Starting phenix.real_space_refine on Thu Jul 2 22:23:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rx2_24722/07_2026/7rx2_24722.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rx2_24722/07_2026/7rx2_24722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rx2_24722/07_2026/7rx2_24722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rx2_24722/07_2026/7rx2_24722.map" model { file = "/net/cci-nas-00/data/ceres_data/7rx2_24722/07_2026/7rx2_24722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rx2_24722/07_2026/7rx2_24722.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7rx2_24722/07_2026/7rx2_24722.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rx2_24722/07_2026/7rx2_24722.cif" } resolution = 2.7 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= 0.003 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 12 5.49 5 S 38 5.16 5 C 6810 2.51 5 N 1664 2.21 5 O 1850 1.98 5 H 12 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10390 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 4969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4969 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 30, 'TRANS': 584} Chain breaks: 4 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 4969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4969 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 30, 'TRANS': 584} Chain breaks: 4 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "B" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 217 Unusual residues: {' CA': 2, 'PGW': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PGW:plan-3': 5} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 217 Unusual residues: {' CA': 2, 'PGW': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PGW:plan-3': 5} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 1.72, per 1000 atoms: 0.17 Number of scatterers: 10390 At special positions: 0 Unit cell: (117.312, 101.058, 98.2313, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 38 16.00 P 12 15.00 O 1850 8.00 N 1664 7.00 C 6810 6.00 H 12 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 252.7 milliseconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 71.5% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'B' and resid 28 through 46 removed outlier: 3.872A pdb=" N VAL B 38 " --> pdb=" O LYS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 86 Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 103 through 117 Processing helix chain 'B' and resid 144 through 155 Processing helix chain 'B' and resid 162 through 174 Processing helix chain 'B' and resid 174 through 191 removed outlier: 3.592A pdb=" N TYR B 180 " --> pdb=" O HIS B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 209 through 238 removed outlier: 3.644A pdb=" N GLU B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 247 removed outlier: 3.618A pdb=" N HIS B 247 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 280 removed outlier: 3.638A pdb=" N ARG B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 311 removed outlier: 3.624A pdb=" N ILE B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 330 Processing helix chain 'B' and resid 331 through 350 Processing helix chain 'B' and resid 354 through 385 removed outlier: 4.037A pdb=" N VAL B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Proline residue: B 377 - end of helix Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 435 through 452 removed outlier: 3.527A pdb=" N ALA B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Proline residue: B 449 - end of helix Processing helix chain 'B' and resid 489 through 501 removed outlier: 4.558A pdb=" N PHE B 493 " --> pdb=" O ASP B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 526 removed outlier: 3.973A pdb=" N ASP B 511 " --> pdb=" O ASP B 507 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 522 " --> pdb=" O GLN B 518 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER B 526 " --> pdb=" O LEU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 554 removed outlier: 3.508A pdb=" N VAL B 542 " --> pdb=" O ILE B 538 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 545 " --> pdb=" O TRP B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 591 removed