Starting phenix.real_space_refine on Thu Jun 19 10:53:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9do0_47070/06_2025/9do0_47070_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9do0_47070/06_2025/9do0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9do0_47070/06_2025/9do0_47070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9do0_47070/06_2025/9do0_47070.map" model { file = "/net/cci-nas-00/data/ceres_data/9do0_47070/06_2025/9do0_47070_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9do0_47070/06_2025/9do0_47070_trim.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'ARG:plan': 1, 'TRP: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: {'ARG:plan': 1, 'TRP: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, 58 Unusual residues: {' CL': 2, 'CLR': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {' CL': 2, 'CLR': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 12.38, per 1000 atoms: 0.56 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: 5.74 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 2.01 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: 8.85 Time building geometry restraints manager: 6.87 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: 0.07 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: 5.900 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: 0.440 Extract box with map and model: 0.890 Check model and map are aligned: 0.180 Set scattering table: 0.190 Process input model: 49.770 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 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:13.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (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 TRP 0.006 0.000 TRP B 350 HIS 0.001 0.000 HIS B 765 PHE 0.007 0.000 PHE A 377 TYR 0.006 0.001 TYR A 303 ARG 0.017 0.001 ARG B 802 Details of bonding type rmsd hydrogen bonds : bond 0.13051 ( 700) hydrogen bonds : angle 6.02021 ( 2049) SS BOND : bond 0.00061 ( 8) SS BOND : angle 0.31805 ( 16) covalent geometry : bond 0.00182 (11314) covalent geometry : angle 0.42716 (15384) *********************** 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 : 1.564 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: 2.1832 time to fit residues: 286.7050 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 : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3799 r_free = 0.3799 target = 0.123078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.081408 restraints weight = 51073.933| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.75 r_work: 0.2952 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 11322 Z= 0.136 Angle : 0.492 6.762 15400 Z= 0.258 Chirality : 0.036 0.136 1752 Planarity : 0.004 0.043 1878 Dihedral : 3.226 22.575 1764 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.30 % Allowed : 16.67 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.23), residues: 1378 helix: 2.77 (0.17), residues: 884 sheet: -1.81 (0.69), residues: 20 loop : -0.61 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 403 HIS 0.003 0.001 HIS B 633 PHE 0.013 0.001 PHE B 556 TYR 0.008 0.001 TYR A 303 ARG 0.007 0.000 ARG B 802 Details of bonding type rmsd hydrogen bonds : bond 0.04821 ( 700) hydrogen bonds : angle 4.47657 ( 2049) SS BOND : bond 0.00556 ( 8) SS BOND : angle 2.84148 ( 16) covalent geometry : bond 0.00308 (11314) covalent geometry : angle 0.48352 (15384) *********************** 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 94 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7051 (ttp-170) cc_final: 0.6750 (tpm170) REVERT: A 675 MET cc_start: 0.6831 (mtp) cc_final: 0.6630 (mtp) REVERT: A 732 VAL cc_start: 0.9099 (t) cc_final: 0.8872 (m) REVERT: B 696 MET cc_start: 0.8618 (tpt) cc_final: 0.8152 (tpt) outliers start: 15 outliers final: 7 residues processed: 88 average time/residue: 1.9693 time to fit residues: 193.6493 Evaluate side-chains 82 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 1.764 ------------------------------------------------------------------------------- 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 B residue 209 MET 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 50 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 121 optimal weight: 0.3980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 765 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.118195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.076288 restraints weight = 51161.518| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.72 r_work: 0.2854 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11322 Z= 0.167 Angle : 0.485 7.530 15400 Z= 0.255 Chirality : 0.037 0.135 1752 Planarity : 0.004 0.041 1878 Dihedral : 3.454 24.476 1764 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.39 % Allowed : 15.54 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.23), residues: 1378 helix: 2.72 (0.17), residues: 898 sheet: -1.55 (0.66), residues: 20 loop : -0.66 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 403 HIS 0.006 0.001 HIS B 633 PHE 0.012 0.001 PHE B 556 TYR 0.011 0.001 TYR A 303 ARG 0.004 0.001 ARG B 802 Details of bonding type rmsd hydrogen bonds : bond 0.05274 ( 700) hydrogen bonds : angle 4.24108 ( 2049) SS BOND : bond 0.00209 ( 8) SS BOND : angle 1.93021 ( 16) covalent geometry : bond 0.00391 (11314) covalent geometry : angle 0.48162 (15384) *********************** 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 97 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 553 HIS cc_start: 0.8323 (p90) cc_final: 0.8015 (t-90) REVERT: A 659 ARG cc_start: 0.7198 (ttp-170) cc_final: 0.6602 (tpm170) REVERT: A 675 MET cc_start: 0.7217 (mtp) cc_final: 0.7009 (mtp) REVERT: B 659 ARG cc_start: 0.6942 (ttm-80) cc_final: 0.6519 (tpm170) REVERT: B 696 MET cc_start: 0.8663 (tpt) cc_final: 0.8158 (tpt) REVERT: B 732 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8327 (m) outliers start: 16 outliers final: 5 residues processed: 91 average time/residue: 2.1873 time to fit residues: 225.3054 Evaluate side-chains 82 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 3.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 732 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 126 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 88 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.118718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.076654 restraints weight = 51408.821| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.75 r_work: 0.2865 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11322 Z= 0.118 Angle : 0.453 4.431 15400 Z= 0.236 Chirality : 0.036 0.131 1752 Planarity : 0.004 0.043 1878 Dihedral : 3.334 22.400 1764 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.22 % Allowed : 15.62 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.23), residues: 1378 helix: 2.80 (0.17), residues: 898 sheet: -1.57 (0.66), residues: 20 loop : -0.70 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 403 HIS 0.004 0.001 HIS B 633 PHE 0.009 0.001 PHE B 556 TYR 0.009 0.001 TYR B 214 ARG 0.002 0.000 ARG B 802 Details of bonding type rmsd hydrogen bonds : bond 0.04674 ( 700) hydrogen bonds : angle 4.12707 ( 2049) SS BOND : bond 0.00312 ( 8) SS BOND : angle 2.44384 ( 16) covalent geometry : bond 0.00260 (11314) covalent geometry : angle 0.44631 (15384) *********************** 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 94 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7216 (ttp-170) cc_final: 0.6630 (tpm170) REVERT: B 696 MET cc_start: 0.8678 (tpt) cc_final: 0.8225 (tpt) outliers start: 14 outliers final: 8 residues processed: 85 average time/residue: 2.0067 time to fit residues: 192.3666 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 : 1.773 ------------------------------------------------------------------------------- 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 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 763 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 93 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.117042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.074699 restraints weight = 51285.421| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.75 r_work: 0.2829 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11322 Z= 0.166 Angle : 0.478 5.647 15400 Z= 0.250 Chirality : 0.036 0.133 1752 Planarity : 0.004 0.044 1878 Dihedral : 3.446 25.344 1764 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.39 % Allowed : 14.84 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.23), residues: 1378 helix: 2.68 (0.17), residues: 900 sheet: -1.39 (0.66), residues: 20 loop : -0.66 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 403 HIS 0.005 0.001 HIS B 633 PHE 0.009 0.001 PHE B 344 TYR 0.010 0.001 TYR B 214 ARG 0.002 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.05135 ( 700) hydrogen bonds : angle 4.13557 ( 2049) SS BOND : bond 0.00248 ( 8) SS BOND : angle 2.27927 ( 16) covalent geometry : bond 0.00390 (11314) covalent geometry : angle 0.47249 (15384) *********************** 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 93 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 1.718 Fit side-chains revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7238 (ttp-170) cc_final: 0.6651 (tpm170) REVERT: B 696 MET cc_start: 0.8689 (tpt) cc_final: 0.8234 (tpt) outliers start: 16 outliers final: 11 residues processed: 86 average time/residue: 1.6995 time to fit residues: 166.9940 Evaluate side-chains 83 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 1.694 ------------------------------------------------------------------------------- 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 A residue 786 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 101 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.118003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.075807 restraints weight = 51145.623| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.74 r_work: 0.2847 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11322 Z= 0.112 Angle : 0.440 5.405 15400 Z= 0.230 Chirality : 0.035 0.132 1752 Planarity : 0.004 0.045 1878 Dihedral : 3.364 23.834 1764 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.39 % Allowed : 15.