Starting phenix.real_space_refine on Mon Oct 26 06:32:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11ah_75585/10_2026/11ah_75585.cif Found real_map, /net/cci-nas-00/data/ceres_data/11ah_75585/10_2026/11ah_75585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11ah_75585/10_2026/11ah_75585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11ah_75585/10_2026/11ah_75585.map" model { file = "/net/cci-nas-00/data/ceres_data/11ah_75585/10_2026/11ah_75585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11ah_75585/10_2026/11ah_75585.cif" } resolution = 3.6 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 50 5.16 5 C 6290 2.51 5 N 1556 2.21 5 O 1692 1.98 5 H 9718 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19306 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 9653 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 33, 'TRANS': 587} Chain breaks: 2 Chain: "B" Number of atoms: 9653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 9653 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 33, 'TRANS': 587} Chain breaks: 2 Time building chain proxies: 3.39, per 1000 atoms: 0.18 Number of scatterers: 19306 At special positions: 0 Unit cell: (115.62, 76.26, 113.16, 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 50 16.00 O 1692 8.00 N 1556 7.00 C 6290 6.00 H 9718 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: 1.71 Conformation dependent library (CDL) restraints added in 633.4 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: 2316 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 4 sheets defined 70.4% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 49 through 85 removed outlier: 3.526A pdb=" N MET A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 61 " --> pdb=" O GLY A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 114 removed outlier: 4.118A pdb=" N TYR A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Proline residue: A 100 - end of helix removed outlier: 3.500A pdb=" N SER A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE A 114 " --> pdb=" O PHE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 130 removed outlier: 3.938A pdb=" N THR A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 143 removed outlier: 6.520A pdb=" N ILE A 141 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LYS A 142 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 158 removed outlier: 3.537A pdb=" N ALA A 148 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 157 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 165 through 188 Processing helix chain 'A' and resid 193 through 214 Processing helix chain 'A' and resid 215 through 228 removed outlier: 3.665A pdb=" N SER A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 257 removed outlier: 3.928A pdb=" N VAL A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 313 removed outlier: 3.787A pdb=" N ILE A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.773A pdb=" N SER A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 339 removed outlier: 3.714A pdb=" N TYR A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.971A pdb=" N LEU A 358 " --> pdb=" O MET A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 374 removed outlier: 3.786A pdb=" N LEU A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 392 Processing helix chain 'A' and resid 397 through 417 removed outlier: 4.024A pdb=" N TRP A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE A 414 " --> pdb=" O PHE A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 448 Processing helix chain 'A' and resid 462 through 480 removed outlier: 3.998A pdb=" N TYR A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 493 removed outlier: 3.867A pdb=" N PHE A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 513 removed outlier: 3.957A pdb=" N VAL A 501 " --> pdb=" O HIS A 497 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 528 Processing helix chain 'A' and resid 546 through 550 removed outlier: 3.563A pdb=" N PHE A 550 " --> pdb=" O VAL A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 575 removed outlier: 3.684A pdb=" N ASP A 575 " --> pdb=" O VAL A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 605 Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 640 through 651 Processing helix chain 'A' and resid 670 through 682 Processing helix chain 'B' and resid 49 through 85 removed outlier: 3.526A pdb=" N MET B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 114 removed outlier: 4.118A pdb=" N TYR B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) Proline residue: B 100 - end of helix removed outlier: 3.500A pdb=" N SER B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE B 114 " --> pdb=" O PHE B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 removed outlier: 3.938A pdb=" N THR B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 143 removed outlier: 6.520A pdb=" N ILE B 141 " --> pdb=" O TYR B 138 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LYS B 142 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 158 removed outlier: 3.537A pdb=" N ALA B 148 " --> pdb=" O PHE B 144 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL B 149 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 157 " --> pdb=" O CYS B 153 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY B 158 " --> pdb=" O THR B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 165 through 188 Processing helix chain 'B' and resid 193 through 