Starting phenix.real_space_refine on Sat Aug 23 06:21:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uc1_42112/08_2025/8uc1_42112.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uc1_42112/08_2025/8uc1_42112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uc1_42112/08_2025/8uc1_42112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uc1_42112/08_2025/8uc1_42112.map" model { file = "/net/cci-nas-00/data/ceres_data/8uc1_42112/08_2025/8uc1_42112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uc1_42112/08_2025/8uc1_42112.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 50 5.16 5 Cl 2 4.86 5 C 6756 2.51 5 N 1660 2.21 5 O 1842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10310 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5154 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 31, 'TRANS': 636} Chain breaks: 1 Chain: "B" Number of atoms: 5154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5154 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 31, 'TRANS': 636} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.53, per 1000 atoms: 0.25 Number of scatterers: 10310 At special positions: 0 Unit cell: (86.508, 114.276, 115.344, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 50 16.00 O 1842 8.00 N 1660 7.00 C 6756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 411.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2464 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 3 sheets defined 70.2% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 41 through 51 removed outlier: 3.658A pdb=" N GLN A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 66 through 71 removed outlier: 3.553A pdb=" N TRP A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 74 No H-bonds generated for 'chain 'A' and resid 72 through 74' Processing helix chain 'A' and resid 78 through 105 removed outlier: 4.327A pdb=" N GLY A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 109 through 116 removed outlier: 3.949A pdb=" N LEU A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 removed outlier: 3.757A pdb=" N MET A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 152 Processing helix chain 'A' and resid 168 through 196 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 231 removed outlier: 4.326A pdb=" N LYS A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 254 through 257 Processing helix chain 'A' and resid 258 through 282 Processing helix chain 'A' and resid 291 through 308 Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 335 through 366 removed outlier: 3.529A pdb=" N TYR A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL A 341 " --> pdb=" O HIS A 337 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 387 Processing helix chain 'A' and resid 397 through 407 removed outlier: 3.742A pdb=" N GLY A 407 " --> pdb=" O GLN A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.632A pdb=" N GLU A 433 " --> pdb=" O PHE A 430 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER A 434 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 448 removed outlier: 3.717A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 448 " --> pdb=" O VAL A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 456 through 465 removed outlier: 3.717A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 484 through 505 removed outlier: 3.915A pdb=" N LEU A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 490 " --> pdb=" O TYR A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 removed outlier: 3.532A pdb=" N THR A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 577 Processing helix chain 'A' and resid 653 through 671 removed outlier: 3.710A pdb=" N VAL A 670 " --> pdb=" O GLU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 690 Processing helix chain 'A' and resid 695 through 700 Processing helix chain 'A' and resid 705 through 722 removed outlier: 3.734A pdb=" N GLN A 722 " --> pdb=" O ALA A 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 32 Processing helix chain 'B' and resid 41 through 51 removed outlier: 3.658A pdb=" N GLN B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'B' and resid 66 through 71 removed outlier: 3.553A pdb=" N TRP B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 78 through 105 removed outlier: 4.327A pdb=" N GLY B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Proline residue: B 96 - end of helix Processing helix chain 'B' and resid 109 through 116 removed outlier: 3.949A pdb=" N LEU B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 127 removed outlier: 3.757A pdb=" N MET B 122 " --> pdb=" O TYR B 118 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 125 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 152 Processing helix chain 'B' and resid 168 through 196 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 206 through 231 removed outlier: 4.326A pdb=" N LYS B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 253 Processing helix chain 'B' and resid 254 through 257 Processing helix chain 'B' and resid 258 through 282 Processing helix chain 'B' and resid 291 through 308 Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'B' and resid 335 through 366 removed outlier: 3.529A pdb=" N TYR B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL B 341 " --> pdb=" O HIS B 337 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 387 Processing helix chain 'B' and resid 397 through 407 removed outlier: 3.742A pdb=" N GLY B 407 " --> pdb=" O GLN B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.632A pdb=" N GLU B 433 " --> pdb=" O PHE B 430 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER B 434 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 448 removed outlier: 3.717A pdb=" N LEU B 440 " --> pdb=" O PRO B 436 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 448 " --> pdb=" O VAL B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 456 through 465 removed outlier: 3.717A pdb=" N PHE B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 482 Processing helix chain 'B' and resid 484 through 505 removed outlier: 3.915A pdb=" N LEU B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR B 490 " --> pdb=" O TYR B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 560 removed outlier: 3.532A pdb=" N THR B 560 " --> pdb=" O LEU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 577 Processing helix chain 'B' and resid 653 through 671 removed outlier: 3.710A pdb=" N VAL B 670 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 690 Processing helix chain 'B' and resid 695 through 700 Processing helix chain 'B' and resid 705 through 722 removed outlier: 3.734A pdb=" N GLN B 722 " --> pdb=" O ALA B 718 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 21 removed outlier: 3.595A pdb=" N VAL A 18 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 18 " --> pdb=" O VAL A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.573A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N GLN A 513 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 11.730A pdb=" N ILE A 535 " --> pdb=" O GLN A 513 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS A 536 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASP A 645 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE A 538 " --> pdb=" O ASP A 645 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N PHE A 703 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A 676 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.573A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N GLN B 513 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 11.730A pdb=" N ILE B 535 " --> pdb=" O GLN B 513 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS B 536 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASP B 645 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE B 538 " --> pdb=" O ASP B 645 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N PHE B 703 " --> pdb=" O VAL B 674 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU B 676 " --> pdb=" O PHE B 703 " (cutoff:3.500A) 650 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1724 1.32 - 1.45: 2658 1.45 - 1.57: 6072 1.57 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 10536 Sorted by residual: bond pdb=" CE1 HIS B 337 " pdb=" NE2 HIS B 337 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.68e+01 bond pdb=" CE1 HIS A 337 " pdb=" NE2 HIS A 337 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.68e+01 bond pdb=" C PRO A 327 " pdb=" O PRO A 327 " ideal model delta sigma weight residual 1.243 1.209 0.034 8.50e-03 1.38e+04 1.58e+01 bond pdb=" C PRO B 327 " pdb=" O PRO B 327 " ideal model delta sigma weight residual 1.243 1.209 0.034 8.50e-03 1.38e+04 1.58e+01 bond pdb=" N GLU A 207 " pdb=" CA GLU A 207 " ideal model delta sigma weight residual 1.462 1.488 -0.026 8.50e-03 1.38e+04 9.12e+00 ... (remaining 10531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 13611 1.57 - 3.14: 596 3.14 - 4.71: 89 4.71 - 6.28: 16 6.28 - 7.84: 6 Bond angle restraints: 14318 Sorted by residual: angle pdb=" C LEU B 326 " pdb=" N PRO B 327 " pdb=" CA PRO B 327 " ideal model delta sigma weight residual 119.66 122.71 -3.05 7.20e-01 1.93e+00 1.79e+01 angle pdb=" C LEU A 326 " pdb=" N PRO A 327 " pdb=" CA PRO A 327 " ideal model delta sigma weight residual 119.66 122.71 -3.05 7.20e-01 1.93e+00 1.79e+01 angle pdb=" CB GLN B 504 " pdb=" CG GLN B 504 " pdb=" CD GLN B 504 " ideal model delta sigma weight residual 112.60 105.56 7.04 1.70e+00 3.46e-01 1.72e+01 angle pdb=" CB GLN A 504 " pdb=" CG GLN A 504 " pdb=" CD GLN A 504 " ideal model delta sigma weight residual 112.60 105.56 7.04 1.70e+00 3.46e-01 1.72e+01 angle pdb=" CA ASN B 382 " pdb=" C ASN B 382 " pdb=" O ASN B 382 " ideal model delta sigma weight residual 120.82 116.47 4.35 1.05e+00 9.07e-01 1.71e+01 ... (remaining 14313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 5538 17.18 - 34.37: 583 34.37 - 51.55: 85 51.55 - 68.73: 24 68.73 - 85.91: 6 Dihedral angle restraints: 6236 sinusoidal: 2388 harmonic: 3848 Sorted by residual: dihedral pdb=" CG ARG A 502 " pdb=" CD ARG A 502 " pdb=" NE ARG A 502 " pdb=" CZ ARG A 502 " ideal model delta sinusoidal sigma weight residual 180.00 138.56 41.44 2 1.50e+01 4.44e-03 9.34e+00 dihedral pdb=" CG ARG B 502 " pdb=" CD ARG B 502 " pdb=" NE ARG B 502 " pdb=" CZ ARG B 502 " ideal model delta sinusoidal sigma weight residual 180.00 138.56 41.44 2 1.50e+01 4.44e-03 9.34e+00 dihedral pdb=" CA ILE A 140 " pdb=" CB ILE A 140 " pdb=" CG1 ILE A 140 " pdb=" CD1 ILE A 140 " ideal model delta sinusoidal sigma weight residual 60.00 114.99 -54.99 3 1.50e+01 4.44e-03 9.32e+00 ... (remaining 6233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1165 0.043 - 0.087: 364 0.087 - 0.130: 127 0.130 - 0.173: 36 0.173 - 0.217: 14 Chirality restraints: 1706 Sorted by residual: chirality pdb=" CA ILE B 393 " pdb=" N ILE B 393 " pdb=" C ILE B 393 " pdb=" CB ILE B 393 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE A 393 " pdb=" N ILE A 393 " pdb=" C ILE A 393 " pdb=" CB ILE A 393 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA VAL B 532 " pdb=" N VAL B 532 " pdb=" C VAL B 532 " pdb=" CB VAL B 532 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.30e-01 ... (remaining 1703 not shown) Planarity restraints: 1784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 150 " -0.248 9.50e-02 1.11e+02 1.11e-01 7.60e+00 pdb=" NE ARG A 150 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 150 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 150 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 150 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 150 " 0.248 9.50e-02 1.11e+02 1.11e-01 7.60e+00 pdb=" NE ARG B 150 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B 150 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 150 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 150 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 288 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO A 289 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " 0.030 5.00e-02 4.00e+02 ... (remaining 1781 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1668 2.76 - 3.29: 10481 3.29 - 3.83: 17174 3.83 - 4.36: 19390 4.36 - 4.90: 34164 Nonbonded interactions: 82877 Sorted by model distance: nonbonded pdb=" O ALA A 495 " pdb=" OG1 THR A 498 " model vdw 2.220 3.040 nonbonded pdb=" O ALA B 495 " pdb=" OG1 THR B 498 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" OE1 GLU B 374 " model vdw 2.245 3.040 nonbonded pdb=" OG1 THR A 128 " pdb=" OE1 GLU A 374 " model vdw 2.245 3.040 nonbonded pdb=" O MET B 63 " pdb=" NE2 GLN B 373 " model vdw 2.320 3.120 ... (remaining 82872 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.400 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 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 : 0.005 0.041 10536 Z= 0.345 Angle : 0.723 7.845 14318 Z= 0.496 Chirality : 0.052 0.217 1706 Planarity : 0.006 0.111 1784 Dihedral : 14.103 85.914 3772 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.71 % Allowed : 10.93 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.24), residues: 