Starting phenix.real_space_refine on Thu Mar 5 04:37:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rtc_4997/03_2026/6rtc_4997.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rtc_4997/03_2026/6rtc_4997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rtc_4997/03_2026/6rtc_4997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rtc_4997/03_2026/6rtc_4997.map" model { file = "/net/cci-nas-00/data/ceres_data/6rtc_4997/03_2026/6rtc_4997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rtc_4997/03_2026/6rtc_4997.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 68 5.16 5 C 6286 2.51 5 N 1536 2.21 5 O 1680 1.98 5 H 9804 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19374 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 9687 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 25, 'TRANS': 595} Chain breaks: 2 Restraints were copied for chains: B Time building chain proxies: 10.65, per 1000 atoms: 0.55 Number of scatterers: 19374 At special positions: 0 Unit cell: (97.825, 121.475, 121.475, 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) S 68 16.00 O 1680 8.00 N 1536 7.00 C 6286 6.00 H 9804 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 377.3 milliseconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 7 sheets defined 63.1% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 70 through 95 Proline residue: A 87 - end of helix removed outlier: 4.060A pdb=" N MET A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 118 Proline residue: A 110 - end of helix removed outlier: 4.160A pdb=" N THR A 113 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 143 removed outlier: 3.646A pdb=" N SER A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 191 Processing helix chain 'A' and resid 200 through 225 removed outlier: 4.198A pdb=" N LYS A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N TYR A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 247 removed outlier: 4.070A pdb=" N PHE A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 276 removed outlier: 3.671A pdb=" N TYR A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 Processing helix chain 'A' and resid 329 through 332 Processing helix chain 'A' and resid 333 through 360 removed outlier: 3.549A pdb=" N ALA A 337 " --> pdb=" O MET A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 380 removed outlier: 3.857A pdb=" N ILE A 370 " --> pdb=" O ASN A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 391 through 401 removed outlier: 3.556A pdb=" N GLY A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 removed outlier: 3.671A pdb=" N VAL A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 442 removed outlier: 4.343A pdb=" N LEU A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 449 Processing helix chain 'A' and resid 450 through 457 removed outlier: 4.221A pdb=" N TYR A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 474 removed outlier: 4.284A pdb=" N CYS A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 498 removed outlier: 4.399A pdb=" N ALA A 483 " --> pdb=" O PRO A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 520 removed outlier: 3.729A pdb=" N THR A 519 " --> pdb=" O ASN A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' Processing helix chain 'A' and resid 542 through 552 removed outlier: 3.661A pdb=" N ALA A 552 " --> pdb=" O GLN A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 672 No H-bonds generated for 'chain 'A' and resid 670 through 672' Processing helix chain 'A' and resid 676 through 692 Processing helix chain 'A' and resid 703 through 712 removed outlier: 3.657A pdb=" N TYR A 707 " --> pdb=" O HIS A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 740 removed outlier: 3.782A pdb=" N ALA A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN A 740 " --> pdb=" O PHE A 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 24 Processing helix chain 'B' and resid 48 through 56 Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 70 through 95 Proline residue: B 87 - end of helix removed outlier: 4.060A pdb=" N MET B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 118 Proline residue: B 110 - end of helix removed outlier: 4.161A pdb=" N THR B 113 " --> pdb=" O PHE B 109 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 117 " --> pdb=" O THR B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 143 removed outlier: 3.646A pdb=" N SER B 132 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 191 Processing helix chain 'B' and resid 200 through 225 removed outlier: 4.199A pdb=" N LYS B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N TYR B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 247 removed outlier: 4.069A pdb=" N PHE B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 247 " --> pdb=" O ASP