Starting phenix.real_space_refine on Thu May 1 04:54:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uc1_42112/05_2025/8uc1_42112.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uc1_42112/05_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_42112/05_2025/8uc1_42112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uc1_42112/05_2025/8uc1_42112.map" model { file = "/net/cci-nas-00/data/ceres_data/8uc1_42112/05_2025/8uc1_42112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uc1_42112/05_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-5669/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: 6.63, per 1000 atoms: 0.64 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: 2.92 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: 0.98 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: 3.20 Time building geometry restraints manager: 3.21 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: 0.05 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: 1.190 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.310 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.960 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.16087 ( 650) hydrogen bonds : angle 6.12242 ( 1890) covalent geometry : bond 0.00513 (10536) covalent geometry : angle 0.72291 (14318) *********************** 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 : 1.046 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 120 average time/residue: 0.2356 time to fit residues: 41.2468 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 : 1.174 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.173404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.125047 restraints weight = 11593.062| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.70 r_work: 0.3114 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10536 Z= 0.216 Angle : 0.598 8.213 14318 Z= 0.310 Chirality : 0.045 0.152 1706 Planarity : 0.005 0.048 1784 Dihedral : 4.061 19.826 1430 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.22 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: 2.02 (0.71), residues: 52 loop : -0.67 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 Details of bonding type rmsd hydrogen bonds : bond 0.04842 ( 650) hydrogen bonds : angle 4.82617 ( 1890) covalent geometry : bond 0.00530 (10536) covalent geometry : angle 0.59752 (14318) *********************** 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 : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 16 residues processed: 140 average time/residue: 0.2548 time to fit residues: 51.9912 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 : 1.150 ------------------------------------------------------------------------------- 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: 3.9990 chunk 97 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 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: 9.9990 chunk 53 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 504 GLN B 707 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.168940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.119092 restraints weight = 11900.796| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.77 r_work: 0.3053 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 10536 Z= 0.330 Angle : 0.678 6.103 14318 Z= 0.357 Chirality : 0.049 0.162 1706 Planarity : 0.005 0.045 1784 Dihedral : 4.227 15.872 1426 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.44 % Favored : 95.41 % Rotamer: Outliers : 3.53 % Allowed : 12.52 % Favored : 83.95 % 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: 1.03 (0.23), residues: 1328 helix: 1.34 (0.18), residues: 862 sheet: 1.89 (0.72), residues: 52 loop : -0.83 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 472 HIS 0.004 0.001 HIS A 640 PHE 0.024 0.002 PHE A 111 TYR 0.020 0.002 TYR A 16 ARG 0.003 0.000 ARG B 558 Details of bonding type rmsd hydrogen bonds : bond 0.05355 ( 650) hydrogen bonds : angle 4.89311 ( 1890) covalent geometry : bond 0.00824 (10536) covalent geometry : angle 0.67803 (14318) *********************** 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 149 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 1.117 Fit side-chains REVERT: A 267 MET cc_start: 0.7476 (ptm) cc_final: 0.7162 (mmt) REVERT: A 394 SER cc_start: 0.8334 (m) cc_final: 0.8082 (p) REVERT: B 267 MET cc_start: 0.7509 (ptm) cc_final: 0.7162 (mmt) REVERT: B 394 SER cc_start: 0.8328 (m) cc_final: 0.8037 (p) outliers start: 40 outliers final: 21 residues processed: 139 average time/residue: 0.2321 time to fit residues: 45.9843 Evaluate side-chains 128 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 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 325 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 342 ASP 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 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 342 ASP 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: 5.