1328 helix: 1.60 (0.18), residues: 824 sheet: 1.89 (0.76), residues: 52 loop : -0.60 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 130 TYR 0.028 0.001 TYR B 123 PHE 0.012 0.001 PHE B 213 TRP 0.018 0.002 TRP B 70 HIS 0.001 0.000 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00513 (10536) covalent geometry : angle 0.72291 (14318) hydrogen bonds : bond 0.16087 ( 650) hydrogen bonds : angle 6.12242 ( 1890) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.423 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 120 average time/residue: 0.1039 time to fit residues: 18.1957 Evaluate side-chains 109 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain B residue 342 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS A 389 GLN B 220 HIS B 389 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.172564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.124130 restraints weight = 11544.915| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.48 r_work: 0.3123 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10536 Z= 0.226 Angle : 0.603 8.303 14318 Z= 0.314 Chirality : 0.045 0.141 1706 Planarity : 0.005 0.048 1784 Dihedral : 4.063 19.964 1430 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.17 % Allowed : 11.90 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.24), residues: 1328 helix: 1.59 (0.18), residues: 864 sheet: 2.05 (0.71), residues: 52 loop : -0.69 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 175 TYR 0.018 0.002 TYR B 16 PHE 0.016 0.002 PHE B 111 TRP 0.008 0.002 TRP A 472 HIS 0.003 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00554 (10536) covalent geometry : angle 0.60308 (14318) hydrogen bonds : bond 0.04867 ( 650) hydrogen bonds : angle 4.85943 ( 1890) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 16 residues processed: 139 average time/residue: 0.1060 time to fit residues: 21.2441 Evaluate side-chains 127 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 260 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 64 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 70 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.174673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.127987 restraints weight = 11599.623| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.60 r_work: 0.3173 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10536 Z= 0.132 Angle : 0.508 5.858 14318 Z= 0.265 Chirality : 0.042 0.156 1706 Planarity : 0.004 0.042 1784 Dihedral : 3.928 15.107 1426 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.99 % Favored : 95.86 % Rotamer: Outliers : 2.47 % Allowed : 12.70 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.24), residues: 1328 helix: 1.79 (0.18), residues: 860 sheet: 1.95 (0.72), residues: 52 loop : -0.50 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 175 TYR 0.012 0.001 TYR B 16 PHE 0.017 0.001 PHE A 566 TRP 0.009 0.001 TRP A 472 HIS 0.002 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00300 (10536) covalent geometry : angle 0.50783 (14318) hydrogen bonds : bond 0.04009 ( 650) hydrogen bonds : angle 4.53968 ( 1890) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.7576 (ptm) cc_final: 0.7243 (mmt) REVERT: B 267 MET cc_start: 0.7562 (ptm) cc_final: 0.7238 (mmt) REVERT: B 389 GLN cc_start: 0.8001 (mm110) cc_final: 0.7738 (mm110) outliers start: 28 outliers final: 15 residues processed: 136 average time/residue: 0.1195 time to fit residues: 22.4088 Evaluate side-chains 122 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 333 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 116 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.177424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.128118 restraints weight = 11831.016| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.74 r_work: 0.3150 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10536 Z= 0.126 Angle : 0.492 6.087 14318 Z= 0.254 Chirality : 0.041 0.125 1706 Planarity : 0.004 0.037 1784 Dihedral : 3.888 15.794 1426 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.31 % Favored : 96.54 % Rotamer: Outliers : 2.12 % Allowed : 13.23 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.24), residues: 1328 helix: 1.76 (0.18), residues: 870 sheet: 1.94 (0.72), residues: 52 loop : -0.22 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 175 TYR 0.011 0.001 TYR B 16 PHE 