Starting phenix.real_space_refine on Sat Jul 4 17:23:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9do0_47070/07_2026/9do0_47070_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9do0_47070/07_2026/9do0_47070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9do0_47070/07_2026/9do0_47070_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9do0_47070/07_2026/9do0_47070_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9do0_47070/07_2026/9do0_47070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9do0_47070/07_2026/9do0_47070.map" } resolution = 2.54 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= 0.041 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: 6 Type Number sf(0) Gaussians S 72 5.16 5 Cl 4 4.86 5 C 7242 2.51 5 N 1802 2.21 5 O 2010 1.98 5 H 11018 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22148 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 10964 Classifications: {'peptide': 697} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 666} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 10964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 10964 Classifications: {'peptide': 697} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 666} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Ad-hoc single atom residues: {' CL': 2} Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Ad-hoc single atom residues: {' CL': 2} Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Time building chain proxies: 3.52, per 1000 atoms: 0.16 Number of scatterers: 22148 At special positions: 0 Unit cell: (96.642, 96.642, 109.032, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 72 16.00 O 2010 8.00 N 1802 7.00 C 7242 6.00 H 11018 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 161 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS A 173 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 463 " - pdb=" SG CYS A 472 " distance=2.03 Simple disulfide: pdb=" SG CYS A 562 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 161 " - pdb=" SG CYS B 172 " distance=2.03 Simple disulfide: pdb=" SG CYS B 173 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 463 " - pdb=" SG CYS B 472 " distance=2.03 Simple disulfide: pdb=" SG CYS B 562 " - pdb=" SG CYS B 568 " distance=2.03 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: 1.69 Conformation dependent library (CDL) restraints added in 538.2 milliseconds 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2568 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 8 sheets defined 68.7% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 92 through 114 Processing helix chain 'A' and resid 114 through 157 removed outlier: 4.476A pdb=" N GLY A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N TRP A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 203 through 232 Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.510A pdb=" N CYS A 237 " --> pdb=" O PRO A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 258 through 276 removed outlier: 3.662A pdb=" N VAL A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 298 Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 306 through 327 Processing helix chain 'A' and resid 328 through 339 Processing helix chain 'A' and resid 345 through 366 removed outlier: 3.605A pdb=" N TRP A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 366 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 419 removed outlier: 3.516A pdb=" N GLY A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 425 removed outlier: 6.606A pdb=" N PHE A 423 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 424 " --> pdb=" O THR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 443 Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 494 through 518 removed outlier: 3.571A pdb=" N SER A 498 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 506 " --> pdb=" O GLN A 502 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR A 514 " --> pdb=" O LYS A 510 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL A 515 " --> pdb=" O ILE A 511 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 516 " --> pdb=" O ILE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 552 Processing helix chain 'A' and resid 555 through 562 Processing helix chain 'A' and resid 570 through 588 Processing helix chain 'A' and resid 590 through 602 Processing helix chain 'A' and resid 603 through 605 No H-bonds generated for 'chain 