR cc_start: 0.8643 (m-10) cc_final: 0.8363 (t80) REVERT: B 168 ASP cc_start: 0.9053 (m-30) cc_final: 0.8696 (m-30) REVERT: B 242 ASN cc_start: 0.9213 (t0) cc_final: 0.8834 (t0) REVERT: B 405 TYR cc_start: 0.8927 (t80) cc_final: 0.8537 (t80) REVERT: B 451 MET cc_start: 0.9057 (mmp) cc_final: 0.8325 (mmp) REVERT: B 476 ASP cc_start: 0.7826 (m-30) cc_final: 0.7093 (p0) REVERT: C 80 TYR cc_start: 0.8708 (m-10) cc_final: 0.8332 (t80) REVERT: C 83 PHE cc_start: 0.8561 (t80) cc_final: 0.8094 (t80) REVERT: C 86 GLU cc_start: 0.9256 (OUTLIER) cc_final: 0.8969 (pm20) REVERT: C 93 GLN cc_start: 0.8586 (pp30) cc_final: 0.8268 (pp30) REVERT: C 184 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8579 (mm-30) REVERT: C 242 ASN cc_start: 0.9130 (t0) cc_final: 0.8735 (t0) REVERT: C 288 TYR cc_start: 0.8925 (t80) cc_final: 0.8564 (t80) REVERT: C 336 LEU cc_start: 0.8915 (tt) cc_final: 0.8593 (pp) REVERT: C 405 TYR cc_start: 0.8977 (t80) cc_final: 0.8650 (t80) REVERT: C 451 MET cc_start: 0.9122 (mmp) cc_final: 0.8363 (mmp) REVERT: C 476 ASP cc_start: 0.7759 (m-30) cc_final: 0.7177 (p0) outliers start: 37 outliers final: 28 residues processed: 235 average time/residue: 0.1771 time to fit residues: 61.5624 Evaluate side-chains 221 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 192 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 187 PHE 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 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 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 86 GLU 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 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 Chi-restraints excluded: chain C residue 485 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 68 optimal weight: 0.0670 chunk 102 optimal weight: 0.5980 chunk 121 optimal weight: 9.9990 chunk 76 optimal weight: 0.0980 chunk 74 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9885 Z= 0.167 Angle : 0.685 12.174 13428 Z= 0.334 Chirality : 0.042 0.188 1689 Planarity : 0.004 0.035 1641 Dihedral : 3.988 23.969 1344 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.31 % Allowed : 25.76 % Favored : 70.93 % 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 (0.24), residues: 1254 helix: 1.33 (0.16), residues: 975 sheet: -1.91 (0.79), residues: 48 loop : -1.98 (0.35), residues: 231 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 0.025 0.001 PHE B 83 TYR 0.020 0.001 TYR B 75 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 259 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 224 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8722 (m-10) cc_final: 0.8296 (t80) REVERT: A 93 GLN cc_start: 0.8605 (pp30) cc_final: 0.8050 (pp30) REVERT: A 184 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8751 (mm-30) REVERT: A 242 ASN cc_start: 0.9039 (t0) cc_final: 0.8728 (t0) REVERT: A 288 TYR cc_start: 0.8966 (t80) cc_final: 0.8414 (t80) REVERT: A 451 MET cc_start: 0.9065 (mmp) cc_final: 0.8606 (mtp) REVERT: B 80 TYR cc_start: 0.8581 (m-10) cc_final: 0.8347 (t80) REVERT: B 93 GLN cc_start: 0.8640 (pp30) cc_final: 0.8225 (pp30) REVERT: B 168 ASP cc_start: 0.9088 (m-30) cc_final: 0.8738 (m-30) REVERT: B 177 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8570 (ttp) REVERT: B 242 ASN cc_start: 0.9164 (t0) cc_final: 0.8878 (t0) REVERT: B 304 MET cc_start: 0.9180 (tmm) cc_final: 0.8699 (tmm) REVERT: B 316 MET cc_start: 0.9370 (mmm) cc_final: 0.9138 (mtm) REVERT: B 405 TYR cc_start: 0.8798 (t80) cc_final: 0.8424 (t80) REVERT: B 451 MET cc_start: 0.9042 (mmp) cc_final: 0.8288 (mmp) REVERT: B 476 ASP cc_start: 0.7642 (m-30) cc_final: 0.7055 (p0) REVERT: C 80 TYR cc_start: 0.8624 (m-10) cc_final: 