214 Processing helix chain 'B' and resid 215 through 228 removed outlier: 3.687A pdb=" N SER B 228 " --> pdb=" O ILE B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 257 removed outlier: 3.927A pdb=" N VAL B 255 " --> pdb=" O ARG B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 313 removed outlier: 3.787A pdb=" N ILE B 282 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 323 removed outlier: 3.773A pdb=" N SER B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 339 removed outlier: 3.714A pdb=" N TYR B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.971A pdb=" N LEU B 358 " --> pdb=" O MET B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 374 removed outlier: 3.786A pdb=" N LEU B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 392 Processing helix chain 'B' and resid 397 through 417 removed outlier: 4.024A pdb=" N TRP B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE B 414 " --> pdb=" O PHE B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 448 Processing helix chain 'B' and resid 462 through 480 removed outlier: 3.998A pdb=" N TYR B 466 " --> pdb=" O MET B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 493 removed outlier: 3.867A pdb=" N PHE B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 513 removed outlier: 3.956A pdb=" N VAL B 501 " --> pdb=" O HIS B 497 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 511 " --> pdb=" O ALA B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 528 Processing helix chain 'B' and resid 546 through 550 removed outlier: 3.563A pdb=" N PHE B 550 " --> pdb=" O VAL B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 575 removed outlier: 3.684A pdb=" N ASP B 575 " --> pdb=" O VAL B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 605 Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 640 through 651 Processing helix chain 'B' and resid 670 through 682 Processing sheet with id=AA1, first strand: chain 'A' and resid 230 through 232 removed outlier: 4.389A pdb=" N PHE A 231 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE B 231 " --> pdb=" O PHE A 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 558 through 559 removed outlier: 6.305A pdb=" N LEU A 558 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY A 592 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 663 through 669 removed outlier: 5.636A pdb=" N ALA A 664 " --> pdb=" O SER A 660 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N SER A 660 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU A 633 " --> pdb=" O PHE A 657 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N THR A 659 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LEU A 635 " --> pdb=" O THR A 659 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 634 " --> pdb=" O LYS B 634 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 634 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU B 633 " --> pdb=" O PHE B 657 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N THR B 659 " --> pdb=" O LEU B 633 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LEU B 635 " --> pdb=" O THR B 659 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N SER B 660 " --> pdb=" O ALA B 664 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ALA B 664 " --> pdb=" O SER B 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 558 through 559 removed outlier: 6.305A pdb=" N LEU B 558 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY B 592 " --> pdb=" O LEU B 581 " (cutoff:3.500A) 606 hydrogen bonds defined for protein. 1764 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: 4.32 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9702 1.03 - 1.23: 16 1.23 - 1.42: 4122 1.42 - 1.62: 5638 1.62 - 1.81: 84 Bond restraints: 19562 Sorted by residual: bond pdb=" N GLU A 48 " pdb=" CA GLU A 48 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" N GLU B 48 " pdb=" CA GLU B 48 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" N GLU B 48 " pdb=" H GLU B 48 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" N GLU A 48 " pdb=" H GLU A 48 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" CG LEU B 502 " pdb=" CD2 LEU B 502 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.26e-01 ... (remaining 19557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 32075 0.94 - 1.88: 3138 1.88 - 2.82: 122 2.82 - 3.77: 65 3.77 - 4.71: 16 Bond angle restraints: 35416 Sorted by residual: angle pdb=" N PHE B 162 " pdb=" CA PHE B 162 " pdb=" CB PHE B 162 " ideal model delta sigma weight residual 111.74 108.76 2.98 1.58e+00 4.01e-01 3.55e+00 angle pdb=" N PHE A 162 " pdb=" CA PHE A 162 " pdb=" CB PHE A 162 " ideal model delta sigma weight residual 111.74 108.76 2.98 1.58e+00 4.01e-01 3.55e+00 angle pdb=" CA PHE B 162 " pdb=" C PHE B 162 " pdb=" N LEU B 163 " ideal model delta sigma weight residual 114.98 117.36 -2.38 1.34e+00 5.57e-01 3.15e+00 angle pdb=" CA PHE A 162 " pdb=" C PHE A 162 " pdb=" N LEU A 163 " ideal model delta sigma weight residual 114.98 117.36 -2.38 1.34e+00 5.57e-01 3.15e+00 angle pdb=" CA PRO A 627 " pdb=" C PRO A 627 " pdb=" O PRO A 627 " ideal model delta sigma weight residual 123.16 120.60 2.56 1.49e+00 4.50e-01 2.96e+00 ... (remaining 35411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 8342 17.80 - 35.61: 656 35.61 - 53.41: 220 53.41 - 71.21: 42 71.21 - 89.02: 22 Dihedral angle restraints: 9282 sinusoidal: 4894 harmonic: 4388 Sorted by residual: dihedral pdb=" CB GLU