'A' and resid 603 through 605' Processing helix chain 'A' and resid 606 through 624 removed outlier: 3.578A pdb=" N ALA A 613 " --> pdb=" O PRO A 609 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 653 through 657 Processing helix chain 'A' and resid 677 through 687 Processing helix chain 'A' and resid 709 through 723 Processing helix chain 'A' and resid 767 through 779 removed outlier: 3.511A pdb=" N VAL A 771 " --> pdb=" O PRO A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 808 Processing helix chain 'B' and resid 92 through 114 Processing helix chain 'B' and resid 114 through 158 removed outlier: 4.472A pdb=" N GLY B 128 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N TRP B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS B 157 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU B 158 " --> pdb=" O THR B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 203 through 232 Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 240 through 249 Processing helix chain 'B' and resid 258 through 276 removed outlier: 3.670A pdb=" N VAL B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 298 Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 306 through 327 Processing helix chain 'B' and resid 328 through 339 Processing helix chain 'B' and resid 345 through 366 removed outlier: 3.599A pdb=" N TRP B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 366 " --> pdb=" O VAL B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 419 removed outlier: 3.519A pdb=" N GLY B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 425 removed outlier: 6.609A pdb=" N PHE B 423 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 424 " --> pdb=" O THR B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 443 Processing helix chain 'B' and resid 445 through 450 Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'B' and resid 494 through 518 removed outlier: 3.566A pdb=" N SER B 498 " --> pdb=" O ILE B 494 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 506 " --> pdb=" O GLN B 502 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 514 " --> pdb=" O LYS B 510 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL B 515 " --> pdb=" O ILE B 511 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 516 " --> pdb=" O ILE B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 552 Processing helix chain 'B' and resid 555 through 562 Processing helix chain 'B' and resid 570 through 588 Processing helix chain 'B' and resid 590 through 602 Processing helix chain 'B' and resid 603 through 605 No H-bonds generated for 'chain 'B' and resid 603 through 605' Processing helix chain 'B' and resid 606 through 624 removed outlier: 3.581A pdb=" N ALA B 613 " --> pdb=" O PRO B 609 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 638 Processing helix chain 'B' and resid 653 through 657 Processing helix chain 'B' and resid 677 through 687 Processing helix chain 'B' and resid 709 through 723 Processing helix chain 'B' and resid 767 through 779 removed outlier: 3.501A pdb=" N VAL B 771 " --> pdb=" O PRO B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 808 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 670 through 671 removed outlier: 6.021A pdb=" N LEU A 670 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 675 through 676 removed outlier: 4.089A pdb=" N MET A 675 " --> pdb=" O VAL A 732 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 761 through 763 removed outlier: 5.991A pdb=" N VAL A 762 " --> pdb=" O THR A 786 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N HIS A 787 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU A 791 " --> pdb=" O HIS A 787 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 160 through 161 Processing sheet with id=AA6, first strand: chain 'B' and resid 670 through 671 removed outlier: 6.047A pdb=" N LEU B 670 " --> pdb=" O ILE B 695 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 675 through 676 removed outlier: 4.111A pdb=" N MET B 675 " --> pdb=" O VAL B 732 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 761 through 763 removed outlier: 6.079A pdb=" N VAL B 762 " --> pdb=" O THR B 786 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N HIS B 787 " --> pdb=" O LEU B 791 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LEU B 791 " --> pdb=" O HIS B 787 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 2049 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: 