Starting phenix.real_space_refine on Fri Sep 19 02:29:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9do0_47070/09_2025/9do0_47070_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9do0_47070/09_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_47070/09_2025/9do0_47070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9do0_47070/09_2025/9do0_47070.map" model { file = "/net/cci-nas-00/data/ceres_data/9do0_47070/09_2025/9do0_47070_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9do0_47070/09_2025/9do0_47070_trim.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 72 5.16 5 Cl 4 4.86 5 C 7242 2.51 5 N 1802 2.21 5 O 2010 1.98 5 H 11018 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22148 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 10964 Classifications: {'peptide': 697} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 666} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 10964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 10964 Classifications: {'peptide': 697} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 666} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 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: 3.90, per 1000 atoms: 0.18 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: 2.08 Conformation dependent library (CDL) restraints added in 612.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2568 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 8 sheets defined 68.7% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 92 through 114 Processing helix chain 'A' and resid 114 through 157 removed outlier: 4.476A pdb=" N GLY A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N TRP A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 203 through 232 Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.510A pdb=" N CYS A 237 " --> pdb=" O PRO A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 258 through 276 removed outlier: 3.662A pdb=" N VAL A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 298 Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 306 through 327 Processing helix chain 'A' and resid 328 through 339 Processing helix chain 'A' and resid 345 through 366 removed outlier: 3.605A pdb=" N TRP A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 366 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 419 removed outlier: 3.516A pdb=" N GLY A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 425 removed outlier: 6.606A pdb=" N PHE A 423 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 424 " --> pdb=" O THR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 443 Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 494 through 518 removed outlier: 3.571A pdb=" N SER A 498 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 506 " --> pdb=" O GLN A 502 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR A 514 " --> pdb=" O LYS A 510 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL A 515 " --> pdb=" O ILE A 511 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 516 " --> pdb=" O ILE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 552 Processing helix chain 'A' and resid 555 through 562 Processing helix chain 'A' and resid 570 through 588 Processing helix chain 'A' and resid 590 through 602 Processing helix chain 'A' and resid 603 through 605 No H-bonds generated for 'chain 'A' and resid 603 through 605' Processing helix chain 'A' and resid 606 through 624 removed outlier: 3.578A pdb=" N ALA A 613 " --> pdb=" O PRO A 609 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 653 through 657 Processing helix chain 'A' and resid 677 through 687 Processing helix chain 'A' and resid 709 through 723 Processing helix chain 'A' and resid 767 through 779 removed outlier: 3.511A pdb=" N VAL A 771 " --> pdb=" O PRO A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 808 Processing helix chain 'B' and resid 92 through 114 Processing helix chain 'B' and resid 114 through 158 removed outlier: 4.472A pdb=" N GLY B 128 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N TRP B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS B 157 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU B 158 " --> pdb=" O THR B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 203 through 232 Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 240 through 249 Processing helix chain 'B' and resid 258 through 276 removed outlier: 3.670A pdb=" N VAL B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 298 Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 306 through 327 Processing helix chain 'B' and resid 328 through 339 Processing helix chain 'B' and resid 345 through 366 removed outlier: 3.599A pdb=" N TRP B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 366 " --> pdb=" O VAL B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 419 removed outlier: 3.519A pdb=" N GLY B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 425 removed outlier: 6.609A pdb=" N PHE B 423 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 424 " --> pdb=" O THR