outlier: 3.519A pdb=" N GLY B 574 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 605 removed outlier: 4.335A pdb=" N THR B 604 " --> pdb=" O GLU B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 634 removed outlier: 3.654A pdb=" N LYS B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 658 Processing helix chain 'B' and resid 701 through 706 Processing helix chain 'B' and resid 711 through 726 removed outlier: 3.932A pdb=" N SER B 715 " --> pdb=" O GLY B 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 46 removed outlier: 3.873A pdb=" N VAL A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 86 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 103 through 117 Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 174 through 191 removed outlier: 3.593A pdb=" N TYR A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 204 Processing helix chain 'A' and resid 209 through 238 removed outlier: 3.643A pdb=" N GLU A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.619A pdb=" N HIS A 247 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 280 removed outlier: 3.638A pdb=" N ARG A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 311 removed outlier: 3.624A pdb=" N ILE A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 330 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'A' and resid 354 through 385 removed outlier: 4.037A pdb=" N VAL A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 424 through 435 Processing helix chain 'A' and resid 435 through 452 removed outlier: 3.527A pdb=" N ALA A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix Processing helix chain 'A' and resid 489 through 501 removed outlier: 4.558A pdb=" N PHE A 493 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 526 removed outlier: 3.973A pdb=" N ASP A 511 " --> pdb=" O ASP A 507 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 522 " --> pdb=" O GLN A 518 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 526 " --> pdb=" O LEU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 554 removed outlier: 3.508A pdb=" N VAL A 542 " --> pdb=" O ILE A 538 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 591 removed outlier: 3.520A pdb=" N GLY A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 582 " --> pdb=" O TRP A 578 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 605 removed outlier: 4.334A pdb=" N THR A 604 " --> pdb=" O GLU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 634 removed outlier: 3.654A pdb=" N LYS A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 658 Processing helix chain 'A' and resid 701 through 706 Processing helix chain 'A' and resid 711 through 726 removed outlier: 3.932A pdb=" N SER A 715 " --> pdb=" O GLY A 711 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 48 through 52 removed outlier: 3.551A pdb=" N TYR B 18 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL B 19 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE B 139 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG B 21 " --> pdb=" O ASP B 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 504 through 505 removed outlier: 6.619A pdb=" N GLU B 504 " --> pdb=" O LYS B 556 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.551A pdb=" N TYR A 18 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL A 19 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE A 139 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG A 21 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 504 through 505 removed outlier: 6.619A pdb=" N GLU A 504 " --> pdb=" O LYS A 556 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 644 hydrogen bonds defined for protein. 