5.24 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 10998 1.04 - 1.23: 172 1.23 - 1.43: 4560 1.43 - 1.63: 6494 1.63 - 1.83: 108 Bond restraints: 22332 Sorted by residual: bond pdb=" CG ARG B 802 " pdb=" CD ARG B 802 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.11e+00 bond pdb=" CB MET B 757 " pdb=" CG MET B 757 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.95e-01 bond pdb=" CG MET B 757 " pdb=" SD MET B 757 " ideal model delta sigma weight residual 1.803 1.826 -0.023 2.50e-02 1.60e+03 8.15e-01 bond pdb=" CG ARG A 802 " pdb=" CD ARG A 802 " ideal model delta sigma weight residual 1.520 1.540 -0.020 3.00e-02 1.11e+03 4.57e-01 bond pdb=" CB GLU B 605 " pdb=" CG GLU B 605 " ideal model delta sigma weight residual 1.520 1.540 -0.020 3.00e-02 1.11e+03 4.42e-01 ... (remaining 22327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 40281 2.43 - 4.86: 96 4.86 - 7.29: 0 7.29 - 9.72: 0 9.72 - 12.15: 1 Bond angle restraints: 40378 Sorted by residual: angle pdb=" CB MET B 757 " pdb=" CG MET B 757 " pdb=" SD MET B 757 " ideal model delta sigma weight residual 112.70 124.85 -12.15 3.00e+00 1.11e-01 1.64e+01 angle pdb=" C PHE B 527 " pdb=" N ILE B 528 " pdb=" CA ILE B 528 " ideal model delta sigma weight residual 120.33 122.56 -2.23 8.00e-01 1.56e+00 7.74e+00 angle pdb=" C ILE B 528 " pdb=" CA ILE B 528 " pdb=" CB ILE B 528 " ideal model delta sigma weight residual 114.00 111.17 2.83 1.31e+00 5.83e-01 4.68e+00 angle pdb=" CB ARG B 802 " pdb=" CG ARG B 802 " pdb=" CD ARG B 802 " ideal model delta sigma weight residual 111.30 116.09 -4.79 2.30e+00 1.89e-01 4.35e+00 angle pdb=" CG MET B 757 " pdb=" SD MET B 757 " pdb=" CE MET B 757 " ideal model delta sigma weight residual 100.90 105.42 -4.52 2.20e+00 2.07e-01 4.23e+00 ... (remaining 40373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 9613 17.96 - 35.91: 764 35.91 - 53.87: 247 53.87 - 71.83: 80 71.83 - 89.78: 6 Dihedral angle restraints: 10710 sinusoidal: 5808 harmonic: 4902 Sorted by residual: dihedral pdb=" CB CYS A 562 " pdb=" SG CYS A 562 " pdb=" SG CYS A 568 " pdb=" CB CYS A 568 " ideal model delta sinusoidal sigma weight residual -86.00 -52.11 -33.89 1 1.00e+01 1.00e-02 1.63e+01 dihedral pdb=" CB CYS B 562 " pdb=" SG CYS B 562 " pdb=" SG CYS B 568 " pdb=" CB CYS B 568 " ideal model delta sinusoidal sigma weight residual -86.00 -54.44 -31.56 1 1.00e+01 1.00e-02 1.42e+01 dihedral pdb=" CA ASP B 124 " pdb=" CB ASP B 124 " pdb=" CG ASP B 124 " pdb=" OD1 ASP B 124 " ideal model delta sinusoidal sigma weight residual -30.00 -89.59 59.59 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 10707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1198 0.026 - 0.051: 316 0.051 - 0.076: 131 0.076 - 0.102: 81 0.102 - 0.127: 26 Chirality restraints: 1752 Sorted by residual: chirality pdb=" CA ILE B 253 " pdb=" N ILE B 253 " pdb=" C ILE B 253 " pdb=" CB ILE B 253 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE A 160 " pdb=" N ILE A 160 " pdb=" C ILE A 160 " pdb=" CB ILE A 160 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA ILE A 253 " pdb=" N ILE A 253 " pdb=" C ILE A 253 " pdb=" CB ILE A 253 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1749 not shown) Planarity restraints: 3208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 802 " -0.263 9.50e-02 1.11e+02 8.80e-02 9.37e+00 pdb=" NE ARG B 802 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG B 802 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG B 802 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 802 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 802 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG B 802 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B 802 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG B 802 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 802 " 0.131 9.50e-02 1.11e+02 4.40e-02 2.46e+00 pdb=" NE ARG A 802 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 802 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 802 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 802 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 802 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 802 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 802 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 802 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 608 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO A 