B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 276 removed outlier: 3.671A pdb=" N TYR B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 Processing helix chain 'B' and resid 329 through 332 Processing helix chain 'B' and resid 333 through 360 removed outlier: 3.549A pdb=" N ALA B 337 " --> pdb=" O MET B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 380 removed outlier: 3.857A pdb=" N ILE B 370 " --> pdb=" O ASN B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 383 No H-bonds generated for 'chain 'B' and resid 381 through 383' Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.556A pdb=" N GLY B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 421 removed outlier: 3.670A pdb=" N VAL B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 442 removed outlier: 4.343A pdb=" N LEU B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 449 Processing helix chain 'B' and resid 450 through 457 removed outlier: 4.221A pdb=" N TYR B 454 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG B 457 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 474 removed outlier: 4.284A pdb=" N CYS B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS B 464 " --> pdb=" O LYS B 460 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 498 removed outlier: 4.399A pdb=" N ALA B 483 " --> pdb=" O PRO B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 520 removed outlier: 3.729A pdb=" N THR B 519 " --> pdb=" O ASN B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 541 No H-bonds generated for 'chain 'B' and resid 539 through 541' Processing helix chain 'B' and resid 542 through 552 removed outlier: 3.661A pdb=" N ALA B 552 " --> pdb=" O GLN B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 672 No H-bonds generated for 'chain 'B' and resid 670 through 672' Processing helix chain 'B' and resid 676 through 692 Processing helix chain 'B' and resid 703 through 712 removed outlier: 3.657A pdb=" N TYR B 707 " --> pdb=" O HIS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 740 removed outlier: 3.782A pdb=" N ALA B 733 " --> pdb=" O SER B 729 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN B 740 " --> pdb=" O PHE B 736 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 150 removed outlier: 3.582A pdb=" N TYR A 159 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 506 through 507 Processing sheet with id=AA4, first strand: chain 'A' and resid 530 through 533 removed outlier: 6.920A pdb=" N LYS A 530 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ASP A 668 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL A 532 " --> pdb=" O ASP A 668 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 665 " --> pdb=" O PHE A 698 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL A 700 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU A 667 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N PHE A 727 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU A 699 " --> pdb=" O PHE A 727 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 150 removed outlier: 3.582A pdb=" N TYR B 159 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 506 through 507 Processing sheet with id=AA7, first strand: chain 'B' and resid 530 through 533 removed outlier: 6.920A pdb=" N LYS B 530 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ASP B 668 " --> pdb=" O LYS B 530 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL B 532 " --> pdb=" O ASP B 668 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU B 665 " --> pdb=" O PHE B 698 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL B 700 " --> pdb=" O LEU B 665 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 667 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N PHE B 727 " --> pdb=" O ILE B 697 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU B 699 " --> pdb=" O PHE B 727 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 506 hydrogen bonds defined for protein. 1482 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: 3.73 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9776 1.03 - 1.22: 30 1.22 - 1.42: 4060 1.42 - 1.62: 5624 1.62 - 1.82: 108 Bond restraints: 19598 Sorted by residual: bond pdb=" CG LEU B 340 " pdb=" CD1 LEU B 340 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.57e+00 bond pdb=" CG LEU A 340 " pdb=" CD1 LEU A 340 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.50e+00 bond pdb=" CB PRO A 537 " pdb=" CG PRO A 537 " ideal model delta sigma weight residual 1.492 1.399 0.093 5.00e-02 4.00e+02 3.46e+00 bond pdb=" CB PRO B 537 " pdb=" CG PRO B 537 " ideal model delta sigma weight residual 1.492 1.399 0.093 5.00e-02 4.00e+02 3.46e+00 bond pdb=" CG1 ILE A 387 " pdb=" CD1 ILE A 387 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.70e+00 ... (remaining 19593 