0.025 0.001 PHE A 111 TRP 0.009 0.002 TRP B 472 HIS 0.001 0.001 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00288 (10536) covalent geometry : angle 0.49176 (14318) hydrogen bonds : bond 0.03724 ( 650) hydrogen bonds : angle 4.39228 ( 1890) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.7483 (ptm) cc_final: 0.7134 (mmt) REVERT: A 482 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8479 (tt) REVERT: A 633 MET cc_start: 0.5782 (ttp) cc_final: 0.5308 (mmt) REVERT: B 267 MET cc_start: 0.7489 (ptm) cc_final: 0.7132 (mmt) REVERT: B 389 GLN cc_start: 0.7816 (mm110) cc_final: 0.7554 (mm110) REVERT: B 394 SER cc_start: 0.7841 (m) cc_final: 0.7635 (p) REVERT: B 482 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8457 (tt) REVERT: B 633 MET cc_start: 0.5783 (ttp) cc_final: 0.5309 (mmt) outliers start: 24 outliers final: 15 residues processed: 125 average time/residue: 0.1013 time to fit residues: 18.6689 Evaluate side-chains 119 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 26 optimal weight: 9.9990 chunk 96 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.0020 chunk 1 optimal weight: 3.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.175408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.126218 restraints weight = 11721.728| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.91 r_work: 0.3157 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10536 Z= 0.135 Angle : 0.494 5.914 14318 Z= 0.255 Chirality : 0.042 0.125 1706 Planarity : 0.004 0.034 1784 Dihedral : 3.830 16.447 1426 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.24 % Favored : 96.61 % Rotamer: Outliers : 3.44 % Allowed : 12.70 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.24), residues: 1328 helix: 1.77 (0.18), residues: 870 sheet: 1.81 (0.71), residues: 52 loop : -0.25 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 150 TYR 0.011 0.001 TYR A 16 PHE 0.022 0.001 PHE A 111 TRP 0.008 0.002 TRP A 472 HIS 0.001 0.001 HIS A 640 Details of bonding type rmsd covalent geometry : bond 0.00318 (10536) covalent geometry : angle 0.49364 (14318) hydrogen bonds : bond 0.03705 ( 650) hydrogen bonds : angle 4.33389 ( 1890) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.7507 (ptm) cc_final: 0.7153 (mmt) REVERT: A 337 HIS cc_start: 0.6762 (p-80) cc_final: 0.5962 (m170) REVERT: A 482 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8489 (tt) REVERT: A 633 MET cc_start: 0.5597 (ttp) cc_final: 0.5293 (mmt) REVERT: B 180 MET cc_start: 0.6494 (mmm) cc_final: 0.6268 (mmm) REVERT: B 267 MET cc_start: 0.7510 (ptm) cc_final: 0.7146 (mmt) REVERT: B 337 HIS cc_start: 0.6752 (p-80) cc_final: 0.5956 (m170) REVERT: B 482 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8501 (tt) REVERT: B 633 MET cc_start: 0.5585 (ttp) cc_final: 0.5284 (mmt) outliers start: 39 outliers final: 25 residues processed: 139 average time/residue: 0.1009 time to fit residues: 20.5823 Evaluate side-chains 131 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 698 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 47 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.176317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.130298 restraints weight = 11858.451| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.82 r_work: 0.3144 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10536 Z= 0.126 Angle : 0.484 6.008 14318 Z= 0.250 Chirality : 0.041 0.125 1706 Planarity : 0.004 0.034 1784 Dihedral : 3.816 17.064 1426 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.39 % Favored : 96.46 % Rotamer: Outliers : 3.17 % Allowed : 13.23 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.24), residues: 1328 helix: 1.81 (0.18), residues: 872 sheet: 1.76 (0.70), residues: 52 loop : -0.16 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 150 TYR 0.011 0.001 TYR B 123 PHE 0.019 0.001 PHE B 111 TRP 0.010 0.002 TRP B 70 HIS 0.001 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00293 (10536) covalent geometry : angle 0.48397 (14318) hydrogen bonds : bond 0.03618 ( 650) hydrogen bonds : angle 4.27208 ( 1890) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 TRP cc_start: 0.6238 (p-90) cc_final: 0.6024 (p-90) REVERT: A 228 TYR cc_start: 0.8297 (m-80) cc_final: 0.7768 (m-80) REVERT: A 267 MET cc_start: 0.7445 (ptm) cc_final: 0.7126 (mmt) REVERT: A 482 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8496 (tt) REVERT: B 70 TRP cc_start: 0.6227 (p-90) cc_final: 0.6011 (p-90) REVERT: B 220 HIS cc_start: 0.7521 (OUTLIER) cc_final: 0.7318 (m170) REVERT: B 228 TYR cc_start: 0.8298 (m-80) cc_final: 0.7768 (m-80) REVERT: B 267 MET cc_start: 0.7454 (ptm) cc_final: 0.7125 (mmt) REVERT: B 482 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8497 (tt) outliers start: 36 outliers final: 26 residues processed: 129 average time/residue: 0.0983 time to fit residues: 18.6743 Evaluate side-chains 128 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 482 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 100 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 63 optimal weight: 0.0980 chunk 55 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.177226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.129037 restraints weight = 11671.955| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.94 r_work: 0.3173 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10536 Z= 0.112 Angle : 0.487 6.793 14318 Z= 0.249 Chirality : 0.041 0.155 1706 Planarity : 0.003 0.035 1784 Dihedral : 3.784 16.403 1426 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.61 % Favored : 96.23 % Rotamer: Outliers : 3.09 % Allowed : 13.93 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.24), residues: 1328 helix: 1.86 (0.18), residues: 870 sheet: 1.79 (0.70), residues: 52 loop : -0.16 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 572 TYR 0.009 0.001 TYR B 16 PHE 0.017 0.001 PHE B 111 TRP 0.009 0.001 TRP A 472 HIS 0.002 0.000 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00250 (10536) covalent geometry : angle 0.48736 (14318) hydrogen bonds : bond 0.03433 ( 650) hydrogen bonds : angle 4.20352 ( 1890) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.7570 (ptm) cc_final: 0.7176 (mmt) REVERT: A 482 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8471 (tt) REVERT: B 267 MET cc_start: 0.7581 (ptm) cc_final: 0.7178 (mmt) REVERT: B 482 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8482 (tt) outliers start: 35 outliers final: 26 residues processed: 131 average time/residue: 0.1050 time to fit residues: 19.8727 Evaluate side-chains 128 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 698 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 104 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.177533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.129013 restraints weight = 11860.177| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.85 r_work: 0.3169 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10536 Z= 0.126 Angle : 0.511 10.981 14318 Z= 0.260 Chirality : 0.042 0.141 1706 Planarity : 0.004 0.057 1784 Dihedral : 3.837 18.428 1426 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.69 % Favored : 96.16 % Rotamer: Outliers : 2.82 % Allowed : 15.08 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.24), residues: 1328 helix: 1.83 (0.18), residues: 872 sheet: 1.80 (0.69), residues: 52 loop : -0.13 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 399 TYR 0.015 0.001 TYR B 123 PHE 0.016 0.001 PHE B 111 TRP 0.013 0.002 TRP A 70 HIS 0.002 0.001 HIS A 640 Details of bonding type rmsd covalent geometry : bond 0.00291 (10536) covalent geometry : angle 0.51083 (14318) hydrogen bonds : bond 0.03490 ( 650) hydrogen bonds : angle 4.19849 ( 1890) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.7593 (ptm) cc_final: 0.7206 (mmt) REVERT: A 482 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8487 (tt) REVERT: B 267 MET cc_start: 0.7605 (ptm) cc_final: 0.7207 (mmt) REVERT: B 482 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8492 (tt) outliers start: 32 outliers final: 26 residues processed: 123 average time/residue: 0.1013 time to fit residues: 18.2650 Evaluate side-chains 121 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 698 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 129 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 76 optimal weight: 0.0770 chunk 34 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.177601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.128972 restraints weight = 11673.978| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.97 r_work: 0.3167 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10536 Z= 0.116 Angle : 0.500 7.547 14318 Z= 0.254 Chirality : 0.041 0.138 1706 Planarity : 