609 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 609 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 609 " 0.021 5.00e-02 4.00e+02 ... (remaining 3205 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.20: 1283 2.20 - 2.80: 46095 2.80 - 3.40: 63774 3.40 - 4.00: 82763 4.00 - 4.60: 127689 Nonbonded interactions: 321604 Sorted by model distance: nonbonded pdb=" HH TYR A 342 " pdb=" O LEU A 642 " model vdw 1.605 2.450 nonbonded pdb=" HH TYR B 342 " pdb=" O LEU B 642 " model vdw 1.608 2.450 nonbonded pdb=" OD2 ASP A 773 " pdb=" HZ3 LYS B 97 " model vdw 1.621 2.450 nonbonded pdb=" OD1 ASP B 643 " pdb=" H LYS B 645 " model vdw 1.638 2.450 nonbonded pdb=" HH TYR B 343 " pdb=" O ARG B 776 " model vdw 1.644 2.450 ... (remaining 321599 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.980 Find NCS groups from input model: 0.200 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:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 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 11322 Z= 0.090 Angle : 0.427 12.152 15400 Z= 0.224 Chirality : 0.035 0.127 1752 Planarity : 0.004 0.116 1878 Dihedral : 14.963 89.783 4224 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.17 % Allowed : 16.49 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.87 (0.24), residues: 1378 helix: 2.08 (0.18), residues: 882 sheet: -1.79 (0.71), residues: 20 loop : -0.20 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 802 TYR 0.006 0.001 TYR A 303 PHE 0.007 0.000 PHE A 377 TRP 0.006 0.000 TRP B 350 HIS 0.001 0.000 HIS B 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.09 (11314) covalent geometry : angle 0.42716 / 0.22 (15384) SS BOND : bond 0.00061 / 0.03 ( 8) SS BOND : angle 0.31805 / 0.21 ( 16) hydrogen bonds : bond 0.13051 / 8.97 ( 700) hydrogen bonds : angle 6.02021 / 4.46 ( 2049) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 0.619 Fit side-chains REVERT: B 696 MET cc_start: 0.8334 (tpt) cc_final: 0.8030 (tpt) outliers start: 2 outliers final: 0 residues processed: 119 average time/residue: 1.0641 time to fit residues: 139.8850 Evaluate side-chains 73 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 ASN A 765 HIS B 371 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.118079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.075983 restraints weight = 51390.398| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.73 r_work: 0.2850 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11322 Z= 0.234 Angle : 0.552 6.761 15400 Z= 0.294 Chirality : 0.039 0.143 1752 Planarity : 0.005 0.049 1878 Dihedral : 3.510 27.516 1764 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.48 % Allowed : 16.23 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.18 (0.23), residues: 1378 helix: 2.54 (0.17), residues: 896 sheet: -1.64 (0.67), residues: 20 loop : -0.67 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 802 TYR 0.013 0.001 TYR A 303 PHE 0.012 0.001 PHE B 556 TRP 0.013 0.001 TRP A 403 HIS 0.006 0.001 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.23 (11314) covalent geometry : angle 0.54588 / 0.29 (15384) SS BOND : bond 0.01208 / 0.43 ( 8) SS BOND : angle 2.58773 / 1.73 ( 16) hydrogen bonds : bond 0.05785 / 3.92 ( 700) hydrogen bonds : angle 4.39562 / 3.27 ( 2049) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7197 (ttp-170) cc_final: 0.6720 (tpm170) REVERT: A 732 VAL cc_start: 0.9090 (t) cc_final: 0.8872 (m) REVERT: B 659 ARG cc_start: 0.7136 (ttp-170) cc_final: 0.6671 (tpm170) REVERT: B 696 MET cc_start: 0.8637 (tpt) cc_final: 0.8262 (tpt) outliers start: 17 outliers final: 7 residues processed: 92 average time/residue: 0.8494 time to fit residues: 88.2218 Evaluate side-chains 83 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 703 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 24 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 765 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.119481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.077503 restraints weight = 51016.078| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.74 r_work: 0.2874 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11322 Z= 0.120 Angle : 0.469 7.068 15400 Z= 0.245 Chirality : 0.036 0.147 1752 Planarity : 0.004 0.042 1878 Dihedral : 3.377 22.771 1764 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.56 % Allowed : 16.06 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.40 (0.23), residues: 