Starting phenix.real_space_refine on Fri Feb 14 13:30:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uc1_42112/02_2025/8uc1_42112.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uc1_42112/02_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_42112/02_2025/8uc1_42112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uc1_42112/02_2025/8uc1_42112.map" model { file = "/net/cci-nas-00/data/ceres_data/8uc1_42112/02_2025/8uc1_42112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uc1_42112/02_2025/8uc1_42112.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.10, per 1000 atoms: 0.59 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: 2.89 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.06 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: 2.98 Time building geometry restraints manager: 3.23 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: 0.06 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: 0.960 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.190 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.610 ------------------------------------------------------------------------------- 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= 0.333 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 (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: 1.30 (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 TRP 0.018 0.002 TRP B 70 HIS 0.001 0.000 HIS B 220 PHE 0.012 0.001 PHE B 213 TYR 0.028 0.001 TYR B 123 ARG 0.002 0.000 ARG A 130 *********************** 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 : 1.112 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 120 average time/residue: 0.2256 time to fit residues: 39.1298 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 : 1.094 ------------------------------------------------------------------------------- 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 111 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 119 optimal weight: 0.3980 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.173288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.124946 restraints weight = 11587.123| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.70 r_work: 0.3116 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10536 Z= 0.350 Angle : 0.597 8.199 14318 Z= 0.310 Chirality : 0.045 0.148 1706 Planarity : 0.005 0.048 1784 Dihedral : 4.065 19.868 1430 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % 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 (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: 1.37 (0.24), residues: 1328 helix: 1.59 (0.18), residues: 864 sheet: 2.01 (0.71), residues: 52 loop : -0.67 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 472 HIS 0.003 0.001 HIS A 640 PHE 0.016 0.002 PHE B 111 TYR 0.018 0.002 TYR B 16 ARG 0.003 0.000 ARG A 175 *********************** 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 154 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 16 residues processed: 140 average time/residue: 0.2223 time to fit residues: 44.6513 Evaluate side-chains 126 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 122 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 504 GLN A 707 HIS B 220 HIS B 707 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.169799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.124761 restraints weight = 11851.638| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.98 r_work: 0.3051 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 10536 Z= 0.435 Angle : 0.615 5.876 14318 Z= 0.324 Chirality : 0.046 0.161 1706 Planarity : 0.005 0.042 1784 Dihedral : 4.132 14.892 1426 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.07 % Favored : 95.78 % Rotamer: Outliers : 3.09 % Allowed : 12.70 % Favored : 84.22 % 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: 1.24 (0.23), residues: 1328 helix: 1.49 (0.18), residues: 862 sheet: 1.96 (0.72), residues: 52 loop : -0.70 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 472 HIS 0.003 0.001 HIS B 337 PHE 0.022 0.002 PHE A 111 TYR 0.018 0.002 TYR A 16 ARG 0.002 0.000 ARG A 558 *********************** 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 148 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.7440 (ptm) cc_final: 0.7155 (mmt) REVERT: A 394 SER cc_start: 0.8193 (m) cc_final: 0.7972 (p) REVERT: B 267 MET cc_start: 0.7457 (ptm) cc_final: 0.7155 (mmt) REVERT: B 389 GLN cc_start: 0.8082 (mm110) cc_final: 0.7780 (mm110) REVERT: B 394 SER cc_start: 0.8225 (m) cc_final: 0.8001 (p) outliers start: 35 outliers final: 20 residues processed: 138 average time/residue: 0.2376 time to fit residues: 46.4213 Evaluate side-chains 131 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 115 SER 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 333 THR Chi-restraints excluded: chain A residue 641 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 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 325 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 641 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 125 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 43 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.174905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.126369 