0.004 0.044 1784 Dihedral : 3.819 20.289 1426 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.84 % Favored : 96.01 % Rotamer: Outliers : 3.00 % Allowed : 14.73 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.24), residues: 1328 helix: 1.83 (0.18), residues: 882 sheet: 1.82 (0.69), residues: 52 loop : -0.12 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 399 TYR 0.009 0.001 TYR A 16 PHE 0.015 0.001 PHE B 111 TRP 0.031 0.003 TRP B 70 HIS 0.001 0.000 HIS A 640 Details of bonding type rmsd covalent geometry : bond 0.00264 (10536) covalent geometry : angle 0.49992 (14318) hydrogen bonds : bond 0.03401 ( 650) hydrogen bonds : angle 4.16441 ( 1890) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.7584 (ptm) cc_final: 0.7195 (mmt) REVERT: A 482 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8466 (tt) REVERT: B 267 MET cc_start: 0.7610 (ptm) cc_final: 0.7197 (mmt) REVERT: B 482 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8465 (tt) outliers start: 34 outliers final: 27 residues processed: 126 average time/residue: 0.0995 time to fit residues: 18.4973 Evaluate side-chains 125 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 698 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 38 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 67 optimal weight: 0.0040 chunk 47 optimal weight: 0.6980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.179078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.129981 restraints weight = 11745.701| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.00 r_work: 0.3158 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10536 Z= 0.117 Angle : 0.512 8.731 14318 Z= 0.260 Chirality : 0.042 0.135 1706 Planarity : 0.004 0.040 1784 Dihedral : 3.836 25.292 1426 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.84 % Favored : 96.01 % Rotamer: Outliers : 2.56 % Allowed : 15.34 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.24), residues: 1328 helix: 1.90 (0.18), residues: 870 sheet: 1.81 (0.69), residues: 52 loop : -0.11 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 399 TYR 0.019 0.001 TYR A 123 PHE 0.014 0.001 PHE A 111 TRP 0.022 0.003 TRP B 70 HIS 0.002 0.000 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00269 (10536) covalent geometry : angle 0.51168 (14318) hydrogen bonds : bond 0.03385 ( 650) hydrogen bonds : angle 4.14980 ( 1890) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.7599 (ptm) cc_final: 0.7198 (mmt) REVERT: A 482 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8488 (tt) REVERT: B 180 MET cc_start: 0.5803 (mmt) cc_final: 0.5527 (mmp) REVERT: B 267 MET cc_start: 0.7617 (ptm) cc_final: 0.7197 (mmt) REVERT: B 482 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8475 (tt) outliers start: 29 outliers final: 27 residues processed: 115 average time/residue: 0.1072 time to fit residues: 17.7763 Evaluate side-chains 120 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 698 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 110 optimal weight: 0.9980 chunk 89 optimal weight: 0.4980 chunk 112 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 129 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 66 optimal weight: 0.2980 chunk 73 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.178477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.130726 restraints weight = 11855.786| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.87 r_work: 0.3163 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10536 Z= 0.108 Angle : 0.500 8.624 14318 Z= 0.254 Chirality : 0.041 0.137 1706 Planarity : 0.004 0.052 1784 Dihedral : 3.845 33.101 1426 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.99 % Favored : 95.86 % Rotamer: Outliers : 2.73 % Allowed : 15.17 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.24), residues: 1328 helix: 1.93 (0.18), residues: 870 sheet: 1.85 (0.69), residues: 52 loop : -0.08 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 399 TYR 0.008 0.001 TYR A 16 PHE 0.014 0.001 PHE A 111 TRP 0.021 0.002 TRP A 70 HIS 0.003 0.000 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00241 (10536) covalent geometry : angle 0.49980 (14318) hydrogen bonds : bond 0.03287 ( 650) hydrogen bonds : angle 4.10840 ( 1890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2497.61 seconds wall clock time: 43 minutes 44.21 seconds (2624.21 seconds total)