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.23), residues: 1378 helix: 2.76 (0.17), residues: 900 sheet: -1.28 (0.68), residues: 20 loop : -0.65 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 403 HIS 0.003 0.000 HIS B 633 PHE 0.009 0.001 PHE B 344 TYR 0.009 0.001 TYR B 214 ARG 0.001 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.04624 ( 700) hydrogen bonds : angle 4.05110 ( 2049) SS BOND : bond 0.00156 ( 8) SS BOND : angle 1.59659 ( 16) covalent geometry : bond 0.00251 (11314) covalent geometry : angle 0.43708 (15384) *********************** 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 88 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7207 (ttp-170) cc_final: 0.6658 (tpm170) outliers start: 16 outliers final: 11 residues processed: 83 average time/residue: 1.7250 time to fit residues: 164.1089 Evaluate side-chains 82 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 1.651 ------------------------------------------------------------------------------- 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 A residue 786 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 33 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.116731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.074439 restraints weight = 51422.792| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.74 r_work: 0.2819 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2662 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= 0.148 Angle : 0.456 5.089 15400 Z= 0.239 Chirality : 0.036 0.132 1752 Planarity : 0.004 0.045 1878 Dihedral : 3.465 26.718 1764 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.30 % Allowed : 15.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.23), residues: 1378 helix: 2.71 (0.17), residues: 896 sheet: -1.05 (0.71), residues: 20 loop : -0.60 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 403 HIS 0.003 0.001 HIS A 633 PHE 0.013 0.001 PHE B 344 TYR 0.010 0.001 TYR B 214 ARG 0.002 0.000 ARG A 416 Details of bonding type rmsd hydrogen bonds : bond 0.04985 ( 700) hydrogen bonds : angle 4.06290 ( 2049) SS BOND : bond 0.00163 ( 8) SS BOND : angle 1.46726 ( 16) covalent geometry : bond 0.00343 (11314) covalent geometry : angle 0.45364 (15384) *********************** 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 90 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7259 (ttp-170) cc_final: 0.6670 (tpm170) outliers start: 15 outliers final: 9 residues processed: 85 average time/residue: 1.9241 time to fit residues: 186.1675 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 : 1.647 ------------------------------------------------------------------------------- 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 652 THR Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 461 THR 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 79 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 chunk 74 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.115595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.073658 restraints weight = 51271.942| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.72 r_work: 0.2805 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11322 Z= 0.166 Angle : 0.473 6.581 15400 Z= 0.250 Chirality : 0.037 0.133 1752 Planarity : 0.004 0.047 1878 Dihedral : 3.615 30.343 1764 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.22 % Allowed : 15.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.23), residues: 1378 helix: 2.62 (0.17), residues: 896 sheet: -1.01 (0.71), residues: 20 loop : -0.65 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 403 HIS 0.003 0.001 HIS A 633 PHE 0.014 0.001 PHE B 344 TYR 0.010 0.001 TYR B 214 ARG 0.002 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.05281 ( 700) hydrogen bonds : angle 4.08294 ( 2049) SS BOND : bond 0.00146 ( 8) SS BOND : angle 1.39663 ( 16) covalent geometry : bond 0.00389 (11314) covalent geometry : angle 0.47129 (15384) *********************** 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 85 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7281 (ttp-170) cc_final: 0.6677 (tpm170) outliers start: 14 outliers final: 9 residues processed: 81 average time/residue: 1.9061 time to fit residues: 176.9914 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 : 1.736 ------------------------------------------------------------------------------- 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 114 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.116318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.074521 restraints weight = 51384.011| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.73 r_work: 0.2819 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11322 Z= 0.130 Angle : 0.453 7.192 15400 Z= 0.237 Chirality : 0.036 0.131 1752 Planarity : 0.004 0.046 1878 Dihedral : 3.555 30.514 1764 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.95 % Allowed : 15.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.23), residues: 1378 helix: 2.69 (0.17), residues: 896 sheet: -1.03 (0.73), residues: 20 loop : -0.65 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 350 HIS 0.003 0.000 HIS A 633 PHE 0.014 0.001 PHE B 344 TYR 0.009 0.001 TYR B 214 ARG 0.002 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.04880 ( 700) hydrogen bonds : angle 4.01303 ( 2049) SS BOND : bond 0.00100 ( 8) SS BOND : angle 1.32948 ( 16) covalent geometry : bond 0.00299 (11314) covalent geometry : angle 0.45113 (15384) *********************** 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: 11 poor density : 68 time to evaluate : 1.631 Fit side-chains revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7236 (ttp-170) cc_final: 0.6654 (tpm170) outliers start: 11 outliers final: 8 residues processed: 76 average time/residue: 1.9262 time to fit residues: 164.2510 Evaluate side-chains 75 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 1.559 ------------------------------------------------------------------------------- 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 52 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.116256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.074509 restraints weight = 51486.249| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.72 r_work: 0.2816 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3040 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= 0.132 Angle : 0.454 7.179 15400 Z= 0.237 Chirality : 0.036 0.131 1752 Planarity : 0.004 0.046 1878 Dihedral : 3.554 31.833 1764 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.52 % Allowed : 16.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.23), residues: 1378 helix: 2.69 (0.17), residues: 896 sheet: -0.98 (0.72), residues: 20 loop : -0.66 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 403 HIS 0.003 0.000 HIS A 633 PHE 0.013 0.001 PHE B 344 TYR 0.009 0.001 TYR A 214 ARG 0.002 0.000 ARG A 416 Details of bonding type rmsd hydrogen bonds : bond 0.04868 ( 700) hydrogen bonds : angle 3.99480 ( 2049) SS BOND : bond 0.00104 ( 8) SS BOND : angle 1.30677 ( 16) covalent geometry : bond 0.00302 (11314) covalent geometry : angle 0.45233 (15384) ********************** 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 73 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 1.664 Fit side-chains revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7269 (ttp-170) cc_final: 0.6685 (tpm170) outliers start: 6 outliers final: 6 residues processed: 73 average time/residue: 2.4055 time to fit residues: 196.6893 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 : 2.053 ------------------------------------------------------------------------------- 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 106 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.116470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.074775 restraints weight = 51547.561| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.72 r_work: 0.2822 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11322 Z= 0.123 Angle : 0.446 5.959 15400 Z= 0.233 Chirality : 0.036 0.130 1752 Planarity : 0.004 0.046 1878 Dihedral : 3.528 32.306 1764 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.52 % Allowed : 15.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.23), residues: 1378 helix: 2.71 (0.17), residues: 896 sheet: -1.09 (0.71), residues: 20 loop : -0.67 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 350 HIS 0.003 0.000 HIS A 633 PHE 0.014 0.001 PHE B 344 TYR 0.009 0.001 TYR A 214 ARG 0.002 0.000 ARG A 416 Details of bonding type rmsd hydrogen bonds : bond 0.04752 ( 700) hydrogen bonds : angle 3.96495 ( 2049) SS BOND : bond 0.00086 ( 8) SS BOND : angle 1.25143 ( 16) covalent geometry : bond 0.00280 (11314) covalent geometry : angle 0.44429 (15384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16012.34 seconds wall clock time: 277 minutes 5.04 seconds (16625.04 seconds total)