B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 443 Processing helix chain 'B' and resid 445 through 450 Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'B' and resid 494 through 518 removed outlier: 3.566A pdb=" N SER B 498 " --> pdb=" O ILE B 494 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 506 " --> pdb=" O GLN B 502 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 514 " --> pdb=" O LYS B 510 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL B 515 " --> pdb=" O ILE B 511 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 516 " --> pdb=" O ILE B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 552 Processing helix chain 'B' and resid 555 through 562 Processing helix chain 'B' and resid 570 through 588 Processing helix chain 'B' and resid 590 through 602 Processing helix chain 'B' and resid 603 through 605 No H-bonds generated for 'chain 'B' and resid 603 through 605' Processing helix chain 'B' and resid 606 through 624 removed outlier: 3.581A pdb=" N ALA B 613 " --> pdb=" O PRO B 609 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 638 Processing helix chain 'B' and resid 653 through 657 Processing helix chain 'B' and resid 677 through 687 Processing helix chain 'B' and resid 709 through 723 Processing helix chain 'B' and resid 767 through 779 removed outlier: 3.501A pdb=" N VAL B 771 " --> pdb=" O PRO B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 808 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 670 through 671 removed outlier: 6.021A pdb=" N LEU A 670 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 675 through 676 removed outlier: 4.089A pdb=" N MET A 675 " --> pdb=" O VAL A 732 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 761 through 763 removed outlier: 5.991A pdb=" N VAL A 762 " --> pdb=" O THR A 786 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N HIS A 787 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU A 791 " --> pdb=" O HIS A 787 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 160 through 161 Processing sheet with id=AA6, first strand: chain 'B' and resid 670 through 671 removed outlier: 6.047A pdb=" N LEU B 670 " --> pdb=" O ILE B 695 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 675 through 676 removed outlier: 4.111A pdb=" N MET B 675 " --> pdb=" O VAL B 732 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 761 through 763 removed outlier: 6.079A pdb=" N VAL B 762 " --> pdb=" O THR B 786 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N HIS B 787 " --> pdb=" O LEU B 791 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LEU B 791 " --> pdb=" O HIS B 787 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 2049 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.47 Time building geometry restraints manager: 2.87 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.420 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:7.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.390 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.24), residues: 1378 helix: 2.08 (0.18), residues: 882 sheet: -1.79 (0.71), residues: 20 loop : -0.20 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 802 TYR 0.006 0.001 TYR A 303 PHE 0.007 0.000 PHE A 377 TRP 0.006 0.000 TRP B 350 HIS 0.001 0.000 HIS B 765 Details of bonding type rmsd covalent geometry : bond 0.00182 (11314) covalent geometry : angle 0.42716 (15384) SS BOND : bond 0.00061 ( 8) SS BOND : angle 0.31805 ( 16) hydrogen bonds : bond 0.13051 ( 700) hydrogen bonds : angle 6.02021 ( 2049) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 0.554 Fit side-chains REVERT: B 696 MET cc_start: 0.8334 (tpt) cc_final: 0.8030 (tpt) outliers start: 2 outliers final: 0 residues processed: 119 average time/residue: 1.0676 time to fit residues: 138.9067 Evaluate side-chains 73 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3736 r_free = 0.3736 target = 0.118388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.076325 restraints weight = 51347.858| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.73 r_work: 0.2859 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 11322 Z= 0.235 Angle : 0.546 6.491 15400 Z= 0.291 Chirality : 0.039 0.142 1752 Planarity : 0.005 0.048 1878 Dihedral : 3.461 27.059 1764 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.48 % Allowed : 16.41 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.23), residues: 1378 helix: 2.56 (0.17), residues: 896 sheet: -1.65 (0.67), residues: 20 loop : -0.67 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 802 TYR 0.013 0.001 TYR A 303 PHE 0.012 0.001 PHE B 556 TRP 0.012 0.001 TRP A 403 HIS 0.006 0.001 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00550 (11314) covalent geometry : angle 0.53648 (15384) SS BOND : bond 0.01539 ( 8) SS BOND : angle 3.15323 ( 16) hydrogen bonds : bond 0.05749 ( 700) hydrogen bonds : angle 4.42813 ( 2049) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7181 (ttp-170) cc_final: 0.6709 (tpm170) REVERT: A 732 VAL cc_start: 0.9098 (t) cc_final: 0.8882 (m) REVERT: B 696 MET cc_start: 