1884 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: 1.12 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 12 1.03 - 1.22: 43 1.22 - 1.42: 4415 1.42 - 1.61: 6086 1.61 - 1.81: 72 Bond restraints: 10628 Sorted by residual: bond pdb=" C1 PGW A1508 " pdb=" O01 PGW A1508 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C1 PGW B 807 " pdb=" O01 PGW B 807 " ideal model delta sigma weight residual 1.332 1.421 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C1 PGW A1504 " pdb=" O01 PGW A1504 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C1 PGW B 803 " pdb=" O01 PGW B 803 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C1 PGW B 805 " pdb=" O01 PGW B 805 " ideal model delta sigma weight residual 1.332 1.419 -0.087 2.00e-02 2.50e+03 1.90e+01 ... (remaining 10623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 13743 2.24 - 4.48: 449 4.48 - 6.72: 109 6.72 - 8.96: 23 8.96 - 11.20: 26 Bond angle restraints: 14350 Sorted by residual: angle pdb=" N ASN A 593 " pdb=" CA ASN A 593 " pdb=" C ASN A 593 " ideal model delta sigma weight residual 113.41 108.17 5.24 1.22e+00 6.72e-01 1.84e+01 angle pdb=" N ASN B 593 " pdb=" CA ASN B 593 " pdb=" C ASN B 593 " ideal model delta sigma weight residual 113.41 108.18 5.23 1.22e+00 6.72e-01 1.84e+01 angle pdb=" C2 PGW B 805 " pdb=" C1 PGW B 805 " pdb=" O01 PGW B 805 " ideal model delta sigma weight residual 110.92 122.12 -11.20 3.00e+00 1.11e-01 1.39e+01 angle pdb=" O11 PGW B 805 " pdb=" P PGW B 805 " pdb=" O12 PGW B 805 " ideal model delta sigma weight residual 98.90 110.10 -11.20 3.00e+00 1.11e-01 1.39e+01 angle pdb=" C2 PGW A1506 " pdb=" C1 PGW A1506 " pdb=" O01 PGW A1506 " ideal model delta sigma weight residual 110.92 122.12 -11.20 3.00e+00 1.11e-01 1.39e+01 ... (remaining 14345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.61: 5918 27.61 - 55.22: 282 55.22 - 82.82: 58 82.82 - 110.43: 2 110.43 - 138.04: 2 Dihedral angle restraints: 6262 sinusoidal: 2640 harmonic: 3622 Sorted by residual: dihedral pdb=" CA ALA B 389 " pdb=" C ALA B 389 " pdb=" N SER B 390 " pdb=" CA SER B 390 " ideal model delta harmonic sigma weight residual 180.00 155.53 24.47 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA ALA A 389 " pdb=" C ALA A 389 " pdb=" N SER A 390 " pdb=" CA SER A 390 " ideal model delta harmonic sigma weight residual 180.00 155.56 24.44 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" C15 PGW A1507 " pdb=" C16 PGW A1507 " pdb=" C17 PGW A1507 " pdb=" C18 PGW A1507 " ideal model delta sinusoidal sigma weight residual 178.71 -43.25 -138.04 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 6259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1038 0.048 - 0.095: 445 0.095 - 0.143: 70 0.143 - 0.190: 13 0.190 - 0.238: 4 Chirality restraints: 1570 Sorted by residual: chirality pdb=" CA VAL B 136 " pdb=" N VAL B 136 " pdb=" C VAL B 136 " pdb=" CB VAL B 136 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA VAL A 136 " pdb=" N VAL A 136 " pdb=" C VAL A 136 " pdb=" CB VAL A 136 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C02 PGW B 808 " pdb=" C01 PGW B 808 " pdb=" C03 PGW B 808 " pdb=" O01 PGW B 808 " both_signs ideal model delta sigma weight residual False 2.36 2.55 -0.19 2.00e-01 2.50e+01 9.29e-01 ... (remaining 1567 not shown) Planarity restraints: 1768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 155 " -0.025 2.00e-02 2.50e+03 1.88e-02 8.85e+00 pdb=" CG TRP A 155 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 155 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 155 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 155 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 155 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 155 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 155 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 155 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 155 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 155 " 0.025 2.00e-02 2.50e+03 1.88e-02 8.80e+00 pdb=" CG TRP B 155 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 155 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 155 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 155 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 155 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 155 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 155 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 155 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 155 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 526 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.54e+00 pdb=" N PRO B 527 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " -0.033 5.00e-02 4.00e+02 ... (remaining 1765 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.30: 