B 442 " pdb=" CG GLU B 442 " pdb=" CD GLU B 442 " pdb=" OE1 GLU B 442 " ideal model delta sinusoidal sigma weight residual 0.00 89.02 -89.02 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU A 442 " pdb=" CG GLU A 442 " pdb=" CD GLU A 442 " pdb=" OE1 GLU A 442 " ideal model delta sinusoidal sigma weight residual 0.00 89.02 -89.02 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU A 259 " pdb=" CG GLU A 259 " pdb=" CD GLU A 259 " pdb=" OE1 GLU A 259 " ideal model delta sinusoidal sigma weight residual 0.00 86.82 -86.82 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 9279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1021 0.026 - 0.052: 308 0.052 - 0.078: 159 0.078 - 0.104: 51 0.104 - 0.130: 21 Chirality restraints: 1560 Sorted by residual: chirality pdb=" CA ILE A 419 " pdb=" N ILE A 419 " pdb=" C ILE A 419 " pdb=" CB ILE A 419 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE B 419 " pdb=" N ILE B 419 " pdb=" C ILE B 419 " pdb=" CB ILE B 419 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE B 535 " pdb=" N ILE B 535 " pdb=" C ILE B 535 " pdb=" CB ILE B 535 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 1557 not shown) Planarity restraints: 2836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 301 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C PHE A 301 " -0.030 2.00e-02 2.50e+03 pdb=" O PHE A 301 " 0.011 2.00e-02 2.50e+03 pdb=" N CYS A 302 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 301 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C PHE B 301 " 0.030 2.00e-02 2.50e+03 pdb=" O PHE B 301 " -0.011 2.00e-02 2.50e+03 pdb=" N CYS B 302 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 303 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" C GLN A 303 " 0.028 2.00e-02 2.50e+03 pdb=" O GLN A 303 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG A 304 " -0.009 2.00e-02 2.50e+03 ... (remaining 2833 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 821 2.18 - 2.79: 37327 2.79 - 3.39: 53215 3.39 - 4.00: 66068 4.00 - 4.60: 104378 Nonbonded interactions: 261809 Sorted by model distance: nonbonded pdb=" O TYR B 531 " pdb="HH12 ARG B 538 " model vdw 1.581 2.450 nonbonded pdb=" O TYR A 531 " pdb="HH12 ARG A 538 " model vdw 1.581 2.450 nonbonded pdb=" O VAL B 570 " pdb=" HG1 THR B 574 " model vdw 1.583 2.450 nonbonded pdb=" O VAL A 570 " pdb=" HG1 THR A 574 " model vdw 1.583 2.450 nonbonded pdb=" OE2 GLU A 225 " pdb=" HE1 TRP B 237 " model vdw 1.595 2.450 ... (remaining 261804 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.720 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.002 0.032 9844 Z= 0.119 Angle : 0.496 4.707 13410 Z= 0.275 Chirality : 0.035 0.130 1560 Planarity : 0.004 0.040 1666 Dihedral : 14.581 89.018 3434 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.07 % Allowed : 11.09 % Favored : 87.84 % 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: 1.20 (0.25), residues: 1230 helix: 1.76 (0.20), residues: 780 sheet: None (None), residues: 0 loop : -0.94 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 182 TYR 0.010 0.001 TYR A 99 PHE 0.010 0.001 PHE A 231 TRP 0.007 0.001 TRP B 388 HIS 0.002 0.000 HIS B 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 9844) covalent geometry : angle 0.49580 / 0.27 (13410) hydrogen bonds : bond 0.13681 / 9.36 ( 606) hydrogen bonds : angle 5.74299 / 4.16 ( 1764) *********************** 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 135 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.432 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 outliers start: 11 outliers final: 5 residues processed: 133 average time/residue: 0.2565 time to fit residues: 46.1042 Evaluate side-chains 84 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain B residue 169 PHE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 411 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: [108, 49, 97, 113, 53, 5, 33, 123, 65, 62, 51] chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.111116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.083114 restraints weight = 53637.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.088213 restraints weight = 23444.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.091669 restraints weight = 14369.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.093884 restraints weight = 10464.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.095294 restraints weight = 8410.683| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9844 Z= 0.163 Angle : 0.522 5.011 13410 Z= 0.277 Chirality : 0.037 0.138 1560 Planarity : 0.004 0.033 1666 Dihedral : 4.340 52.418 1326 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.58 % Allowed : 13.04 % Favored : 86.38 % 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: 1.74 (0.25), residues: 1230 helix: 2.28 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -1.04 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 182 TYR 0.012 0.001 TYR A 99 PHE 0.012 0.001 PHE B 231 TRP 0.008 0.001 TRP B 388 HIS 0.002 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 9844) covalent geometry : angle 0.52217 / 0.28 (13410) hydrogen bonds : bond 0.05191 / 3.45 ( 606) hydrogen bonds : angle 4.16813 / 3.06 ( 1764) *********************** 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 80 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 79 average time/residue: 0.2342 time to fit residues: 26.1626 Evaluate side-chains 77 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain B residue 169 PHE Chi-restraints excluded: chain B residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: [106, 45, 112, 84, 97, 98, 79, 49, 11, 24, 68] chunk 106 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 84 optimal weight: 0.1980 chunk 97 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 68 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.115406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.087744 restraints weight = 53730.