restraints weight = 11618.102| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.82 r_work: 0.3136 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1615 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= 0.170 Angle : 0.492 5.718 14318 Z= 0.257 Chirality : 0.041 0.125 1706 Planarity : 0.004 0.038 1784 Dihedral : 3.993 15.745 1426 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.16 % Favored : 96.69 % Rotamer: Outliers : 3.88 % Allowed : 12.87 % Favored : 83.25 % 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: 1.62 (0.24), residues: 1328 helix: 1.68 (0.18), residues: 870 sheet: 1.67 (0.70), residues: 52 loop : -0.24 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 472 HIS 0.001 0.001 HIS B 704 PHE 0.037 0.001 PHE B 111 TYR 0.011 0.001 TYR B 673 ARG 0.001 0.000 ARG B 15 *********************** 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 152 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 108 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.7411 (ptm) cc_final: 0.7075 (mmt) REVERT: A 336 PHE cc_start: 0.8117 (m-10) cc_final: 0.7580 (m-10) REVERT: A 394 SER cc_start: 0.8034 (m) cc_final: 0.7820 (p) REVERT: A 399 ARG cc_start: 0.7910 (ttp80) cc_final: 0.7519 (ttp80) REVERT: A 482 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8341 (tt) REVERT: A 566 PHE cc_start: 0.7852 (m-80) cc_final: 0.7510 (m-80) REVERT: A 633 MET cc_start: 0.5838 (ttp) cc_final: 0.5334 (mmt) REVERT: B 267 MET cc_start: 0.7430 (ptm) cc_final: 0.7075 (mmt) REVERT: B 399 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7505 (ttp80) REVERT: B 482 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8345 (tt) REVERT: B 566 PHE cc_start: 0.7840 (m-80) cc_final: 0.7494 (m-80) REVERT: B 633 MET cc_start: 0.5831 (ttp) cc_final: 0.5330 (mmt) outliers start: 44 outliers final: 23 residues processed: 138 average time/residue: 0.2250 time to fit residues: 44.4754 Evaluate side-chains 128 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 325 LEU Chi-restraints excluded: chain A residue 333 THR 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 243 VAL Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 333 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.170588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.125798 restraints weight = 11897.025| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.06 r_work: 0.3034 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 10536 Z= 0.439 Angle : 0.611 9.295 14318 Z= 0.319 Chirality : 0.046 0.144 1706 Planarity : 0.004 0.040 1784 Dihedral : 4.080 16.819 1426 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.22 % Favored : 95.63 % Rotamer: Outliers : 3.70 % Allowed : 12.96 % 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: 1.35 (0.24), residues: 1328 helix: 1.53 (0.18), residues: 872 sheet: 1.46 (0.70), residues: 52 loop : -0.52 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 472 HIS 0.003 0.001 HIS B 640 PHE 0.050 0.002 PHE A 111 TYR 0.014 0.002 TYR B 16 ARG 0.002 0.000 ARG A 716 *********************** 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: 42 poor density : 107 time to evaluate : 1.099 Fit side-chains REVERT: A 180 MET cc_start: 0.6819 (mmm) cc_final: 0.6577 (mmm) REVERT: A 267 MET cc_start: 0.7441 (ptm) cc_final: 0.7120 (mmt) REVERT: A 633 MET cc_start: 0.5751 (ttp) cc_final: 0.5483 (mmt) REVERT: B 180 MET cc_start: 0.6637 (mmm) cc_final: 0.6381 (mmm) REVERT: B 267 MET cc_start: 0.7454 (ptm) cc_final: 0.7119 (mmt) REVERT: B 633 MET cc_start: 0.5751 (ttp) cc_final: 0.5479 (mmt) outliers start: 42 outliers final: 32 residues processed: 138 average time/residue: 0.2234 time to fit residues: 44.4284 Evaluate side-chains 136 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 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 298 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 395 CYS 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 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 257 LEU Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 453 MET 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 23 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 14 optimal weight: 0.0770 chunk 78 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.175233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.127935 restraints weight = 11768.011| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.81 r_work: 0.3149 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10536 Z= 0.174 Angle : 0.505 9.337 14318 Z= 0.256 Chirality : 0.041 0.129 1706 Planarity : 0.004 0.035 1784 Dihedral : 3.970 17.973 1426 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.61 % Favored : 96.23 % Rotamer: Outliers : 3.35 % Allowed : 14.37 % 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 (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: 1.63 (0.24), residues: 1328 helix: 1.64 (0.18), residues: 884 sheet: 1.41 (0.69), residues: 52 loop : -0.17 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 472 HIS 0.002 0.000 HIS B 704 PHE 0.033 0.001 PHE A 111 TYR 0.024 0.001 TYR B 123 ARG 0.001 0.000 ARG A 150 *********************** 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 140 