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 34006 1.94 - 3.88: 1342 3.88 - 5.81: 136 5.81 - 7.75: 12 7.75 - 9.69: 6 Bond angle restraints: 35502 Sorted by residual: angle pdb=" CD1 LEU B 538 " pdb=" CG LEU B 538 " pdb=" CD2 LEU B 538 " ideal model delta sigma weight residual 110.80 104.18 6.62 2.20e+00 2.07e-01 9.06e+00 angle pdb=" CD1 LEU A 538 " pdb=" CG LEU A 538 " pdb=" CD2 LEU A 538 " ideal model delta sigma weight residual 110.80 104.20 6.60 2.20e+00 2.07e-01 8.99e+00 angle pdb=" CA LEU A 538 " pdb=" CB LEU A 538 " pdb=" CG LEU A 538 " ideal model delta sigma weight residual 116.30 125.99 -9.69 3.50e+00 8.16e-02 7.66e+00 angle pdb=" N GLY B 193 " pdb=" CA GLY B 193 " pdb=" C GLY B 193 " ideal model delta sigma weight residual 113.18 119.74 -6.56 2.37e+00 1.78e-01 7.65e+00 angle pdb=" CA LEU B 538 " pdb=" CB LEU B 538 " pdb=" CG LEU B 538 " ideal model delta sigma weight residual 116.30 125.98 -9.68 3.50e+00 8.16e-02 7.65e+00 ... (remaining 35497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 7992 16.13 - 32.25: 916 32.25 - 48.38: 244 48.38 - 64.50: 108 64.50 - 80.63: 10 Dihedral angle restraints: 9270 sinusoidal: 4914 harmonic: 4356 Sorted by residual: dihedral pdb=" CA PHE B 662 " pdb=" C PHE B 662 " pdb=" N HIS B 663 " pdb=" CA HIS B 663 " ideal model delta harmonic sigma weight residual 180.00 157.45 22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA PHE A 662 " pdb=" C PHE A 662 " pdb=" N HIS A 663 " pdb=" CA HIS A 663 " ideal model delta harmonic sigma weight residual 180.00 157.47 22.53 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA PHE A 108 " pdb=" C PHE A 108 " pdb=" N PHE A 109 " pdb=" CA PHE A 109 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 9267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1437 0.089 - 0.178: 121 0.178 - 0.267: 4 0.267 - 0.356: 0 0.356 - 0.445: 2 Chirality restraints: 1564 Sorted by residual: chirality pdb=" CG LEU B 340 " pdb=" CB LEU B 340 " pdb=" CD1 LEU B 340 " pdb=" CD2 LEU B 340 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 4.95e+00 chirality pdb=" CG LEU A 340 " pdb=" CB LEU A 340 " pdb=" CD1 LEU A 340 " pdb=" CD2 LEU A 340 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" CB ILE B 131 " pdb=" CA ILE B 131 " pdb=" CG1 ILE B 131 " pdb=" CG2 ILE B 131 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1561 not shown) Planarity restraints: 2832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 536 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO B 537 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 537 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 537 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 536 " -0.048 5.00e-02 4.00e+02 7.22e-02 8.34e+00 pdb=" N PRO A 537 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 537 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 537 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 228 " 0.038 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO A 229 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " 0.032 5.00e-02 4.00e+02 ... (remaining 2829 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.29: 3745 2.29 - 2.87: 42627 2.87 - 3.45: 47241 3.45 - 4.02: 62540 4.02 - 4.60: 96516 Nonbonded interactions: 252669 Sorted by model distance: nonbonded pdb=" HH TYR B 345 " pdb=" O SER B 365 " model vdw 1.716 2.450 nonbonded pdb=" HH TYR A 345 " pdb=" O SER A 365 " model vdw 1.716 2.450 nonbonded pdb=" O GLN A 405 " pdb=" HG SER A 408 " model vdw 1.718 2.450 nonbonded pdb=" O GLN B 405 " pdb=" HG SER B 408 " model vdw 1.718 2.450 nonbonded pdb=" HH TYR B 114 " pdb=" OE2 GLU B 368 " model vdw 1.720 2.450 ... (remaining 252664 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.110 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 24.680 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 : 0.007 0.093 9794 Z= 0.290 Angle : 0.910 9.688 13294 Z= 0.479 Chirality : 0.051 0.445 1564 Planarity : 0.007 0.072 1646 Dihedral : 14.958 80.630 3450 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.83 (0.19), residues: 1230 helix: -1.98 (0.15), residues: 708 sheet: -3.02 (0.54), residues: 38 loop : -3.26 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.027 0.002 TYR A 690 PHE 0.020 0.002 PHE A 546 TRP 0.008 0.001 TRP A 61 HIS 0.005 0.002 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00709 ( 9794) covalent geometry : angle 0.91029 (13294) hydrogen bonds : bond 0.15738 ( 506) hydrogen bonds : angle 5.68677 ( 1482) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 PHE cc_start: 0.8527 (t80) cc_final: 0.8272 (t80) REVERT: A 123 MET cc_start: 0.8382 (ptm) cc_final: 0.8130 (ptt) REVERT: A 145 GLU cc_start: 0.7086 (mp0) cc_final: 0.6750 (mp0) REVERT: A 168 GLU cc_start: 0.7556 (tp30) cc_final: 0.7353 (tp30) REVERT: A 191 GLN cc_start: 0.7908 (tm-30) cc_final: 0.7539 (tm-30) REVERT: A 243 ASP cc_start: 0.8407 (t0) cc_final: 0.7891 (t0) REVERT: A 258 PHE cc_start: 0.6413 (t80) cc_final: 0.6110 (t80) REVERT: A 542 ASN cc_start: 0.8212 (t0) cc_final: 0.7672 (t0) REVERT: B 123 MET cc_start: 0.8367 (ptm) cc_final: 0.8128 (ptt) REVERT: B 168 GLU cc_start: 0.7506 (tp30) cc_final: 0.7300 (tp30) REVERT: B 191 GLN cc_start: 0.7895 (tm-30) cc_final: 0.7538 (tm-30) REVERT: B 243 ASP cc_start: 0.8432 (t0) cc_final: 0.7926 (t0) REVERT: B 258 PHE cc_start: 0.6358 (t80) cc_final: 0.6076 (t80) REVERT: B 542 ASN cc_start: 0.8267 (t0) cc_final: 0.7724 (t0) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1685 time to fit residues: 50.1226 Evaluate side-chains 130 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.4980 chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN A 273 ASN A 348 ASN A 359 HIS B 122 GLN B 273 ASN B 348 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.146152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.113980 restraints weight = 44910.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.118801 restraints weight = 21930.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.121532 restraints weight = 14424.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.123827 restraints weight = 11430.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.125053 restraints weight = 9749.118| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3327 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9794 Z= 0.114 Angle : 0.553 6.776 13294 Z= 0.295 Chirality : 0.039 0.133 1564 Planarity : 0.004 0.040 1646 Dihedral : 4.692 21.655 1314 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.47 % Favored : 95.37 % Rotamer: Outliers : 1.81 % Allowed : 11.52 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.24), residues: 1230 helix: 0.26 (0.19), residues: 708 sheet: -2.14 (0.64), residues: 52 loop : -2.70 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 316 TYR 0.017 0.001 TYR B 539 PHE 0.020 0.001 PHE B 499 TRP 0.004 0.001 TRP A 61 HIS 0.005 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9794) covalent geometry : angle 0.55262 (13294) hydrogen bonds : bond 0.04676 ( 506) hydrogen bonds : angle 4.16827 ( 1482) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 GLU cc_start: 0.7546 (tp30) cc_final: 0.7338 (tp30) REVERT: A 243 ASP cc_start: 0.8344 (t0) cc_final: 0.7937 (t0) REVERT: A 348 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.8252 (t0) REVERT: B 191 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7980 (tm-30) REVERT: B 243 ASP cc_start: 0.8326 (t0) cc_final: 0.7915 (t0) REVERT: B 348 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.8243 (t0) outliers start: 19 outliers final: 8 residues processed: 164 average time/residue: 0.1419 time to fit residues: 36.8196 Evaluate side-chains 144 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 17 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 26 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.141545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.108966 restraints weight = 44681.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.113536 restraints weight = 21990.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.116411 restraints weight = 14689.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.118342 restraints weight = 11617.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.119319 restraints weight = 10023.851| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9794 Z= 0.128 Angle : 0.528 6.436 13294 Z= 0.285 Chirality : 0.039 0.133 1564 Planarity : 0.003 0.033 1646 Dihedral : 4.387 20.262 1314 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.47 % Favored : 95.37 % Rotamer: Outliers : 1.14 % Allowed : 14.29 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.25), residues: 1230 helix: 0.98 (0.20), residues: 722 sheet: -2.00 (0.66), residues: 52 loop : -2.57 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 316 TYR 0.019 0.001 TYR B 539 PHE 0.017 0.001 PHE A 499 TRP 0.002 0.000 TRP B 61 HIS 0.004 0.001 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9794) covalent geometry : angle 0.52828 (13294) hydrogen bonds : bond 0.04365 ( 506) hydrogen bonds : angle 4.01296 ( 1482) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8541 (ptm) cc_final: 0.8235 (ptp) REVERT: A 243 ASP cc_start: 0.8395 (t0) cc_final: 0.8022 (t0) REVERT: B 123 MET cc_start: 0.8538 (ptm) cc_final: 0.8208 (ptp) REVERT: B 243 ASP cc_start: 0.8372 (t0) cc_final: 0.8008 (t0) outliers start: 12 outliers final: 7 residues processed: 153 average time/residue: 0.1267 time to fit residues: 31.8836 Evaluate side-chains 142 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 98 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 367 GLN B 121 HIS B 367 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.133400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.103402 restraints weight = 45846.