Starting phenix.real_space_refine on Thu May 22 04:35:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9do0_47070/05_2025/9do0_47070_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9do0_47070/05_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_47070/05_2025/9do0_47070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9do0_47070/05_2025/9do0_47070.map" model { file = "/net/cci-nas-00/data/ceres_data/9do0_47070/05_2025/9do0_47070_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9do0_47070/05_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-5687/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: 11.63, per 1000 atoms: 0.53 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: 5.61 Conformation dependent library (CDL) restraints added in 1.8 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: 1.66 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: 8.66 Time building geometry restraints manager: 6.72 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: 3.440 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: 0.350 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 47.390 Find NCS groups from input model: 0.570 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: 0.000 Load rotamer database and sin/cos tables:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.310 ------------------------------------------------------------------------------- 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 : 1.574 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: 2.1284 time to fit residues: 279.8838 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 = 0.123095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.081429 restraints weight = 51074.795| |-----------------------------------------------------------------------------| 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: 0.7740 moved from start: 0.1398 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 6.769 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 4.47744 ( 2049) SS BOND : bond 0.00561 ( 8) SS BOND : angle 2.84295 ( 16) covalent geometry : bond 0.00309 (11314) covalent geometry : angle 0.48351 (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 : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7052 (ttp-170) cc_final: 0.6751 (tpm170) REVERT: A 675 MET cc_start: 0.6836 (mtp) cc_final: 0.6635 (mtp) REVERT: A 732 VAL cc_start: 0.9105 (t) cc_final: 0.8877 (m) REVERT: B 696 MET cc_start: 0.8621 (tpt) cc_final: 0.8156 (tpt) outliers start: 15 outliers final: 7 residues processed: 88 average time/residue: 1.9820 time to fit residues: 195.9443 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 : 1.559 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.6980 chunk 49 optimal weight: 1.9990 chunk 121 optimal weight: 0.2980 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.118894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.077121 restraints weight = 51190.952| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.72 r_work: 0.2868 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11322 Z= 0.163 Angle : 0.478 6.265 15400 Z= 0.252 Chirality : 0.037 0.134 1752 Planarity : 0.004 0.041 1878 Dihedral : 3.391 23.890 1764 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.30 % Allowed : 15.71 % Favored : 82.99 % 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: 2.42 (0.23), residues: 1378 helix: 2.78 (0.17), residues: 896 sheet: -1.58 (0.66), residues: 20 loop : -0.69 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 403 HIS 0.005 0.001 HIS B 633 PHE 0.011 0.001 PHE B 556 TYR 0.010 0.001 TYR A 303 ARG 0.006 0.001 ARG B 802 Details of bonding type rmsd hydrogen bonds : bond 0.05160 ( 700) hydrogen bonds : angle 4.24979 ( 2049) SS BOND : bond 0.00299 ( 8) SS BOND : angle 2.01975 ( 16) covalent geometry : bond 0.00382 (11314) covalent geometry : angle 0.47401 (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 93 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7176 (ttp-170) cc_final: 0.6579 (tpm170) REVERT: A 675 MET cc_start: 0.7152 (mtp) cc_final: 0.6938 (mtp) REVERT: B 696 MET cc_start: 0.8659 (tpt) cc_final: 0.8163 (tpt) outliers start: 15 outliers final: 6 residues processed: 86 average time/residue: 1.8776 time to fit residues: 181.3771 Evaluate side-chains 80 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 THR 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=4.00 ------------------------------------------------------------------------------- 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: 1.9990 chunk 38 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 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 = 0.3735 r_free = 0.3735 target = 0.118536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.076330 restraints weight = 51314.883| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.75 r_work: 0.2856 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11322 Z= 0.132 Angle : 0.468 6.253 15400 Z= 0.243 Chirality : 0.036 0.131 1752 Planarity : 0.004 0.044 1878 Dihedral : 3.350 22.982 1764 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.30 % Allowed : 15.45 % 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 (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: 2.42 (0.23), residues: 1378 helix: 2.77 (0.17), residues: 898 sheet: -1.47 (0.67), residues: 20 loop : -0.71 (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 0.04808 ( 700) hydrogen bonds : angle 4.13924 ( 2049) SS BOND : bond 0.00228 ( 8) SS BOND : angle 2.78670 ( 16) covalent geometry : bond 0.00300 (11314) covalent geometry : angle 0.45980 (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: 