1378 helix: 2.76 (0.17), residues: 896 sheet: -1.79 (0.63), residues: 20 loop : -0.71 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 802 TYR 0.009 0.001 TYR B 214 PHE 0.011 0.001 PHE B 556 TRP 0.010 0.001 TRP A 403 HIS 0.004 0.001 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (11314) covalent geometry : angle 0.46065 / 0.24 (15384) SS BOND : bond 0.00327 / 0.13 ( 8) SS BOND : angle 2.73360 / 1.55 ( 16) hydrogen bonds : bond 0.04903 / 3.32 ( 700) hydrogen bonds : angle 4.26924 / 3.16 ( 2049) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7173 (ttp-170) cc_final: 0.6817 (tpm170) REVERT: A 732 VAL cc_start: 0.9077 (t) cc_final: 0.8874 (m) REVERT: A 760 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7204 (m-80) REVERT: B 696 MET cc_start: 0.8628 (tpt) cc_final: 0.8201 (tpt) REVERT: B 760 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.7199 (m-80) outliers start: 18 outliers final: 6 residues processed: 83 average time/residue: 0.9026 time to fit residues: 84.3780 Evaluate side-chains 81 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 760 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 94 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.117306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.075164 restraints weight = 51115.002| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.73 r_work: 0.2836 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11322 Z= 0.165 Angle : 0.481 4.680 15400 Z= 0.253 Chirality : 0.036 0.134 1752 Planarity : 0.004 0.043 1878 Dihedral : 3.463 25.177 1764 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.39 % Allowed : 14.93 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.34 (0.23), residues: 1378 helix: 2.69 (0.17), residues: 900 sheet: -1.58 (0.63), residues: 20 loop : -0.70 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 802 TYR 0.009 0.001 TYR B 214 PHE 0.009 0.001 PHE B 556 TRP 0.009 0.001 TRP A 403 HIS 0.005 0.001 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (11314) covalent geometry : angle 0.47566 / 0.25 (15384) SS BOND : bond 0.00280 / 0.12 ( 8) SS BOND : angle 2.35406 / 1.41 ( 16) hydrogen bonds : bond 0.05191 / 3.51 ( 700) hydrogen bonds : angle 4.20707 / 3.11 ( 2049) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7229 (ttp-170) cc_final: 0.6609 (tpm170) REVERT: B 696 MET cc_start: 0.8663 (tpt) cc_final: 0.8214 (tpt) outliers start: 16 outliers final: 11 residues processed: 85 average time/residue: 0.7999 time to fit residues: 77.3240 Evaluate side-chains 84 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 763 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 111 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.117902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.075880 restraints weight = 51087.227| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.73 r_work: 0.2848 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11322 Z= 0.119 Angle : 0.447 4.503 15400 Z= 0.234 Chirality : 0.036 0.132 1752 Planarity : 0.004 0.044 1878 Dihedral : 3.377 23.939 1764 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.30 % Allowed : 15.28 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.43 (0.23), residues: 1378 helix: 2.75 (0.17), residues: 900 sheet: -1.38 (0.66), residues: 20 loop : -0.65 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 802 TYR 0.009 0.001 TYR B 214 PHE 0.009 0.001 PHE B 556 TRP 0.009 0.001 TRP A 403 HIS 0.004 0.001 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (11314) covalent geometry : angle 0.44284 / 0.23 (15384) SS BOND : bond 0.00183 / 0.08 ( 8) SS BOND : angle 1.83549 / 1.08 ( 16) hydrogen bonds : bond 0.04724 / 3.19 ( 700) hydrogen bonds : angle 4.10565 / 3.03 ( 2049) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7241 (ttp-170) cc_final: 0.6645 (tpm170) REVERT: A 732 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8223 (m) REVERT: A 760 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.7202 (m-80) REVERT: B 696 MET cc_start: 0.8693 (tpt) cc_final: 0.8248 (tpt) REVERT: B 760 PHE cc_start: 0.7632 (OUTLIER) cc_final: 0.7151 (m-80) outliers start: 15 outliers final: 8 residues processed: 81 average time/residue: 0.7785 time to fit residues: 71.8941 Evaluate side-chains 84 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 760 PHE Chi-restraints excluded: chain B residue 763 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 0.0570 