0.8331 (t80) REVERT: C 83 PHE cc_start: 0.8335 (t80) cc_final: 0.7924 (t80) REVERT: C 177 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8559 (ttp) REVERT: C 242 ASN cc_start: 0.9045 (t0) cc_final: 0.8748 (t0) REVERT: C 288 TYR cc_start: 0.8921 (t80) cc_final: 0.8571 (t80) REVERT: C 303 GLU cc_start: 0.9091 (pp20) cc_final: 0.8844 (pp20) REVERT: C 336 LEU cc_start: 0.8934 (tt) cc_final: 0.8705 (pp) REVERT: C 405 TYR cc_start: 0.8879 (t80) cc_final: 0.8583 (t80) REVERT: C 451 MET cc_start: 0.9103 (mmp) cc_final: 0.8428 (mmp) outliers start: 35 outliers final: 26 residues processed: 240 average time/residue: 0.1774 time to fit residues: 62.2806 Evaluate side-chains 221 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 193 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 464 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 LEU 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 281 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 326 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 116 optimal weight: 0.0670 chunk 106 optimal weight: 2.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3677 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= 0.180 Angle : 0.694 11.410 13428 Z= 0.339 Chirality : 0.042 0.192 1689 Planarity : 0.004 0.034 1641 Dihedral : 3.961 23.200 1344 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.41 % Allowed : 26.33 % Favored : 70.27 % 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: 0.84 (0.23), residues: 1254 helix: 1.29 (0.16), residues: 975 sheet: -1.89 (0.79), residues: 48 loop : -1.93 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 473 HIS 0.002 0.000 HIS C 328 PHE 0.021 0.001 PHE A 83 TYR 0.019 0.001 TYR A 75 ARG 0.001 0.000 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 238 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 202 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8686 (m-10) cc_final: 0.8358 (t80) REVERT: A 93 GLN cc_start: 0.8529 (pp30) cc_final: 0.7998 (pp30) REVERT: A 184 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8770 (mm-30) REVERT: A 242 ASN cc_start: 0.9009 (t0) cc_final: 0.8729 (t0) REVERT: A 288 TYR cc_start: 0.8956 (t80) cc_final: 0.8369 (t80) REVERT: A 451 MET cc_start: 0.8987 (mmp) cc_final: 0.8395 (mmp) REVERT: B 80 TYR cc_start: 0.8617 (m-10) cc_final: 0.8347 (t80) REVERT: B 168 ASP cc_start: 0.9052 (m-30) cc_final: 0.8700 (m-30) REVERT: B 177 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8496 (ttp) REVERT: B 242 ASN cc_start: 0.9162 (t0) cc_final: 0.8882 (t0) REVERT: B 304 MET cc_start: 0.9263 (tmm) cc_final: 0.8865 (tmm) REVERT: B 316 MET cc_start: 0.9405 (mmm) cc_final: 0.9136 (mpp) REVERT: B 405 TYR cc_start: 0.8750 (t80) cc_final: 0.8405 (t80) REVERT: B 451 MET cc_start: 0.9036 (mmp) cc_final: 0.8270 (mmp) REVERT: B 476 ASP cc_start: 0.7600 (m-30) cc_final: 0.7049 (p0) REVERT: C 80 TYR cc_start: 0.8610 (m-10) cc_final: 0.8298 (t80) REVERT: C 177 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8577 (ttp) REVERT: C 242 ASN cc_start: 0.9079 (t0) cc_final: 0.8798 (t0) REVERT: C 269 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8389 (mp0) REVERT: C 288 TYR cc_start: 0.8932 (t80) cc_final: 0.8564 (t80) REVERT: C 336 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8724 (pp) REVERT: C 405 TYR cc_start: 0.8903 (t80) cc_final: 0.8613 (t80) REVERT: C 451 MET cc_start: 0.9087 (mmp) cc_final: 0.8251 (mmp) outliers start: 36 outliers final: 28 residues processed: 218 average time/residue: 0.1759 time to fit residues: 56.6926 Evaluate side-chains 219 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 188 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 