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.7378 (ptm) cc_final: 0.7094 (mmt) REVERT: A 399 ARG cc_start: 0.7982 (ttp80) cc_final: 0.7663 (ttp80) REVERT: B 267 MET cc_start: 0.7405 (ptm) cc_final: 0.7097 (mmt) REVERT: B 399 ARG cc_start: 0.7962 (ttp80) cc_final: 0.7645 (ttp80) outliers start: 38 outliers final: 27 residues processed: 128 average time/residue: 0.2386 time to fit residues: 43.5103 Evaluate side-chains 124 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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 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 333 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 395 CYS 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 243 VAL Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 698 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 42 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.4004 r_free = 0.4004 target = 0.174215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.126131 restraints weight = 12011.636| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.06 r_work: 0.3098 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10536 Z= 0.243 Angle : 0.530 8.188 14318 Z= 0.271 Chirality : 0.043 0.174 1706 Planarity : 0.004 0.035 1784 Dihedral : 3.971 17.787 1426 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.84 % Favored : 96.01 % Rotamer: Outliers : 3.17 % Allowed : 14.11 % Favored : 82.72 % 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: 1.58 (0.24), residues: 1328 helix: 1.62 (0.18), residues: 886 sheet: 1.20 (0.69), residues: 52 loop : -0.20 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 70 HIS 0.002 0.001 HIS B 337 PHE 0.032 0.001 PHE A 111 TYR 0.009 0.001 TYR B 16 ARG 0.001 0.000 ARG A 572 *********************** 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 140 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 TYR cc_start: 0.8296 (m-80) cc_final: 0.7798 (m-80) REVERT: A 267 MET cc_start: 0.7450 (ptm) cc_final: 0.7126 (mmt) REVERT: A 399 ARG cc_start: 0.7962 (ttp80) cc_final: 0.7625 (ttp80) REVERT: A 566 PHE cc_start: 0.7908 (m-80) cc_final: 0.7625 (m-80) REVERT: B 228 TYR cc_start: 0.8294 (m-80) cc_final: 0.7801 (m-80) REVERT: B 267 MET cc_start: 0.7461 (ptm) cc_final: 0.7127 (mmt) REVERT: B 399 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7613 (ttp80) REVERT: B 566 PHE cc_start: 0.7898 (m-80) cc_final: 0.7616 (m-80) outliers start: 36 outliers final: 31 residues processed: 133 average time/residue: 0.2247 time to fit residues: 43.1543 Evaluate side-chains 132 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 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 333 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 641 THR 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 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 333 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 641 THR 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 95 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 63 optimal weight: 0.2980 chunk 87 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.174515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.127093 restraints weight = 11826.483| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.92 r_work: 0.3123 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10536 Z= 0.214 Angle : 0.522 8.125 14318 Z= 0.264 Chirality : 0.042 0.143 1706 Planarity : 0.004 0.036 1784 Dihedral : 3.986 18.443 1426 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.31 % Favored : 96.54 % Rotamer: Outliers : 3.35 % Allowed : 14.46 % Favored : 82.19 % 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: 1.60 (0.24), residues: 1328 helix: 1.63 (0.18), residues: 886 sheet: 1.17 (0.69), residues: 52 loop : -0.18 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 70 HIS 0.002 0.001 HIS B 640 PHE 0.029 0.001 PHE A 111 TYR 0.029 0.001 TYR B 123 ARG 0.001 0.000 ARG A 571 *********************** 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 142 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 104 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 TYR cc_start: 0.8252 (m-80) cc_final: 0.7748 (m-80) REVERT: A 267 MET cc_start: 0.7445 (ptm) cc_final: 0.7121 (mmt) REVERT: A 399 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7617 (ttp80) REVERT: B 180 MET cc_start: 0.7039 (mmm) cc_final: 0.6671 (mmm) REVERT: B 228 TYR cc_start: 0.8264 (m-80) cc_final: 0.7775 (m-80) REVERT: B 267 MET cc_start: 0.7455 (ptm) cc_final: 0.7125 (mmt) REVERT: B 399 ARG cc_start: 0.7934 (ttp80) cc_final: 0.7600 (ttp80) outliers start: 38 outliers final: 33 residues processed: 133 average time/residue: 0.2310 time to fit residues: 43.8063 Evaluate side-chains 133 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 206 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 532 VAL 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 243 VAL Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 532 VAL 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 54 optimal weight: 0.1980 chunk 6 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 67 optimal weight: 0.4980 chunk 68 optimal weight: 8.9990 chunk 86 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.176020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.128083 