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.104982 restraints weight = 26054.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.106255 restraints weight = 23811.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.106992 restraints weight = 16823.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.107517 restraints weight = 15323.114| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9794 Z= 0.227 Angle : 0.602 6.665 13294 Z= 0.334 Chirality : 0.041 0.146 1564 Planarity : 0.004 0.036 1646 Dihedral : 4.511 19.726 1314 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.53 % Favored : 94.31 % Rotamer: Outliers : 2.67 % Allowed : 15.52 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.24), residues: 1230 helix: 1.04 (0.19), residues: 712 sheet: -1.81 (0.67), residues: 52 loop : -2.56 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 353 TYR 0.019 0.002 TYR A 539 PHE 0.022 0.002 PHE A 499 TRP 0.006 0.001 TRP A 61 HIS 0.007 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 9794) covalent geometry : angle 0.60183 (13294) hydrogen bonds : bond 0.05365 ( 506) hydrogen bonds : angle 4.35934 ( 1482) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 ASP cc_start: 0.7797 (t0) cc_final: 0.7563 (t0) REVERT: B 123 MET cc_start: 0.8729 (ptm) cc_final: 0.8234 (ptt) REVERT: B 362 ASP cc_start: 0.7775 (t0) cc_final: 0.7558 (t0) REVERT: B 409 LEU cc_start: 0.8339 (mt) cc_final: 0.7869 (mp) outliers start: 28 outliers final: 20 residues processed: 158 average time/residue: 0.1286 time to fit residues: 33.3635 Evaluate side-chains 158 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.137255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.106610 restraints weight = 45730.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.108969 restraints weight = 25937.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.111865 restraints weight = 20419.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.112318 restraints weight = 14514.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.112532 restraints weight = 13764.151| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9794 Z= 0.113 Angle : 0.518 6.471 13294 Z= 0.275 Chirality : 0.039 0.130 1564 Planarity : 0.003 0.032 1646 Dihedral : 4.220 18.834 1314 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.72 % Favored : 95.12 % Rotamer: Outliers : 1.33 % Allowed : 18.00 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.25), residues: 1230 helix: 1.27 (0.19), residues: 726 sheet: -1.71 (0.70), residues: 52 loop : -2.41 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 353 TYR 0.031 0.001 TYR A 276 PHE 0.018 0.001 PHE B 51 TRP 0.002 0.001 TRP A 61 HIS 0.003 0.001 HIS B 385 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9794) covalent geometry : angle 0.51768 (13294) hydrogen bonds : bond 0.04301 ( 506) hydrogen bonds : angle 3.86029 ( 1482) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8680 (t80) cc_final: 0.8336 (t80) REVERT: A 243 ASP cc_start: 0.8365 (t0) cc_final: 0.7900 (t0) REVERT: B 243 ASP cc_start: 0.8375 (t0) cc_final: 0.7895 (t0) outliers start: 14 outliers final: 7 residues processed: 155 average time/residue: 0.1211 time to fit residues: 30.7072 Evaluate side-chains 147 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 398 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 8 optimal weight: 0.0030 chunk 104 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 42 optimal weight: 0.0870 chunk 111 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 overall best weight: 0.4768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS B 731 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.138096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.104606 restraints weight = 44951.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.108881 restraints weight = 22862.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.111631 restraints weight = 15470.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.113374 restraints weight = 12372.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.114219 restraints weight = 10797.187| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9794 Z= 0.096 Angle : 0.496 6.448 13294 Z= 0.260 Chirality : 0.038 0.134 1564 Planarity : 0.003 0.029 1646 Dihedral : 4.027 18.227 1314 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.63 % Favored : 95.20 % Rotamer: Outliers : 2.29 % Allowed : 16.