B residue 53 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 LEU 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 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 333 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 281 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 30.0000 chunk 116 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9885 Z= 0.210 Angle : 0.709 10.587 13428 Z= 0.354 Chirality : 0.043 0.247 1689 Planarity : 0.004 0.034 1641 Dihedral : 4.079 25.713 1344 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.22 % Allowed : 26.80 % Favored : 69.98 % 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: 1.26 (0.16), residues: 972 sheet: -1.76 (0.79), residues: 48 loop : -1.65 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 473 HIS 0.002 0.001 HIS C 328 PHE 0.022 0.001 PHE C 170 TYR 0.019 0.001 TYR B 317 ARG 0.002 0.000 ARG A 72 *********************** 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 fitting. rotamer outliers: 34 poor density : 201 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8686 (m-10) cc_final: 0.8345 (t80) REVERT: A 93 GLN cc_start: 0.8590 (pp30) cc_final: 0.8045 (pp30) REVERT: A 242 ASN cc_start: 0.9042 (t0) cc_final: 0.8703 (t0) REVERT: A 288 TYR cc_start: 0.8991 (t80) cc_final: 0.8352 (t80) REVERT: A 451 MET cc_start: 0.9025 (mmp) cc_final: 0.8449 (mmp) REVERT: B 80 TYR cc_start: 0.8616 (m-10) cc_final: 0.8342 (t80) REVERT: B 168 ASP cc_start: 0.9060 (m-30) cc_final: 0.8694 (m-30) REVERT: B 177 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8517 (ttp) REVERT: B 242 ASN cc_start: 0.9173 (t0) cc_final: 0.8821 (t0) REVERT: B 304 MET cc_start: 0.9295 (tmm) cc_final: 0.8831 (tmm) REVERT: B 405 TYR cc_start: 0.8797 (t80) cc_final: 0.8458 (t80) REVERT: B 451 MET cc_start: 0.9034 (mmp) cc_final: 0.8431 (mmp) REVERT: B 476 ASP cc_start: 0.7647 (m-30) cc_final: 0.7097 (p0) REVERT: C 80 TYR cc_start: 0.8618 (m-10) cc_final: 0.8311 (t80) REVERT: C 93 GLN cc_start: 0.8679 (pp30) cc_final: 0.8339 (pp30) REVERT: C 94 MET cc_start: 0.8931 (ttm) cc_final: 0.8496 (ttm) REVERT: C 170 PHE cc_start: 0.9191 (t80) cc_final: 0.8940 (t80) REVERT: C 177 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8472 (ttp) REVERT: C 242 ASN cc_start: 0.9087 (t0) cc_final: 0.8698 (t0) REVERT: C 288 TYR cc_start: 0.8935 (t80) cc_final: 0.8580 (t80) REVERT: C 336 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8778 (pp) REVERT: C 405 TYR cc_start: 0.8935 (t80) cc_final: 0.8638 (t80) REVERT: C 451 MET cc_start: 0.9115 (mmp) cc_final: 0.8299 (mmp) REVERT: C 476 ASP cc_start: 0.7656 (m-30) cc_final: 0.7111 (p0) outliers start: 34 outliers final: 28 residues processed: 216 average time/residue: 0.1731 time to fit residues: 55.4462 Evaluate side-chains 219 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 188 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 B residue 53 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 LEU 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 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 333 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 281 LEU 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 73 optimal weight: 0.0970 chunk 56 optimal weight: 0.1980 chunk 83 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 115 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9885 Z= 0.206 Angle : 0.732 11.998 13428 Z= 0.363 Chirality : 0.043 0.211 1689 Planarity : 0.004 0.035 1641 Dihedral : 4.165 26.093 1344 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.22 % Allowed : 27.37 % 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: 0.76 (0.23), residues: 1254 helix: 1.16 (0.16), residues: 