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 633 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.116885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.075048 restraints weight = 51380.220| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.72 r_work: 0.2828 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11322 Z= 0.140 Angle : 0.450 4.376 15400 Z= 0.237 Chirality : 0.036 0.133 1752 Planarity : 0.004 0.044 1878 Dihedral : 3.430 25.942 1764 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.56 % Allowed : 15.19 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.41 (0.23), residues: 1378 helix: 2.73 (0.17), residues: 898 sheet: -1.14 (0.68), residues: 20 loop : -0.65 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 311 TYR 0.009 0.001 TYR B 214 PHE 0.010 0.001 PHE B 344 TRP 0.009 0.001 TRP A 403 HIS 0.005 0.001 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (11314) covalent geometry : angle 0.44822 / 0.24 (15384) SS BOND : bond 0.00150 / 0.06 ( 8) SS BOND : angle 1.43619 / 0.86 ( 16) hydrogen bonds : bond 0.04892 / 3.30 ( 700) hydrogen bonds : angle 4.07882 / 3.01 ( 2049) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7245 (ttp-170) cc_final: 0.6662 (tpm170) REVERT: B 696 MET cc_start: 0.8721 (tpt) cc_final: 0.8266 (tpt) outliers start: 18 outliers final: 10 residues processed: 85 average time/residue: 0.8019 time to fit residues: 77.3861 Evaluate side-chains 80 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 763 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 20 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 110 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.116590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.074876 restraints weight = 51201.542| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.71 r_work: 0.2826 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11322 Z= 0.134 Angle : 0.449 5.099 15400 Z= 0.236 Chirality : 0.036 0.131 1752 Planarity : 0.004 0.043 1878 Dihedral : 3.439 26.872 1764 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.56 % Allowed : 14.93 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.45 (0.23), residues: 1378 helix: 2.75 (0.17), residues: 896 sheet: -1.06 (0.71), residues: 20 loop : -0.58 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 416 TYR 0.009 0.001 TYR B 214 PHE 0.006 0.001 PHE B 251 TRP 0.010 0.001 TRP A 403 HIS 0.003 0.000 HIS A 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (11314) covalent geometry : angle 0.44648 / 0.23 (15384) SS BOND : bond 0.00215 / 0.09 ( 8) SS BOND : angle 1.53602 / 0.84 ( 16) hydrogen bonds : bond 0.04854 / 3.27 ( 700) hydrogen bonds : angle 4.05184 / 2.99 ( 2049) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7261 (ttp-170) cc_final: 0.6669 (tpm170) REVERT: B 696 MET cc_start: 0.8727 (tpp) cc_final: 0.8261 (tpt) outliers start: 18 outliers final: 9 residues processed: 83 average time/residue: 0.7940 time to fit residues: 75.2828 Evaluate side-chains 76 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 763 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 121 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.116150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.074387 restraints weight = 51199.560| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.72 r_work: 0.2815 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11322 Z= 0.149 Angle : 0.456 5.380 15400 Z= 0.240 Chirality : 0.036 0.130 1752 Planarity : 0.004 0.044 1878 Dihedral : 3.503 28.666 1764 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.13 % Allowed : 15.36 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.41 (0.23), residues: 1378 helix: 2.72 (0.17), residues: 896 sheet: -1.02 (0.71), residues: 20 loop : -0.60 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 311 TYR 0.010 0.001 TYR B 214 PHE 0.007 0.001 PHE A 251 TRP 0.010 0.001 TRP A 403 HIS 0.003 0.000 HIS A 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (11314) covalent geometry : angle 0.45347 / 0.24 (15384) SS BOND : bond 0.00172 / 0.08 ( 8) SS BOND : angle 1.62084 / 1.05 ( 16) hydrogen bonds : bond 0.05007 / 3.37 ( 700) hydrogen bonds : angle 4.04701 / 2.98 ( 2049) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7274 (ttp-170) cc_final: 0.6667 (tpm170) outliers start: 13 outliers final: 9 residues processed: 79 average time/residue: 0.9583 time to fit residues: 84.7785 Evaluate side-chains 76 