16 2.30 - 2.87: 3794 2.87 - 3.45: 11620 3.45 - 4.02: 20470 4.02 - 4.60: 31098 Nonbonded interactions: 66998 Sorted by model distance: nonbonded pdb=" O PHE B 173 " pdb=" H1 HOH B2301 " model vdw 1.724 2.450 nonbonded pdb=" O PHE A 173 " pdb=" H1 HOH A2301 " model vdw 1.724 2.450 nonbonded pdb=" O PRO A 558 " pdb=" H2 HOH A2302 " model vdw 1.769 2.450 nonbonded pdb=" O PRO B 558 " pdb=" H2 HOH B2302 " model vdw 1.769 2.450 nonbonded pdb=" OH TYR A 312 " pdb=" O PRO A 315 " model vdw 2.196 2.800 ... (remaining 66993 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 727 or resid 1502 or (resid 1504 and (name C01 \ or name C02 or name C03 or name C1 or name C19 or name C2 or name C20 or name C2 \ 1 or name C22 or name C23 or name C24 or name C25 or name C26 or name C3 or name \ C4 or name C5 or name C6 or name C7 or name C8 or name O01 or name O02 or name \ O03 or name O04 or name O11)) or (resid 1505 and (name C01 or name C02 or name C \ 03 or name C1 or name C19 or name C2 or name C20 or name C21 or name C22 or name \ C23 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name O \ 01 or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or na \ me O14 or name P )) or resid 1506 or (resid 1507 and (name C01 or name C02 or na \ me C03 or name C06 or name C19 or name C2 or name C20 or name C21 or name C22 or \ name C23 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name O01 or name O02 or name O03 or name O04 or name O11 or name O12 o \ r name O13 or name O14 or name P )) or resid 1508 or (resid 1509 and (name C01 o \ r name C02 or name C03 or name C1 or name C19 or name C2 or name C20 or name C21 \ or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or \ name O01 or name O02 or name O03 or name O04 or name O11 or name O12 or name O1 \ 3 or name O14 or name P )))) selection = (chain 'B' and (resid 11 through 727 or resid 802 or (resid 804 and (name C01 or \ name C02 or name C03 or name C1 or name C19 or name C2 or name C20 or name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name O01 or name O02 or name O0 \ 3 or name O04 or name O11)) or (resid 805 and (name C01 or name C02 or name C03 \ or name C1 or name C19 or name C2 or name C20 or name C21 or name C22 or name C2 \ 3 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name O01 \ or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or name \ O14 or name P )) or (resid 806 and (name C01 or name C02 or name C03 or name C1 \ or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C \ 3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O01 \ or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or name \ O14 or name P )) or (resid 807 and (name C01 or name C02 or name C03 or name C06 \ or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name \ C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O01 \ or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or name \ O14 or name P )) or resid 808 through 809)) } 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: 3.610 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: 0.060 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.010 Process input model: 7.640 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 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:5.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 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 : 0.010 0.090 10616 Z= 0.443 Angle : 1.079 11.200 14344 Z= 0.509 Chirality : 0.052 0.238 1570 Planarity : 0.005 0.059 1768 Dihedral : 16.125 138.040 3910 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.19 % Allowed : 4.73 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.48 (0.19), residues: 1210 helix: -2.88 (0.12), residues: 810 sheet: -0.67 (0.86), residues: 44 loop : -2.97 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 170 TYR 0.014 0.003 TYR A 352 PHE 0.017 0.002 PHE B 61 TRP 0.050 0.003 TRP A 155 HIS 0.006 0.002 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00960 / 0.44 (10616) covalent geometry : angle 1.07907 / 0.51 (14344) hydrogen bonds : bond 0.26029 / 17.15 ( 644) hydrogen bonds : angle 9.70080 / 7.03 ( 1884) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 148 time to evaluate : 0.338 Fit