restraints weight = 11866.296| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.94 r_work: 0.3131 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2085 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= 0.177 Angle : 0.517 8.829 14318 Z= 0.263 Chirality : 0.042 0.134 1706 Planarity : 0.004 0.037 1784 Dihedral : 3.954 18.960 1426 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.99 % Favored : 95.86 % Rotamer: Outliers : 3.26 % Allowed : 14.73 % Favored : 82.01 % 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: 1.66 (0.24), residues: 1328 helix: 1.66 (0.18), residues: 886 sheet: 1.21 (0.68), residues: 52 loop : -0.12 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP B 70 HIS 0.001 0.000 HIS B 704 PHE 0.024 0.001 PHE A 111 TYR 0.007 0.001 TYR B 16 ARG 0.001 0.000 ARG A 150 *********************** 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 142 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.7463 (ptm) cc_final: 0.7140 (mmt) REVERT: A 399 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7675 (ttp80) REVERT: A 566 PHE cc_start: 0.7826 (m-80) cc_final: 0.7594 (m-80) REVERT: B 180 MET cc_start: 0.7029 (mmm) cc_final: 0.6574 (mmm) REVERT: B 228 TYR cc_start: 0.8285 (m-80) cc_final: 0.7764 (m-80) REVERT: B 267 MET cc_start: 0.7476 (ptm) cc_final: 0.7141 (mmt) REVERT: B 399 ARG cc_start: 0.7940 (ttp80) cc_final: 0.7644 (ttp80) REVERT: B 566 PHE cc_start: 0.7820 (m-80) cc_final: 0.7589 (m-80) outliers start: 37 outliers final: 34 residues processed: 134 average time/residue: 0.2270 time to fit residues: 43.6434 Evaluate side-chains 136 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 298 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 532 VAL 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 298 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 532 VAL 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 66 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.174072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.125515 restraints weight = 11848.884| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.11 r_work: 0.3092 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10536 Z= 0.261 Angle : 0.547 9.035 14318 Z= 0.278 Chirality : 0.043 0.135 1706 Planarity : 0.004 0.036 1784 Dihedral : 3.989 20.938 1426 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.07 % Favored : 95.78 % Rotamer: Outliers : 3.17 % Allowed : 16.31 % Favored : 80.51 % 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: 1.60 (0.24), residues: 1328 helix: 1.60 (0.18), residues: 886 sheet: 1.20 (0.69), residues: 52 loop : -0.11 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 70 HIS 0.002 0.001 HIS B 640 PHE 0.025 0.001 PHE A 111 TYR 0.035 0.001 TYR B 123 ARG 0.002 0.000 ARG A 175 ********************** 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 137 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 TYR cc_start: 0.8289 (m-80) cc_final: 0.7727 (m-80) REVERT: A 267 MET cc_start: 0.7454 (ptm) cc_final: 0.7091 (mmt) REVERT: A 399 ARG cc_start: 0.7967 (ttp80) cc_final: 0.7655 (ttp80) REVERT: A 423 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6430 (tp) REVERT: A 566 PHE cc_start: 0.7846 (m-80) cc_final: 0.7621 (m-80) REVERT: B 180 MET cc_start: 0.6886 (mmm) cc_final: 0.6495 (mmm) REVERT: B 228 TYR cc_start: 0.8290 (m-80) cc_final: 0.7737 (m-80) REVERT: B 267 MET cc_start: 0.7452 (ptm) cc_final: 0.7091 (mmt) REVERT: B 399 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7625 (ttp80) REVERT: B 423 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6429 (tp) REVERT: B 566 PHE cc_start: 0.7845 (m-80) cc_final: 0.7621 (m-80) outliers start: 36 outliers final: 33 residues processed: 127 average time/residue: 0.2270 time to fit residues: 41.4714 Evaluate side-chains 133 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 298 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 532 VAL 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 298 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 532 VAL 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 128 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 48 optimal weight: 0.3980 chunk 50 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.174847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.126979 restraints weight = 11737.051| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.97 r_work: 0.3124 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10536 Z= 0.203 Angle : 0.527 8.937 14318 Z= 0.268 Chirality : 0.042 0.131 1706 Planarity : 0.004 0.037 1784 Dihedral : 3.961 22.231 1426 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.07 % Favored : 95.78 % Rotamer: Outliers : 3.26 % Allowed : 16.05 % Favored : 80.69 % 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: 1.66 (0.24), residues: 1328 helix: 1.64 (0.18), residues: 886 sheet: 1.18 (0.68), residues: 52 loop : -0.07 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 70 HIS 0.002 0.000 HIS B 640 PHE 0.024 0.001 PHE A 111 TYR 0.030 0.001 TYR B 123 ARG 0.001 0.000 ARG A 399 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4603.41 seconds wall clock time: 82 minutes 37.04 seconds (4957.04 seconds total)