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 763 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 55 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 104 optimal weight: 0.3980 chunk 57 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 106 optimal weight: 0.0070 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.116959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.075447 restraints weight = 51419.620| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.72 r_work: 0.2837 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11322 Z= 0.104 Angle : 0.438 5.955 15400 Z= 0.228 Chirality : 0.035 0.131 1752 Planarity : 0.004 0.044 1878 Dihedral : 3.420 27.272 1764 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.04 % Allowed : 15.45 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.50 (0.23), residues: 1378 helix: 2.79 (0.17), residues: 896 sheet: -1.07 (0.72), residues: 20 loop : -0.57 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 802 TYR 0.009 0.001 TYR B 214 PHE 0.005 0.001 PHE B 399 TRP 0.010 0.001 TRP A 403 HIS 0.002 0.000 HIS A 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (11314) covalent geometry : angle 0.43580 / 0.23 (15384) SS BOND : bond 0.00325 / 0.15 ( 8) SS BOND : angle 1.30867 / 0.77 ( 16) hydrogen bonds : bond 0.04563 / 3.07 ( 700) hydrogen bonds : angle 3.99048 / 2.94 ( 2049) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7247 (ttp-170) cc_final: 0.6653 (tpm170) outliers start: 12 outliers final: 8 residues processed: 76 average time/residue: 0.8001 time to fit residues: 69.0118 Evaluate side-chains 73 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 763 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 111 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.117162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.075748 restraints weight = 51496.551| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.71 r_work: 0.2842 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11322 Z= 0.106 Angle : 0.439 7.557 15400 Z= 0.228 Chirality : 0.035 0.130 1752 Planarity : 0.004 0.043 1878 Dihedral : 3.382 27.252 1764 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.61 % Allowed : 15.80 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.53 (0.23), residues: 1378 helix: 2.82 (0.17), residues: 896 sheet: -1.07 (0.71), residues: 20 loop : -0.57 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 802 TYR 0.009 0.001 TYR B 214 PHE 0.005 0.001 PHE A 251 TRP 0.010 0.001 TRP A 403 HIS 0.002 0.000 HIS A 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (11314) covalent geometry : angle 0.43676 / 0.23 (15384) SS BOND : bond 0.00357 / 0.17 ( 8) SS BOND : angle 1.34538 / 0.81 ( 16) hydrogen bonds : bond 0.04488 / 3.01 ( 700) hydrogen bonds : angle 3.95892 / 2.92 ( 2049) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7262 (ttp-170) cc_final: 0.6926 (tpm170) outliers start: 7 outliers final: 6 residues processed: 73 average time/residue: 0.9063 time to fit residues: 74.8950 Evaluate side-chains 72 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 763 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 36 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 118 optimal weight: 0.1980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.116222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.074566 restraints weight = 51289.921| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.72 r_work: 0.2818 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11322 Z= 0.137 Angle : 0.453 6.144 15400 Z= 0.236 Chirality : 0.036 0.131 1752 Planarity : 0.004 0.043 1878 Dihedral : 3.468 30.022 1764 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.61 % Allowed : 15.71 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.44 (0.23), residues: 1378 helix: 2.75 (0.17), residues: 896 sheet: -1.01 (0.71), residues: 20 loop : -0.61 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 311 TYR 0.010 0.001 TYR B 214 PHE 0.007 0.001 PHE A 251 TRP 0.010 0.001 TRP A 403 HIS 0.003 0.000 HIS A 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (11314) covalent geometry : angle 0.45100 / 0.24 (15384) SS BOND : bond 0.00169 / 0.07 ( 8) SS BOND : angle 1.27842 / 0.76 ( 16) hydrogen bonds : bond 0.04852 / 3.27 ( 700) hydrogen bonds : angle 3.97962 / 2.94 ( 2049) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7424.05 seconds wall clock time: 126 minutes 15.61 seconds (7575.61 seconds total)