0.8648 (tpt) cc_final: 0.8278 (tpt) outliers start: 17 outliers final: 7 residues processed: 92 average time/residue: 0.9781 time to fit residues: 100.6851 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 : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 703 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 24 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 94 optimal weight: 0.0970 chunk 97 optimal weight: 4.9990 chunk 132 optimal weight: 0.0870 chunk 10 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 overall best weight: 0.6356 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.119869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.078258 restraints weight = 50982.793| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.72 r_work: 0.2888 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11322 Z= 0.114 Angle : 0.465 6.539 15400 Z= 0.242 Chirality : 0.036 0.145 1752 Planarity : 0.004 0.042 1878 Dihedral : 3.327 21.582 1764 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.39 % Allowed : 16.23 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.23), residues: 1378 helix: 2.80 (0.17), residues: 896 sheet: -1.86 (0.63), residues: 20 loop : -0.69 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 802 TYR 0.009 0.001 TYR B 214 PHE 0.011 0.001 PHE B 556 TRP 0.009 0.001 TRP A 403 HIS 0.003 0.001 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00249 (11314) covalent geometry : angle 0.45554 (15384) SS BOND : bond 0.00385 ( 8) SS BOND : angle 2.85325 ( 16) hydrogen bonds : bond 0.04737 ( 700) hydrogen bonds : angle 4.25514 ( 2049) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7144 (ttp-170) cc_final: 0.6808 (tpm170) REVERT: A 732 VAL cc_start: 0.9076 (t) cc_final: 0.8870 (m) REVERT: A 760 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.7150 (m-80) REVERT: B 696 MET cc_start: 0.8614 (tpt) cc_final: 0.8184 (tpt) REVERT: B 760 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.7165 (m-80) outliers start: 16 outliers final: 6 residues processed: 82 average time/residue: 0.9402 time to fit residues: 85.9242 Evaluate side-chains 82 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 760 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 94 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 41 optimal weight: 0.4980 chunk 97 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 11 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.120451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.078725 restraints weight = 50940.052| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.73 r_work: 0.2902 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11322 Z= 0.100 Angle : 0.443 4.523 15400 Z= 0.230 Chirality : 0.035 0.131 1752 Planarity : 0.004 0.044 1878 Dihedral : 3.218 20.756 1764 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.13 % Allowed : 15.45 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.54 (0.23), residues: 1378 helix: 2.90 (0.17), residues: 898 sheet: -1.77 (0.64), residues: 20 loop : -0.71 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 802 TYR 0.008 0.001 TYR B 214 PHE 0.010 0.001 PHE B 556 TRP 0.008 0.001 TRP A 403 HIS 0.003 0.001 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00216 (11314) covalent geometry : angle 0.43635 (15384) SS BOND : bond 0.00325 ( 8) SS BOND : angle 2.49451 ( 16) hydrogen bonds : bond 0.04250 ( 700) hydrogen bonds : angle 4.09884 ( 2049) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7157 (ttp-170) cc_final: 0.6825 (tpm170) REVERT: A 760 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.7159 (m-80) REVERT: B 696 MET cc_start: 0.8620 (tpt) cc_final: 0.8172 (tpt) REVERT: B 760 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7185 (m-80) outliers start: 13 outliers final: 8 residues processed: 82 average time/residue: 0.8877 time to fit residues: 82.4046 Evaluate side-chains 84 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain B residue 187 CYS 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 760 PHE Chi-restraints excluded: chain B residue 763 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 111 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.116035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.074013 restraints weight = 51004.475| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.70 r_work: 0.2803 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11322 Z= 0.192 Angle : 0.502 5.642 15400 Z= 0.267 Chirality : 0.038 0.137 1752 Planarity : 0.004 0.044 1878 Dihedral : 3.621 28.274 1764 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.39 % Allowed : 15.10 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.24 (0.23), residues: 1378 helix: 2.59 (0.17), residues: 898 sheet: -1.22 (0.67), residues: 20 loop : -0.70 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 311 TYR 0.010 0.001 TYR B 214 PHE 0.011 0.001 PHE B 460 TRP 0.011 0.001 TRP A 403 HIS 0.007 0.001 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00449 (11314) covalent geometry : angle 0.49776 (15384) SS BOND : bond 