975 sheet: -1.73 (0.78), residues: 48 loop : -1.64 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 473 HIS 0.002 0.001 HIS C 328 PHE 0.027 0.001 PHE C 170 TYR 0.025 0.001 TYR B 317 ARG 0.004 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 230 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 196 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.8676 (m-10) cc_final: 0.8311 (t80) REVERT: A 93 GLN cc_start: 0.8598 (pp30) cc_final: 0.8052 (pp30) REVERT: A 242 ASN cc_start: 0.8997 (t0) cc_final: 0.8650 (t0) REVERT: A 288 TYR cc_start: 0.8973 (t80) cc_final: 0.8403 (t80) REVERT: A 451 MET cc_start: 0.9023 (mmp) cc_final: 0.8450 (mmp) REVERT: B 80 TYR cc_start: 0.8643 (m-10) cc_final: 0.8337 (t80) REVERT: B 168 ASP cc_start: 0.9089 (m-30) cc_final: 0.8711 (m-30) REVERT: B 177 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8552 (ttp) REVERT: B 242 ASN cc_start: 0.9187 (t0) cc_final: 0.8794 (t0) REVERT: B 304 MET cc_start: 0.9286 (tmm) cc_final: 0.8852 (tmm) REVERT: B 405 TYR cc_start: 0.8825 (t80) cc_final: 0.8483 (t80) REVERT: B 451 MET cc_start: 0.9047 (mmp) cc_final: 0.8315 (mmp) REVERT: B 476 ASP cc_start: 0.7786 (m-30) cc_final: 0.7210 (p0) REVERT: C 80 TYR cc_start: 0.8637 (m-10) cc_final: 0.8304 (t80) REVERT: C 93 GLN cc_start: 0.8685 (pp30) cc_final: 0.8359 (pp30) REVERT: C 94 MET cc_start: 0.8933 (ttm) cc_final: 0.8504 (ttm) REVERT: C 177 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8601 (ttp) REVERT: C 242 ASN cc_start: 0.9100 (t0) cc_final: 0.8710 (t0) REVERT: C 288 TYR cc_start: 0.8928 (t80) cc_final: 0.8571 (t80) REVERT: C 336 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8787 (pp) REVERT: C 405 TYR cc_start: 0.8932 (t80) cc_final: 0.8630 (t80) REVERT: C 451 MET cc_start: 0.9096 (mmp) cc_final: 0.8273 (mmp) REVERT: C 476 ASP cc_start: 0.7740 (m-30) cc_final: 0.7203 (p0) outliers start: 34 outliers final: 29 residues processed: 211 average time/residue: 0.1697 time to fit residues: 53.5360 Evaluate side-chains 221 residues out of total 1065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 189 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 294 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 LEU 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 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 333 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 232 VAL 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 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 27 optimal weight: 0.0020 chunk 100 optimal weight: 0.7980 chunk 41 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.102556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.075195 restraints weight = 34727.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.077394 restraints weight = 18070.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.078831 restraints weight = 11896.514| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4032 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= 0.188 Angle : 0.737 11.999 13428 Z= 0.359 Chirality : 0.044 0.228 1689 Planarity : 0.004 0.034 1641 Dihedral : 4.097 27.189 1344 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.12 % Allowed : 27.56 % Favored : 69.32 % 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: 0.74 (0.23), residues: 1254 helix: 1.15 (0.16), residues: 972 sheet: -1.69 (0.80), residues: 48 loop : -1.67 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 287 HIS 0.002 0.000 HIS C 328 PHE 0.022 0.001 PHE A 83 TYR 0.019 0.001 TYR B 317 ARG 0.003 0.000 ARG A 479 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2144.36 seconds wall clock time: 39 minutes 6.40 seconds (2346.40 seconds total)