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.25), residues: 1230 helix: 1.57 (0.20), residues: 728 sheet: -1.57 (0.70), residues: 52 loop : -2.25 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 205 TYR 0.030 0.001 TYR A 276 PHE 0.017 0.001 PHE B 51 TRP 0.002 0.000 TRP A 456 HIS 0.003 0.001 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 9794) covalent geometry : angle 0.49642 (13294) hydrogen bonds : bond 0.03794 ( 506) hydrogen bonds : angle 3.66148 ( 1482) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.8396 (t0) cc_final: 0.7930 (t0) REVERT: B 243 ASP cc_start: 0.8387 (t0) cc_final: 0.7923 (t0) outliers start: 24 outliers final: 15 residues processed: 159 average time/residue: 0.1334 time to fit residues: 34.7750 Evaluate side-chains 156 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 532 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 42 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 66 optimal weight: 0.0570 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.134452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.103150 restraints weight = 45571.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.106364 restraints weight = 25764.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.108387 restraints weight = 19339.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.108831 restraints weight = 14167.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.109222 restraints weight = 13429.100| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9794 Z= 0.170 Angle : 0.546 6.590 13294 Z= 0.293 Chirality : 0.040 0.137 1564 Planarity : 0.003 0.032 1646 Dihedral : 4.113 17.886 1314 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.77 % Favored : 94.07 % Rotamer: Outliers : 2.67 % Allowed : 17.90 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.25), residues: 1230 helix: 1.46 (0.19), residues: 728 sheet: -1.58 (0.70), residues: 52 loop : -2.22 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 353 TYR 0.031 0.001 TYR A 276 PHE 0.019 0.001 PHE A 51 TRP 0.004 0.001 TRP A 61 HIS 0.004 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 9794) covalent geometry : angle 0.54579 (13294) hydrogen bonds : bond 0.04337 ( 506) hydrogen bonds : angle 3.90821 ( 1482) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.8517 (t0) cc_final: 0.8269 (t0) REVERT: B 243 ASP cc_start: 0.8517 (t0) cc_final: 0.8271 (t0) outliers start: 28 outliers final: 18 residues processed: 152 average time/residue: 0.1319 time to fit residues: 32.9768 Evaluate side-chains 147 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 81 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 120 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.136764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.104859 restraints weight = 45270.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.108194 restraints weight = 29593.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.109434 restraints weight = 17126.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.110433 restraints weight = 14697.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.110648 restraints weight = 13538.612| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9794 Z= 0.101 Angle : 0.499 6.429 13294 Z= 0.262 Chirality : 0.039 0.154 1564 Planarity : 0.003 0.030 1646 Dihedral : 3.954 17.442 1314 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.29 % Allowed : 17.33 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.25), residues: 1230 helix: 1.71 (0.20), residues: 726 sheet: -1.18 (0.76), residues: 46 loop : -2.01 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 353 TYR 0.030 0.001 TYR A 276 PHE 0.019 0.001 PHE A 51 TRP 0.002 0.000 TRP A 61 HIS 0.003 0.001 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 9794) covalent geometry : angle 0.49860 (13294) hydrogen bonds : bond 0.03792 ( 506) hydrogen bonds : angle 3.64195 ( 1482) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 MET cc_start: 0.8482 (mmm) cc_final: 0.8279 (mmt) REVERT: A 237 ILE cc_start: 0.8914 (tp) cc_final: 0.8620 (tp) REVERT: A 243 ASP cc_start: 0.8459 (t0) cc_final: 0.8214 (t0) REVERT: B 237 ILE cc_start: 0.8916 (tp) cc_final: 0.8622 (tp) REVERT: B 243 ASP cc_start: 0.8453 (t0) cc_final: 0.8208 (t0) outliers start: 24 outliers final: 19 residues processed: 156 average time/residue: 0.1325 time to fit residues: 33.8123 Evaluate side-chains 155 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.136402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.102419 restraints weight = 44944.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.106663 restraints weight = 22747.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.109343 restraints weight = 15446.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.111035 restraints weight = 12417.