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.092921 restraints weight = 22758.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.096446 restraints weight = 13720.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.098724 restraints weight = 9856.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.100053 restraints weight = 7864.508| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9844 Z= 0.104 Angle : 0.464 4.731 13410 Z= 0.240 Chirality : 0.035 0.134 1560 Planarity : 0.004 0.032 1666 Dihedral : 3.861 52.772 1320 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.97 % Allowed : 12.65 % Favored : 86.38 % 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: 2.12 (0.25), residues: 1230 helix: 2.63 (0.19), residues: 790 sheet: None (None), residues: 0 loop : -0.98 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 182 TYR 0.010 0.001 TYR A 99 PHE 0.020 0.001 PHE B 231 TRP 0.005 0.000 TRP B 388 HIS 0.004 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 9844) covalent geometry : angle 0.46392 / 0.24 (13410) hydrogen bonds : bond 0.04459 / 2.94 ( 606) hydrogen bonds : angle 3.80318 / 2.78 ( 1764) *********************** 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 90 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.7737 (mmt) cc_final: 0.7378 (mmt) REVERT: B 427 MET cc_start: 0.7738 (mmt) cc_final: 0.7375 (mmt) outliers start: 10 outliers final: 5 residues processed: 87 average time/residue: 0.2092 time to fit residues: 26.1090 Evaluate side-chains 75 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain B residue 169 PHE Chi-restraints excluded: chain B residue 224 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: [97, 90, 114, 110, 20, 52, 58, 38, 45, 118, 102] chunk 97 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 513 GLN B 513 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.112383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.085178 restraints weight = 54826.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.090063 restraints weight = 24261.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.093369 restraints weight = 14977.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.095491 restraints weight = 10920.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.096743 restraints weight = 8845.523| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9844 Z= 0.185 Angle : 0.508 4.918 13410 Z= 0.269 Chirality : 0.037 0.134 1560 Planarity : 0.004 0.033 1666 Dihedral : 3.881 53.143 1320 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.46 % Allowed : 13.52 % Favored : 85.02 % 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: 2.04 (0.25), residues: 1230 helix: 2.60 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -1.09 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.013 0.001 TYR A 99 PHE 0.009 0.001 PHE B 162 TRP 0.008 0.001 TRP B 388 HIS 0.002 0.001 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 ( 9844) covalent geometry : angle 0.50825 / 0.27 (13410) hydrogen bonds : bond 0.04861 / 3.22 ( 606) hydrogen bonds : angle 3.96385 / 2.90 ( 1764) *********************** 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 93 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 90 average time/residue: 0.2190 time to fit residues: 27.8578 Evaluate side-chains 82 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 414 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: [88, 20, 60, 110, 4, 111, 79, 114, 31, 24, 94] chunk 88 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.112292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.084580 restraints weight = 54736.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.089563 restraints weight = 23408.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.092959 restraints weight = 14228.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.095203 restraints weight = 10319.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.096437 restraints weight = 8253.204| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9844 Z= 0.159 Angle : 0.492 4.799 13410 Z= 0.258 Chirality : 0.036 0.133 1560 Planarity : 0.004 0.032 1666 Dihedral : 3.262 12.006 1316 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.26 % Allowed : 13.81 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.25), residues: 1230 helix: 2.65 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -1.11 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 351 TYR 0.012 0.001 TYR A 99 PHE 0.008 0.001 PHE A 162 TRP 0.008 0.001 TRP B 388 HIS 0.002 0.001 HIS B 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 9844) covalent geometry : angle 0.49184 / 0.26 (13410) hydrogen bonds : bond 0.04754 / 3.14 ( 606) hydrogen bonds : angle 3.86134 / 2.82 ( 1764) *********************** 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 89 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.7966 (mmt) cc_final: 0.7627 (mmt) REVERT: B 427 MET cc_start: 0.7962 (mmt) cc_final: 0.7622 (mmt) outliers start: 13 outliers final: 9 residues processed: 88 average time/residue: 0.1941 time to fit residues: 25.3374 Evaluate side-chains 84 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 414 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: [54, 44, 103, 22, 78, 115, 85, 9, 11, 90, 61] chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.110679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.082911 restraints weight = 54994.