0.00343 ( 8) SS BOND : angle 2.07433 ( 16) hydrogen bonds : bond 0.05663 ( 700) hydrogen bonds : angle 4.18505 ( 2049) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7266 (ttp-170) cc_final: 0.6660 (tpm170) REVERT: A 732 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8184 (m) REVERT: B 696 MET cc_start: 0.8710 (tpt) cc_final: 0.8237 (tpt) REVERT: B 760 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7651 (m-80) outliers start: 16 outliers final: 8 residues processed: 90 average time/residue: 1.0243 time to fit residues: 102.8659 Evaluate side-chains 81 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 732 VAL 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 677 VAL Chi-restraints excluded: chain B residue 760 PHE Chi-restraints excluded: chain B residue 763 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 0.0670 chunk 74 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.116285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.074382 restraints weight = 51354.346| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.72 r_work: 0.2814 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11322 Z= 0.147 Angle : 0.463 5.417 15400 Z= 0.244 Chirality : 0.036 0.133 1752 Planarity : 0.004 0.044 1878 Dihedral : 3.548 27.699 1764 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.65 % Allowed : 15.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.23), residues: 1378 helix: 2.63 (0.17), residues: 898 sheet: -1.08 (0.70), residues: 20 loop : -0.69 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 588 TYR 0.009 0.001 TYR A 214 PHE 0.008 0.001 PHE B 344 TRP 0.010 0.001 TRP A 403 HIS 0.004 0.001 HIS B 633 Details of bonding type rmsd covalent geometry : bond 0.00338 (11314) covalent geometry : angle 0.46070 (15384) SS BOND : bond 0.00181 ( 8) SS BOND : angle 1.46814 ( 16) hydrogen bonds : bond 0.05134 ( 700) hydrogen bonds : angle 4.11526 ( 2049) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7250 (ttp-170) cc_final: 0.6662 (tpm170) REVERT: A 760 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7481 (m-80) REVERT: B 696 MET cc_start: 0.8721 (tpt) cc_final: 0.8257 (tpt) outliers start: 19 outliers final: 12 residues processed: 83 average time/residue: 0.9758 time to fit residues: 90.9741 Evaluate side-chains 80 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 677 VAL Chi-restraints excluded: chain A residue 760 PHE 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 20 optimal weight: 0.0770 chunk 88 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.0142 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.116781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.074904 restraints weight = 50992.350| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.72 r_work: 0.2824 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2729 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= 0.126 Angle : 0.457 6.954 15400 Z= 0.238 Chirality : 0.036 0.131 1752 Planarity : 0.004 0.044 1878 Dihedral : 3.506 27.676 1764 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.48 % Allowed : 14.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.23), residues: 1378 helix: 2.71 (0.17), residues: 896 sheet: -1.04 (0.72), residues: 20 loop : -0.65 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 416 TYR 0.009 0.001 TYR B 214 PHE 0.006 0.001 PHE A 251 TRP 0.010 0.001 TRP A 403 HIS 0.003 0.000 HIS A 633 Details of bonding type rmsd covalent geometry : bond 0.00284 (11314) covalent geometry : angle 0.45406 (15384) SS BOND : bond 0.00168 ( 8) SS BOND : angle 1.56653 ( 16) hydrogen bonds : bond 0.04879 ( 700) hydrogen bonds : angle 4.05867 ( 2049) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7259 (ttp-170) cc_final: 0.6659 (tpm170) REVERT: B 760 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7414 (m-80) outliers start: 17 outliers final: 10 residues processed: 80 average time/residue: 1.0591 time to fit residues: 94.2172 Evaluate side-chains 77 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 733 CYS 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 500 ILE Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 760 PHE Chi-restraints excluded: chain B residue 763 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 121 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.115456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.073555 restraints weight = 51040.309| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.71 r_work: 0.2799 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11322 Z= 0.166 Angle : 0.472 7.187 15400 Z= 0.248 Chirality : 0.037 0.132 1752 Planarity : 0.004 0.045 1878 Dihedral : 3.621 31.119 1764 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.04 % Allowed : 14.84 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.30 (0.23), residues: 1378 helix: 2.63 (0.17), residues: 896 sheet: -0.92 (0.72), residues: 20 loop : -0.66 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 311 TYR 0.011 0.001 TYR B 214 PHE 0.007 0.001 PHE A 251 TRP 0.010 0.001 TRP A 403 HIS 0.003 0.000 HIS A 