side-chains REVERT: B 74 ARG cc_start: 0.7520 (tpp-160) cc_final: 0.7310 (ttm-80) REVERT: B 95 PRO cc_start: 0.8153 (Cg_endo) cc_final: 0.7886 (Cg_exo) REVERT: B 192 MET cc_start: 0.8460 (mtt) cc_final: 0.8117 (mtp) REVERT: B 257 LYS cc_start: 0.6986 (mtpt) cc_final: 0.6622 (mmmm) REVERT: B 289 LEU cc_start: 0.8441 (tt) cc_final: 0.8118 (tt) REVERT: B 626 TYR cc_start: 0.8186 (t80) cc_final: 0.7915 (t80) REVERT: B 641 ARG cc_start: 0.7525 (ttp80) cc_final: 0.7196 (ttp80) REVERT: B 647 ARG cc_start: 0.8051 (ttp80) cc_final: 0.7834 (ttm110) REVERT: B 704 ARG cc_start: 0.7062 (ttm170) cc_final: 0.6820 (mtm-85) REVERT: B 708 ARG cc_start: 0.7018 (tpp-160) cc_final: 0.6702 (ttm-80) REVERT: B 725 LYS cc_start: 0.7818 (tmtt) cc_final: 0.7615 (tmtp) REVERT: A 192 MET cc_start: 0.8484 (mtt) cc_final: 0.8135 (mtp) REVERT: A 257 LYS cc_start: 0.7000 (mtpt) cc_final: 0.6728 (mmmm) REVERT: A 258 GLU cc_start: 0.7438 (tp30) cc_final: 0.7224 (tp30) REVERT: A 289 LEU cc_start: 0.8418 (tt) cc_final: 0.8162 (tt) REVERT: A 626 TYR cc_start: 0.8312 (t80) cc_final: 0.8005 (t80) REVERT: A 641 ARG cc_start: 0.7572 (ttp80) cc_final: 0.7117 (ttp80) REVERT: A 704 ARG cc_start: 0.7030 (ttm170) cc_final: 0.6825 (mtm-85) outliers start: 2 outliers final: 0 residues processed: 150 average time/residue: 0.5877 time to fit residues: 93.6728 Evaluate side-chains 114 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 102 GLN B 148 ASN B 150 GLN B 370 ASN B 499 ASN B 539 ASN B 639 ASN A 102 GLN A 148 ASN A 150 GLN A 370 ASN A 499 ASN A 639 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.101707 restraints weight = 11679.597| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.55 r_work: 0.2951 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10616 Z= 0.122 Angle : 0.519 5.716 14344 Z= 0.286 Chirality : 0.040 0.148 1570 Planarity : 0.005 0.045 1768 Dihedral : 13.421 92.978 1598 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.42 % Allowed : 11.25 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.23), residues: 1210 helix: 0.36 (0.17), residues: 834 sheet: -0.73 (0.80), residues: 44 loop : -2.36 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 170 TYR 0.011 0.001 TYR B 180 PHE 0.011 0.001 PHE A 61 TRP 0.020 0.002 TRP B 155 HIS 0.003 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (10616) covalent geometry : angle 0.51870 / 0.29 (14344) hydrogen bonds : bond 0.05073 / 3.31 ( 644) hydrogen bonds : angle 4.58548 / 3.23 ( 1884) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.236 Fit side-chains REVERT: B 74 ARG cc_start: 0.8037 (tpp-160) cc_final: 0.7772 (ttm-80) REVERT: B 626 TYR cc_start: 0.8627 (t80) cc_final: 0.8310 (t80) REVERT: B 641 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7420 (ttp80) REVERT: B 642 ARG cc_start: 0.7603 (ttp-170) cc_final: 0.7390 (ttm170) REVERT: B 647 ARG cc_start: 0.8204 (ttp80) cc_final: 0.7866 (ttm110) REVERT: B 704 ARG cc_start: 0.7387 (ttm170) cc_final: 0.6801 (mtt-85) REVERT: B 707 MET cc_start: 0.7988 (mmt) cc_final: 0.7500 (mpt) REVERT: B 708 ARG cc_start: 0.7356 (tpp-160) cc_final: 0.6943 (ttm-80) REVERT: B 725 LYS cc_start: 0.7630 (tmtt) cc_final: 0.7356 (tmtp) REVERT: A 200 SER cc_start: 0.8211 (m) cc_final: 0.7986 (m) REVERT: A 257 LYS cc_start: 0.7017 (mtpt) cc_final: 0.6786 (mmmm) REVERT: A 438 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.6318 (mp10) REVERT: A 626 TYR cc_start: 0.8696 (t80) cc_final: 0.8396 (t80) REVERT: A 641 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7275 (ttp80) REVERT: A 704 ARG cc_start: 0.7345 (ttm170) cc_final: 0.6972 (mtm-85) REVERT: A 708 ARG cc_start: 0.7514 (tpp-160) cc_final: 0.7242 (ttm-80) outliers start: 15 outliers final: 8 residues processed: 133 average time/residue: 0.5029 time to fit residues: 71.7135 Evaluate side-chains 117 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 720 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 28 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.128254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.097974 restraints weight = 11704.702| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.55 r_work: 0.2868 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 10616 Z= 0.304 Angle : 