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.087822 restraints weight = 23690.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.091155 restraints weight = 14484.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.093208 restraints weight = 10567.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.094706 restraints weight = 8599.659| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9844 Z= 0.197 Angle : 0.521 4.956 13410 Z= 0.276 Chirality : 0.037 0.135 1560 Planarity : 0.004 0.033 1666 Dihedral : 3.322 12.390 1316 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.65 % Allowed : 13.23 % Favored : 85.12 % 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: 1.97 (0.25), residues: 1230 helix: 2.58 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -1.22 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 351 TYR 0.014 0.001 TYR A 99 PHE 0.010 0.001 PHE A 162 TRP 0.009 0.001 TRP A 388 HIS 0.004 0.001 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 ( 9844) covalent geometry : angle 0.52098 / 0.28 (13410) hydrogen bonds : bond 0.05047 / 3.34 ( 606) hydrogen bonds : angle 3.99599 / 2.92 ( 1764) *********************** 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 96 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 TYR cc_start: 0.8768 (m-80) cc_final: 0.8439 (m-80) REVERT: B 466 TYR cc_start: 0.8763 (m-80) cc_final: 0.8431 (m-80) outliers start: 17 outliers final: 13 residues processed: 93 average time/residue: 0.1986 time to fit residues: 27.2888 Evaluate side-chains 86 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 414 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: [9, 98, 115, 68, 35, 85, 51, 4, 37, 74, 78] chunk 9 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 115 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.112651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.085719 restraints weight = 54213.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.090598 restraints weight = 23619.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.093836 restraints weight = 14414.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.095933 restraints weight = 10468.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.097344 restraints weight = 8422.355| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9844 Z= 0.109 Angle : 0.466 4.779 13410 Z= 0.241 Chirality : 0.036 0.130 1560 Planarity : 0.004 0.032 1666 Dihedral : 3.229 12.190 1316 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.97 % Allowed : 14.20 % Favored : 84.82 % 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: 2.22 (0.25), residues: 1230 helix: 2.76 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -1.06 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 351 TYR 0.011 0.001 TYR A 99 PHE 0.009 0.001 PHE B 231 TRP 0.006 0.001 TRP A 388 HIS 0.002 0.001 HIS B 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 9844) covalent geometry : angle 0.46597 / 0.24 (13410) hydrogen bonds : bond 0.04319 / 2.85 ( 606) hydrogen bonds : angle 3.66977 / 2.68 ( 1764) *********************** 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 89 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.7913 (mmt) cc_final: 0.7688 (mmt) REVERT: B 427 MET cc_start: 0.7911 (mmt) cc_final: 0.7680 (mmt) outliers start: 10 outliers final: 10 residues processed: 87 average time/residue: 0.1802 time to fit residues: 23.3900 Evaluate side-chains 84 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 414 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: [48, 100, 17, 6, 60, 62, 27, 55, 56, 87, 102] chunk 48 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.110673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.083741 restraints weight = 54930.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.088479 restraints weight = 24178.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.091695 restraints weight = 14885.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.093762 restraints weight = 10833.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.095024 restraints weight = 8770.142| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9844 Z= 0.194 Angle : 0.512 4.942 13410 Z= 0.270 Chirality : 0.037 0.132 1560 Planarity : 0.004 0.033 1666 Dihedral : 3.267 12.381 1316 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.26 % Allowed : 13.52 % Favored : 85.21 % 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: 2.04 (0.25), residues: 1230 helix: 2.65 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -1.21 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 351 TYR 0.015 0.001 TYR A 99 PHE 0.010 0.001 PHE A 162 TRP 0.008 0.001 TRP B 388 HIS 0.002 0.001 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 ( 9844) covalent geometry : angle 0.51184 / 0.27 (13410) hydrogen bonds : bond 0.04801 / 3.18 ( 606) hydrogen bonds : angle 3.91510 / 2.86 ( 1764) *********************** 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 87 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 TYR cc_start: 0.8760 (m-80) cc_final: 0.8441 (m-80) REVERT: B 466 TYR cc_start: 0.8754 (m-80) cc_final: 0.8432 (m-80) outliers start: 13 outliers final: 11 residues processed: 85 average time/residue: 0.1943 time to fit residues: 24.3216 Evaluate side-chains 85 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 414 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: [56, 89, 102, 109, 17, 108, 1, 14, 82, 119, 30] chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 82 optimal weight: 0.3980 chunk 119 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.112631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.085841 restraints weight = 53414.