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 51 optimal weight: 0.0870 chunk 43 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.175898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.126247 restraints weight = 11648.393| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.72 r_work: 0.3132 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10536 Z= 0.120 Angle : 0.506 5.506 14318 Z= 0.263 Chirality : 0.042 0.149 1706 Planarity : 0.004 0.038 1784 Dihedral : 4.039 15.447 1426 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.39 % Favored : 96.46 % Rotamer: Outliers : 3.44 % Allowed : 13.40 % Favored : 83.16 % 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: 1.52 (0.24), residues: 1328 helix: 1.61 (0.18), residues: 870 sheet: 1.61 (0.71), residues: 52 loop : -0.30 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 472 HIS 0.001 0.001 HIS B 704 PHE 0.017 0.001 PHE A 111 TYR 0.023 0.001 TYR B 123 ARG 0.001 0.000 ARG A 150 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 650) hydrogen bonds : angle 4.48874 ( 1890) covalent geometry : bond 0.00266 (10536) covalent geometry : angle 0.50631 (14318) *********************** 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 153 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.7367 (ptm) cc_final: 0.7064 (mmt) REVERT: A 399 ARG cc_start: 0.7858 (ttp80) cc_final: 0.7492 (ttp80) REVERT: A 482 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8215 (tt) REVERT: A 566 PHE cc_start: 0.7841 (m-80) cc_final: 0.7503 (m-80) REVERT: A 633 MET cc_start: 0.5854 (ttp) cc_final: 0.5368 (mmt) REVERT: B 267 MET cc_start: 0.7379 (ptm) cc_final: 0.7065 (mmt) REVERT: B 389 GLN cc_start: 0.7882 (mm110) cc_final: 0.7592 (mm110) REVERT: B 399 ARG cc_start: 0.7836 (ttp80) cc_final: 0.7502 (ttp80) REVERT: B 482 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8219 (tt) REVERT: B 566 PHE cc_start: 0.7836 (m-80) cc_final: 0.7494 (m-80) REVERT: B 633 MET cc_start: 0.5853 (ttp) cc_final: 0.5368 (mmt) outliers start: 39 outliers final: 20 residues processed: 139 average time/residue: 0.2963 time to fit residues: 59.6780 Evaluate side-chains 125 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 260 CYS 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 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 260 CYS 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 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: 7.9990 chunk 121 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 128 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.171118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.126646 restraints weight = 11903.632| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 3.09 r_work: 0.3026 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10536 Z= 0.253 Angle : 0.623 11.056 14318 Z= 0.320 Chirality : 0.046 0.315 1706 Planarity : 0.004 0.038 1784 Dihedral : 4.086 16.098 1426 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.99 % Favored : 95.86 % Rotamer: Outliers : 3.35 % Allowed : 13.84 % Favored : 82.80 % 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: 1.50 (0.18), residues: 872 sheet: 1.38 (0.70), residues: 52 loop : -0.54 (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 0.048 0.002 PHE A 111 TYR 0.014 0.002 TYR B 16 ARG 0.002 0.000 ARG A 716 Details of bonding type rmsd hydrogen bonds : bond 0.04603 ( 650) hydrogen bonds : angle 4.66195 ( 1890) covalent geometry : bond 0.00628 (10536) covalent geometry : angle 0.62319 (14318) *********************** 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 143 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.6783 (mmm) cc_final: 0.6481 (mmm) REVERT: A 267 MET cc_start: 0.7431 (ptm) cc_final: 0.7122 (mmt) REVERT: A 633 MET cc_start: 0.5777 (ttp) cc_final: 0.5505 (mmt) REVERT: B 267 MET cc_start: 0.7451 (ptm) cc_final: 0.7122 (mmt) REVERT: B 633 MET cc_start: 0.5760 (ttp) cc_final: 0.5494 (mmt) outliers start: 38 outliers final: 29 residues processed: 131 average time/residue: 0.2080 time to fit residues: 40.3574 Evaluate side-chains 132 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 257 LEU 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 257 LEU 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 393 ILE Chi-restraints excluded: chain B residue 395 CYS 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: 0.9980 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.173157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.123979 restraints weight = 11774.960| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.78 r_work: 0.3107 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10536 Z= 0.151 Angle : 0.536 9.705 14318 Z= 0.272 Chirality : 0.043 0.199 1706 Planarity : 0.004 0.036 1784 Dihedral : 4.031 17.427 1426 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.61 % Favored : 96.23 % Rotamer: Outliers : 3.88 % Allowed : 14.20 % Favored : 81.92 % 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: 1.48 (0.24), residues: 1328 helix: 1.55 (0.18), residues: 884 sheet: 1.24 (0.70), residues: 52 loop : -0.26 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 472 HIS 0.002 0.001 HIS B 707 PHE 0.036 0.001 PHE B 111 TYR 0.012 0.001 TYR B 123 ARG 0.001 0.000 ARG A 150 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 650) hydrogen bonds : angle 4.46732 ( 1890) covalent geometry : bond 0.00361 (10536) covalent geometry : angle 0.53639 (14318) *********************** 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 146 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 102 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.7425 (ptm) cc_final: 0.7077 (mmt) REVERT: A 399 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7677 (ttp80) REVERT: A 633 MET cc_start: 0.5658 (ttp) cc_final: 0.5447 (mmt) REVERT: B 180 MET cc_start: 0.6401 (mmm) cc_final: 0.6028 (mmp) REVERT: B 267 MET cc_start: 0.7455 (ptm) cc_final: 0.7082 (mmt) REVERT: B 399 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7623 (ttp80) REVERT: B 633 MET cc_start: 0.5650 (ttp) cc_final: 0.5440 (mmt) outliers start: 44 outliers final: 36 residues processed: 137 average time/residue: 0.2184 time to fit residues: 43.0662 Evaluate side-chains 134 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 2.417 ------------------------------------------------------------------------------- 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 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 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 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 393 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 42 optimal weight: 5.9990 chunk 110 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 127 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.174778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.127683 restraints weight = 11981.918| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.88 r_work: 0.3130 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10536 Z= 0.130 Angle : 0.518 8.137 14318 Z= 0.263 Chirality : 0.042 0.126 1706 Planarity : 0.004 0.036 1784 Dihedral : 3.981 18.230 1426 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.46 % Favored : 96.39 % Rotamer: Outliers : 3.44 % Allowed : 14.55 % 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: 1.61 (0.24), residues: 1328 helix: 1.64 (0.18), residues: 884 sheet: 1.09 (0.68), residues: 52 loop : -0.16 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 70 HIS 0.002 0.001 HIS B 704 PHE 0.029 0.001 PHE B 111 TYR 0.014 0.001 TYR B 123 ARG 0.001 0.000 ARG A 175 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 650) hydrogen bonds : angle 4.36092 ( 1890) covalent geometry : bond 0.00301 (10536) covalent geometry : angle 0.51848 (14318) *********************** 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 144 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 105 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.6656 (mmm) cc_final: 0.6398 (mmm) REVERT: A 228 TYR cc_start: 0.8334 (m-80) cc_final: 0.7880 (m-80) REVERT: A 267 MET cc_start: 0.7443 (ptm) cc_final: 0.7146 (mmt) REVERT: A 399 ARG cc_start: 0.8002 (ttp80) cc_final: 0.7699 (ttp80) REVERT: A 566 PHE cc_start: 0.7940 (m-80) cc_final: 0.7676 (m-80) REVERT: B 228 TYR cc_start: 0.8335 (m-80) cc_final: 0.7879 (m-80) REVERT: B 267 MET cc_start: 0.7462 (ptm) cc_final: 0.7148 (mmt) REVERT: B 399 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7666 (ttp80) REVERT: B 566 PHE cc_start: 0.7932 (m-80) cc_final: 0.7670 (m-80) outliers start: 39 outliers final: 32 residues processed: 135 average time/residue: 0.2267 time to fit residues: 43.7439 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 : 1.110 ------------------------------------------------------------------------------- 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 317 VAL 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 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 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 333 THR Chi-restraints excluded: chain B residue 393 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 95 optimal weight: 10.0000 chunk 104 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 80 optimal weight: 0.2980 chunk 110 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.175683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.127207 restraints weight = 11796.944| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.96 r_work: 0.3143 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2040 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= 0.118 Angle : 0.504 7.828 14318 Z= 0.256 Chirality : 0.042 0.163 1706 Planarity : 0.004 0.037 1784 Dihedral : 3.950 17.762 1426 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.16 % Favored : 96.69 % Rotamer: Outliers : 3.62 % Allowed : 14.73 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.65 (0.24), residues: 1328 helix: 1.68 (0.18), residues: 886 sheet: 1.06 (0.68), residues: 52 loop : -0.15 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 70 HIS 0.002 0.001 HIS B 704 PHE 0.026 0.001 PHE B 111 TYR 0.013 0.001 TYR A 123 ARG 0.002 0.000 ARG A 631 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 650) hydrogen bonds : angle 4.26270 ( 1890) covalent geometry : bond 0.00267 (10536) covalent geometry : angle 0.50442 (14318) *********************** 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 151 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.6409 (mmm) cc_final: 0.5159 (mmt) REVERT: A 228 TYR cc_start: 0.8208 (m-80) cc_final: 0.7695 (m-80) REVERT: A 267 MET cc_start: 0.7442 (ptm) cc_final: 0.7119 (mmt) REVERT: A 399 ARG cc_start: 0.7949 (ttp80) cc_final: 0.7641 (ttp80) REVERT: B 228 TYR cc_start: 0.8212 (m-80) cc_final: 0.7701 (m-80) REVERT: B 267 MET cc_start: 0.7465 (ptm) cc_final: 0.7125 (mmt) REVERT: B 399 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7578 (ttp80) outliers start: 41 outliers final: 32 residues processed: 140 average time/residue: 0.2053 time to fit residues: 41.6112 Evaluate side-chains 133 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 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 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 393 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 54 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 128 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 86 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.177175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.127860 restraints weight = 11921.911| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.81 r_work: 0.3162 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10536 Z= 0.124 Angle : 0.544 12.773 14318 Z= 0.269 Chirality : 0.044 0.403 1706 Planarity : 0.004 0.037 1784 Dihedral : 3.921 19.075 1426 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.84 % Favored : 96.01 % Rotamer: Outliers : 