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.112090 restraints weight = 10888.667| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9794 Z= 0.110 Angle : 0.505 6.446 13294 Z= 0.266 Chirality : 0.039 0.168 1564 Planarity : 0.003 0.031 1646 Dihedral : 3.903 17.645 1314 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.29 % Allowed : 17.90 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.25), residues: 1230 helix: 1.76 (0.20), residues: 726 sheet: -1.14 (0.76), residues: 46 loop : -1.97 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 353 TYR 0.031 0.001 TYR A 276 PHE 0.019 0.001 PHE A 51 TRP 0.002 0.001 TRP B 466 HIS 0.003 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9794) covalent geometry : angle 0.50537 (13294) hydrogen bonds : bond 0.03804 ( 506) hydrogen bonds : angle 3.65771 ( 1482) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 MET cc_start: 0.8458 (mmm) cc_final: 0.8225 (mmt) REVERT: A 237 ILE cc_start: 0.8896 (tp) cc_final: 0.8609 (tp) REVERT: A 243 ASP cc_start: 0.8531 (t0) cc_final: 0.8272 (t0) REVERT: B 237 ILE cc_start: 0.8897 (tp) cc_final: 0.8610 (tp) REVERT: B 243 ASP cc_start: 0.8517 (t0) cc_final: 0.8265 (t0) REVERT: B 409 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8355 (mt) outliers start: 24 outliers final: 17 residues processed: 151 average time/residue: 0.1307 time to fit residues: 32.6621 Evaluate side-chains 154 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 71 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 28 optimal weight: 0.0870 chunk 89 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.137473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.104890 restraints weight = 45869.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.109010 restraints weight = 27591.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.110309 restraints weight = 16405.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.110664 restraints weight = 14269.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.111047 restraints weight = 13711.732| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9794 Z= 0.104 Angle : 0.503 6.409 13294 Z= 0.264 Chirality : 0.039 0.198 1564 Planarity : 0.003 0.030 1646 Dihedral : 3.838 17.563 1314 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.10 % Allowed : 18.29 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.26), residues: 1230 helix: 1.87 (0.20), residues: 724 sheet: -1.11 (0.76), residues: 46 loop : -1.90 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 353 TYR 0.031 0.001 TYR A 276 PHE 0.019 0.001 PHE B 51 TRP 0.002 0.000 TRP A 466 HIS 0.003 0.001 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9794) covalent geometry : angle 0.50307 (13294) hydrogen bonds : bond 0.03721 ( 506) hydrogen bonds : angle 3.59994 ( 1482) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 MET cc_start: 0.8473 (mmm) cc_final: 0.8214 (mmt) REVERT: A 237 ILE cc_start: 0.8895 (tp) cc_final: 0.8614 (tp) REVERT: A 243 ASP cc_start: 0.8523 (t0) cc_final: 0.8257 (t0) REVERT: B 237 ILE cc_start: 0.8891 (tp) cc_final: 0.8616 (tp) REVERT: B 243 ASP cc_start: 0.8514 (t0) cc_final: 0.8254 (t0) REVERT: B 409 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8354 (mt) outliers start: 22 outliers final: 18 residues processed: 153 average time/residue: 0.1304 time to fit residues: 32.9781 Evaluate side-chains 155 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 711 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 66 optimal weight: 0.0970 chunk 52 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.137506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.105097 restraints weight = 45868.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.110386 restraints weight = 30212.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.111799 restraints weight = 15927.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.111638 restraints weight = 12880.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.111984 restraints weight = 12816.996| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9794 Z= 0.105 Angle : 0.505 6.526 13294 Z= 0.265 Chirality : 0.039 0.205 1564 Planarity : 0.003 0.031 1646 Dihedral : 3.780 17.462 1314 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.81 % Allowed : 18.86 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.25), residues: 1230 helix: 1.90 (0.20), residues: 722 sheet: -1.07 (0.76), residues: 46 loop : -1.84 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 353 TYR 0.031 0.001 TYR A 276 PHE 0.019 0.001 PHE B 51 TRP 0.002 0.000 TRP A 61 HIS 0.005 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9794) covalent geometry : angle 0.50547 (13294) hydrogen bonds : bond 0.03698 ( 506) hydrogen bonds : angle 3.58271 ( 1482) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2695.93 seconds wall clock time: 47 minutes 55.78 seconds (2875.78 seconds total)