15 poor density : 79 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7202 (ttp-170) cc_final: 0.6615 (tpm170) REVERT: B 696 MET cc_start: 0.8682 (tpt) cc_final: 0.8231 (tpt) outliers start: 15 outliers final: 9 residues processed: 86 average time/residue: 1.7243 time to fit residues: 169.3244 Evaluate side-chains 82 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 1.681 ------------------------------------------------------------------------------- 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 249 SER 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: 2.9990 chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 94 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.118489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.076346 restraints weight = 51062.965| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.73 r_work: 0.2855 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2311 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= 0.121 Angle : 0.447 4.676 15400 Z= 0.234 Chirality : 0.036 0.131 1752 Planarity : 0.004 0.045 1878 Dihedral : 3.329 22.912 1764 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.22 % Allowed : 15.28 % 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: 2.46 (0.23), residues: 1378 helix: 2.80 (0.17), residues: 898 sheet: -1.43 (0.68), residues: 20 loop : -0.69 (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 0.008 0.001 PHE B 344 TYR 0.009 0.001 TYR B 214 ARG 0.002 0.000 ARG B 802 Details of bonding type rmsd hydrogen bonds : bond 0.04675 ( 700) hydrogen bonds : angle 4.10041 ( 2049) SS BOND : bond 0.00478 ( 8) SS BOND : angle 1.79364 ( 16) covalent geometry : bond 0.00273 (11314) covalent geometry : angle 0.44307 (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 90 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 1.752 Fit side-chains revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7215 (ttp-170) cc_final: 0.6639 (tpm170) REVERT: B 696 MET cc_start: 0.8697 (tpt) cc_final: 0.8255 (tpt) outliers start: 14 outliers final: 10 residues processed: 83 average time/residue: 1.7231 time to fit residues: 162.8439 Evaluate side-chains 82 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 1.586 ------------------------------------------------------------------------------- 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 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 703 LEU 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: 2.9990 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 123 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.117835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.075523 restraints weight = 51121.284| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.75 r_work: 0.2844 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2505 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= 0.124 Angle : 0.442 4.548 15400 Z= 0.232 Chirality : 0.036 0.130 1752 Planarity : 0.004 0.046 1878 Dihedral : 3.340 23.974 1764 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.39 % Allowed : 14.58 % Favored : 84.03 % 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: 2.48 (0.23), residues: 1378 helix: 2.78 (0.17), residues: 900 sheet: -1.27 (0.70), residues: 20 loop : -0.61 (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 0.012 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 0.04656 ( 700) hydrogen bonds : angle 4.04025 ( 2049) SS BOND : bond 0.00140 ( 8) SS BOND : angle 1.55967 ( 16) covalent geometry : bond 0.00280 (11314) covalent geometry : angle 0.43890 (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 93 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7205 (ttp-170) cc_final: 0.6647 (tpm170) outliers start: 16 outliers final: 9 residues processed: 88 average time/residue: 1.7496 time to fit residues: 174.1246 Evaluate side-chains 81 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 1.543 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- 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: 3.9990 chunk 46 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.115662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.073815 restraints weight = 51496.636| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.72 r_work: 0.2802 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11322 Z= 0.168 Angle : 0.475 5.043 15400 Z= 0.251 Chirality : 0.037 0.132 1752 Planarity : 0.004 0.058 1878 Dihedral : 3.592 28.787 1764 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: 2.33 (0.23), residues: 1378 helix: 2.66 (0.17), residues: 896 sheet: -1.06 (0.72), residues: 20 loop : -0.64 (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 0.018 0.001 PHE B 344 TYR 0.010 0.001 TYR A 214 ARG 0.003 0.001 ARG A 416 Details of bonding type rmsd hydrogen bonds : bond 0.05364 ( 700) hydrogen bonds : angle 4.10659 ( 2049) SS BOND : bond 0.00222 ( 8) SS BOND : angle 1.47378 ( 16) covalent geometry : bond 0.00393 (11314) covalent geometry : angle 0.47301 (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 93 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 1.581 Fit side-chains REVERT: A 659 ARG cc_start: 0.7281 (ttp-170) cc_final: 0.6675 (tpm170) outliers start: 16 outliers final: 8 residues processed: 86 average time/residue: 1.9885 time to fit residues: 190.7567 Evaluate side-chains 77 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 1.698 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.115733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.073828 restraints weight = 51286.498| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.72 r_work: 0.2806 