3.35 % Allowed : 15.70 % Favored : 80.95 % 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: 1.64 (0.24), residues: 1328 helix: 1.66 (0.18), residues: 886 sheet: 1.09 (0.68), residues: 52 loop : -0.13 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 70 HIS 0.001 0.001 HIS A 640 PHE 0.028 0.001 PHE A 111 TYR 0.031 0.001 TYR B 123 ARG 0.001 0.000 ARG B 399 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 650) hydrogen bonds : angle 4.28880 ( 1890) covalent geometry : bond 0.00286 (10536) covalent geometry : angle 0.54414 (14318) *********************** 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 141 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.6488 (mmm) cc_final: 0.5298 (mmt) REVERT: A 267 MET cc_start: 0.7443 (ptm) cc_final: 0.7124 (mmt) REVERT: A 399 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7665 (ttp80) REVERT: A 423 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6435 (tp) REVERT: A 566 PHE cc_start: 0.7800 (m-80) cc_final: 0.7556 (m-80) REVERT: B 267 MET cc_start: 0.7463 (ptm) cc_final: 0.7132 (mmt) REVERT: B 399 ARG cc_start: 0.7923 (ttp80) cc_final: 0.7583 (ttp80) REVERT: B 423 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6431 (tp) REVERT: B 566 PHE cc_start: 0.7796 (m-80) cc_final: 0.7553 (m-80) outliers start: 38 outliers final: 33 residues processed: 132 average time/residue: 0.2094 time to fit residues: 39.7047 Evaluate side-chains 136 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 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 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 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 393 ILE Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 423 LEU 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: 2.9990 chunk 57 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.174298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.123881 restraints weight = 11911.764| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.06 r_work: 0.3086 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10536 Z= 0.180 Angle : 0.575 10.950 14318 Z= 0.290 Chirality : 0.045 0.340 1706 Planarity : 0.004 0.036 1784 Dihedral : 3.997 21.063 1426 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.92 % Favored : 95.93 % Rotamer: Outliers : 3.26 % Allowed : 16.40 % Favored : 80.34 % 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: 1.57 (0.24), residues: 1328 helix: 1.59 (0.18), residues: 886 sheet: 0.98 (0.67), residues: 52 loop : -0.13 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 70 HIS 0.003 0.001 HIS A 640 PHE 0.033 0.001 PHE A 111 TYR 0.030 0.002 TYR B 123 ARG 0.001 0.000 ARG A 502 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 650) hydrogen bonds : angle 4.37691 ( 1890) covalent geometry : bond 0.00442 (10536) covalent geometry : angle 0.57519 (14318) ********************** 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 141 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.6495 (mmm) cc_final: 0.5195 (mmt) REVERT: A 228 TYR cc_start: 0.8288 (m-80) cc_final: 0.7725 (m-80) REVERT: A 267 MET cc_start: 0.7428 (ptm) cc_final: 0.7079 (mmt) REVERT: A 399 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7609 (ttp80) REVERT: A 423 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6273 (tp) REVERT: A 566 PHE cc_start: 0.7821 (m-80) cc_final: 0.7597 (m-80) REVERT: B 228 TYR cc_start: 0.8292 (m-80) cc_final: 0.7725 (m-80) REVERT: B 267 MET cc_start: 0.7450 (ptm) cc_final: 0.7088 (mmt) REVERT: B 423 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.6430 (tp) REVERT: B 566 PHE cc_start: 0.7812 (m-80) cc_final: 0.7589 (m-80) outliers start: 37 outliers final: 34 residues processed: 130 average time/residue: 0.2180 time to fit residues: 40.8112 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 : 0.993 ------------------------------------------------------------------------------- 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 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 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 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 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 393 ILE Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 423 LEU 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: 6.9990 chunk 107 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 48 optimal weight: 0.0970 chunk 50 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4013 r_free = 0.4013 target = 0.174933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.126670 restraints weight = 11788.678| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.94 r_work: 0.3108 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 0.037 10536 Z= 0.131 Angle : 0.539 10.748 14318 Z= 0.269 Chirality : 0.044 0.325 1706 Planarity : 0.004 0.037 1784 Dihedral : 3.974 21.956 1426 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.77 % Favored : 96.08 % Rotamer: Outliers : 3.35 % Allowed : 16.40 % Favored : 80.25 % 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: 1.66 (0.24), residues: 1328 helix: 1.65 (0.18), residues: 886 sheet: 1.11 (0.68), residues: 52 loop : -0.04 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 70 HIS 0.002 0.001 HIS A 640 PHE 0.028 0.001 PHE A 111 TYR 0.028 0.001 TYR B 123 ARG 0.001 0.000 ARG B 399 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 650) hydrogen bonds : angle 4.31227 ( 1890) covalent geometry : bond 0.00306 (10536) covalent geometry : angle 0.53949 (14318) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4955.68 seconds wall clock time: 88 minutes 3.69 seconds (5283.69 seconds total)