633 Details of bonding type rmsd covalent geometry : bond 0.00391 (11314) covalent geometry : angle 0.46997 (15384) SS BOND : bond 0.00207 ( 8) SS BOND : angle 1.43158 ( 16) hydrogen bonds : bond 0.05283 ( 700) hydrogen bonds : angle 4.08823 ( 2049) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7281 (ttp-170) cc_final: 0.6668 (tpm170) outliers start: 12 outliers final: 8 residues processed: 76 average time/residue: 1.1355 time to fit residues: 95.3611 Evaluate side-chains 74 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 55 optimal weight: 0.2980 chunk 128 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 132 optimal weight: 0.3980 chunk 125 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.4982 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.117264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.075531 restraints weight = 51215.606| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.72 r_work: 0.2839 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11322 Z= 0.098 Angle : 0.444 6.552 15400 Z= 0.230 Chirality : 0.035 0.132 1752 Planarity : 0.004 0.045 1878 Dihedral : 3.454 28.462 1764 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.95 % Allowed : 15.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.50 (0.23), residues: 1378 helix: 2.80 (0.17), residues: 896 sheet: -1.07 (0.72), residues: 20 loop : -0.61 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 416 TYR 0.008 0.001 TYR B 214 PHE 0.005 0.001 PHE B 399 TRP 0.011 0.001 TRP A 403 HIS 0.002 0.000 HIS A 633 Details of bonding type rmsd covalent geometry : bond 0.00208 (11314) covalent geometry : angle 0.44226 (15384) SS BOND : bond 0.00103 ( 8) SS BOND : angle 1.24960 ( 16) hydrogen bonds : bond 0.04478 ( 700) hydrogen bonds : angle 3.99227 ( 2049) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7224 (ttp-170) cc_final: 0.6904 (tpm170) outliers start: 11 outliers final: 7 residues processed: 77 average time/residue: 1.0212 time to fit residues: 88.0624 Evaluate side-chains 74 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 763 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 111 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.116517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.074718 restraints weight = 51347.408| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.72 r_work: 0.2822 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2969 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= 0.126 Angle : 0.449 5.520 15400 Z= 0.234 Chirality : 0.036 0.132 1752 Planarity : 0.004 0.043 1878 Dihedral : 3.468 30.013 1764 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.43 % Allowed : 15.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.45 (0.23), residues: 1378 helix: 2.77 (0.17), residues: 896 sheet: -1.02 (0.72), residues: 20 loop : -0.64 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 311 TYR 0.009 0.001 TYR B 214 PHE 0.006 0.001 PHE A 251 TRP 0.010 0.001 TRP B 350 HIS 0.003 0.000 HIS A 633 Details of bonding type rmsd covalent geometry : bond 0.00286 (11314) covalent geometry : angle 0.44772 (15384) SS BOND : bond 0.00136 ( 8) SS BOND : angle 1.25342 ( 16) hydrogen bonds : bond 0.04727 ( 700) hydrogen bonds : angle 3.98290 ( 2049) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2756 Ramachandran restraints generated. 1378 Oldfield, 0 Emsley, 1378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 659 ARG cc_start: 0.7236 (ttp-170) cc_final: 0.6648 (tpm170) outliers start: 5 outliers final: 5 residues processed: 69 average time/residue: 1.0917 time to fit residues: 83.8066 Evaluate side-chains 69 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 763 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 36 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 11 optimal weight: 0.2980 chunk 118 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.116302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.074581 restraints weight = 51095.518| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.72 r_work: 0.2818 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3018 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= 0.129 Angle : 0.453 5.789 15400 Z= 0.236 Chirality : 0.036 0.131 1752 Planarity : 0.004 0.043 1878 Dihedral : 3.501 31.323 1764 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.43 % Allowed : 15.71 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.23), residues: 1378 helix: 2.75 (0.17), residues: 896 sheet: -1.05 (0.71), residues: 20 loop : -0.65 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 101 TYR 0.009 0.001 TYR B 214 PHE 0.006 0.001 PHE A 251 TRP 0.010 0.001 TRP A 403 HIS 0.003 0.000 HIS A 633 Details of bonding type rmsd covalent geometry : bond 0.00295 (11314) covalent geometry : angle 0.45114 (15384) SS BOND : bond 0.00111 ( 8) SS BOND : angle 1.21492 ( 16) hydrogen bonds : bond 0.04792 ( 700) hydrogen bonds : angle 3.98583 ( 2049) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7899.96 seconds wall clock time: 134 minutes 15.20 seconds (8055.20 seconds total)