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.090745 restraints weight = 22369.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.094022 restraints weight = 13399.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.096164 restraints weight = 9633.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.097418 restraints weight = 7684.474| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9844 Z= 0.108 Angle : 0.468 4.775 13410 Z= 0.240 Chirality : 0.036 0.130 1560 Planarity : 0.004 0.032 1666 Dihedral : 3.207 12.466 1316 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.88 % Allowed : 13.81 % Favored : 85.31 % 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: 2.28 (0.26), residues: 1230 helix: 2.83 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -1.08 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 351 TYR 0.011 0.001 TYR A 99 PHE 0.007 0.001 PHE A 217 TRP 0.007 0.001 TRP A 388 HIS 0.002 0.001 HIS B 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 9844) covalent geometry : angle 0.46755 / 0.24 (13410) hydrogen bonds : bond 0.04265 / 2.81 ( 606) hydrogen bonds : angle 3.61719 / 2.64 ( 1764) *********************** 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 82 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 9 residues processed: 81 average time/residue: 0.1966 time to fit residues: 23.3819 Evaluate side-chains 82 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 414 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: [41, 6, 60, 74, 80, 17, 89, 64, 9, 59, 83] chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 83 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.113307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.086502 restraints weight = 53738.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.091454 restraints weight = 22455.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.094762 restraints weight = 13418.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.096840 restraints weight = 9619.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.098311 restraints weight = 7695.064| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9844 Z= 0.105 Angle : 0.458 4.732 13410 Z= 0.233 Chirality : 0.035 0.131 1560 Planarity : 0.004 0.033 1666 Dihedral : 3.118 12.376 1316 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.68 % Allowed : 14.40 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.26), residues: 1230 helix: 2.91 (0.19), residues: 794 sheet: None (None), residues: 0 loop : -1.13 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 351 TYR 0.011 0.001 TYR A 99 PHE 0.008 0.001 PHE A 162 TRP 0.005 0.001 TRP A 388 HIS 0.002 0.000 HIS B 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 9844) covalent geometry : angle 0.45774 / 0.23 (13410) hydrogen bonds : bond 0.03912 / 2.58 ( 606) hydrogen bonds : angle 3.50931 / 2.56 ( 1764) ********************** 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 80 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 79 average time/residue: 0.2045 time to fit residues: 23.6640 Evaluate side-chains 77 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 414 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: [27, 83, 69, 29, 71, 12, 121, 41, 108, 63, 20] chunk 27 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.112809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.086029 restraints weight = 53752.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.090952 restraints weight = 22506.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.094251 restraints weight = 13454.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.096260 restraints weight = 9646.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.097765 restraints weight = 7765.564| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9844 Z= 0.124 Angle : 0.466 4.731 13410 Z= 0.239 Chirality : 0.035 0.129 1560 Planarity : 0.004 0.033 1666 Dihedral : 3.113 12.370 1316 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.68 % Allowed : 14.59 % Favored : 84.73 % 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: 2.33 (0.26), residues: 1230 helix: 2.90 (0.19), residues: 794 sheet: None (None), residues: 0 loop : -1.16 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 351 TYR 0.012 0.001 TYR A 99 PHE 0.007 0.001 PHE B 231 TRP 0.006 0.001 TRP A 388 HIS 0.001 0.000 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 9844) covalent geometry : angle 0.46619 / 0.24 (13410) hydrogen bonds : bond 0.04060 / 2.68 ( 606) hydrogen bonds : angle 3.55822 / 2.60 ( 1764) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2667.46 seconds wall clock time: 46 minutes 7.82 seconds (2767.82 seconds total)