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11322 Z= 0.153 Angle : 0.461 4.678 15400 Z= 0.244 Chirality : 0.036 0.132 1752 Planarity : 0.004 0.047 1878 Dihedral : 3.597 30.584 1764 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.04 % Allowed : 15.54 % 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: 2.32 (0.23), residues: 1378 helix: 2.65 (0.17), residues: 896 sheet: -0.99 (0.73), residues: 20 loop : -0.66 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 B 214 ARG 0.003 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.05159 ( 700) hydrogen bonds : angle 4.07856 ( 2049) SS BOND : bond 0.00119 ( 8) SS BOND : angle 1.38428 ( 16) covalent geometry : bond 0.00355 (11314) covalent geometry : angle 0.45883 (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 82 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7280 (ttp-170) cc_final: 0.6677 (tpm170) outliers start: 12 outliers final: 8 residues processed: 78 average time/residue: 1.9716 time to fit residues: 172.2143 Evaluate side-chains 76 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 1.558 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- 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: 0.6980 chunk 137 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.116353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.074630 restraints weight = 51338.510| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.72 r_work: 0.2820 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11322 Z= 0.122 Angle : 0.452 7.155 15400 Z= 0.236 Chirality : 0.036 0.132 1752 Planarity : 0.004 0.048 1878 Dihedral : 3.538 30.436 1764 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.87 % Allowed : 15.45 % 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 (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: -1.05 (0.74), residues: 20 loop : -0.66 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 403 HIS 0.003 0.000 HIS A 633 PHE 0.016 0.001 PHE B 344 TYR 0.009 0.001 TYR B 214 ARG 0.002 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.04828 ( 700) hydrogen bonds : angle 4.01177 ( 2049) SS BOND : bond 0.00111 ( 8) SS BOND : angle 1.32726 ( 16) covalent geometry : bond 0.00278 (11314) covalent geometry : angle 0.44986 (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: 10 poor density : 69 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7231 (ttp-170) cc_final: 0.6661 (tpm170) outliers start: 10 outliers final: 8 residues processed: 77 average time/residue: 2.0011 time to fit residues: 172.8109 Evaluate side-chains 76 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 1.598 ------------------------------------------------------------------------------- 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 52 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.115815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.074054 restraints weight = 51493.372| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.72 r_work: 0.2809 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3054 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= 0.144 Angle : 0.461 6.984 15400 Z= 0.241 Chirality : 0.036 0.131 1752 Planarity : 0.004 0.047 1878 Dihedral : 3.584 32.524 1764 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.87 % Allowed : 15.62 % 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: 2.32 (0.23), residues: 1378 helix: 2.67 (0.17), residues: 896 sheet: -1.04 (0.72), residues: 20 loop : -0.69 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 403 HIS 0.003 0.000 HIS A 633 PHE 0.015 0.001 PHE B 344 TYR 0.010 0.001 TYR B 214 ARG 0.002 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.05025 ( 700) hydrogen bonds : angle 4.01462 ( 2049) SS BOND : bond 0.00128 ( 8) SS BOND : angle 1.31983 ( 16) covalent geometry : bond 0.00335 (11314) covalent geometry : angle 0.45919 (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 78 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7281 (ttp-170) cc_final: 0.6686 (tpm170) outliers start: 10 outliers final: 8 residues processed: 75 average time/residue: 2.0523 time to fit residues: 171.9689 Evaluate side-chains 76 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 1.668 ------------------------------------------------------------------------------- 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 106 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.116062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.074388 restraints weight = 51533.412| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.72 r_work: 0.2815 rms_B_bonded: 3.07 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: 0.7943 moved from start: 0.3114 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= 0.131 Angle : 0.450 5.728 15400 Z= 0.236 Chirality : 0.036 0.131 1752 Planarity : 0.004 0.048 1878 Dihedral : 3.577 33.945 1764 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.78 % Allowed : 15.54 % 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 (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: 2.70 (0.17), residues: 896 sheet: -1.13 (0.72), residues: 20 loop : -0.70 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 403 HIS 0.003 0.000 HIS A 633 PHE 0.017 0.001 PHE B 344 TYR 0.009 0.001 TYR B 214 ARG 0.002 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.04859 ( 700) hydrogen bonds : angle 3.98609 ( 2049) SS BOND : bond 0.00087 ( 8) SS BOND : angle 1.26211 ( 16) covalent geometry : bond 0.00298 (11314) covalent geometry : angle 0.44835 (15384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15066.40 seconds wall clock time: 257 minutes 53.85 seconds (15473.85 seconds total)