0.690 10.541 14344 Z= 0.367 Chirality : 0.049 0.199 1570 Planarity : 0.005 0.042 1768 Dihedral : 13.050 79.943 1598 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.21 % Allowed : 12.29 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.24), residues: 1210 helix: 1.15 (0.17), residues: 828 sheet: -0.88 (0.72), residues: 48 loop : -2.42 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 170 TYR 0.018 0.003 TYR A 212 PHE 0.026 0.002 PHE B 61 TRP 0.022 0.003 TRP B 155 HIS 0.009 0.002 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.30 (10616) covalent geometry : angle 0.69022 / 0.37 (14344) hydrogen bonds : bond 0.06280 / 4.12 ( 644) hydrogen bonds : angle 4.57302 / 3.18 ( 1884) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.348 Fit side-chains REVERT: B 74 ARG cc_start: 0.8065 (tpp-160) cc_final: 0.7779 (ttm-80) REVERT: B 89 ARG cc_start: 0.8123 (mtp85) cc_final: 0.7908 (ttt90) REVERT: B 129 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6774 (ptt180) REVERT: B 289 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8276 (tp) REVERT: B 438 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.6060 (mp10) REVERT: B 641 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7628 (ttt90) REVERT: B 647 ARG cc_start: 0.8423 (ttp80) cc_final: 0.7956 (ttm110) REVERT: B 704 ARG cc_start: 0.7478 (ttm170) cc_final: 0.6672 (mtt-85) REVERT: B 708 ARG cc_start: 0.7372 (tpp-160) cc_final: 0.6974 (ttm-80) REVERT: A 257 LYS cc_start: 0.7156 (mtpt) cc_final: 0.6856 (mmmm) REVERT: A 289 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8288 (tp) REVERT: A 438 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.6043 (mp10) REVERT: A 641 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7544 (ttt90) REVERT: A 704 ARG cc_start: 0.7263 (ttm170) cc_final: 0.6458 (mtt-85) REVERT: A 707 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7806 (mtt) REVERT: A 708 ARG cc_start: 0.7414 (tpp-160) cc_final: 0.7098 (ttm-80) outliers start: 34 outliers final: 23 residues processed: 126 average time/residue: 0.5624 time to fit residues: 75.6810 Evaluate side-chains 135 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 720 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.132951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.102765 restraints weight = 11598.934| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.55 r_work: 0.2934 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10616 Z= 0.121 Angle : 0.470 6.450 14344 Z= 0.258 Chirality : 0.039 0.146 1570 Planarity : 0.003 0.037 1768 Dihedral : 11.903 79.188 1598 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.27 % Allowed : 14.08 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.26), residues: 1210 helix: 1.94 (0.18), residues: 840 sheet: -0.72 (0.74), residues: 48 loop : -2.18 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 21 TYR 0.010 0.001 TYR B 180 PHE 0.015 0.001 PHE A 61 TRP 0.016 0.002 TRP A 155 HIS 0.004 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (10616) covalent geometry : angle 0.47023 / 0.26 (14344) hydrogen bonds : bond 0.04538 / 2.97 ( 644) hydrogen bonds : angle 4.12486 / 2.88 ( 1884) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.413 Fit side-chains REVERT: B 74 ARG cc_start: 0.7947 (tpp-160) cc_final: 0.7708 (ttm-80) REVERT: B 289 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8322 (tp) REVERT: B 438 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.6014 (mp10) REVERT: B 641 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7496 (ttt90) REVERT: B 647 ARG cc_start: 0.8313 (ttp80) cc_final: 0.7921 (ttm110) REVERT: B 704 ARG cc_start: 0.7461 (ttm170) cc_final: 0.6703 (mtt-85) REVERT: B 708 ARG cc_start: 0.7381 (tpp-160) cc_final: 0.7064 (ttm-80) REVERT: A 200 SER cc_start: 0.8196 (m) cc_final: 0.7976 (m) REVERT: A 257 LYS cc_start: 0.7166 (mtpt) cc_final: 0.6884 (mmmm) REVERT: A 641 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7468 (ttt90) REVERT: A 704 ARG cc_start: 0.7278 (ttm170) cc_final: 0.6923 (mtm-85) REVERT: A 708 ARG cc_start: 0.7482 (tpp-160) cc_final: 0.7229 (ttm-80) outliers start: 24 outliers final: 13 residues processed: 130 average time/residue: 0.5691 time to fit residues: 78.9097 Evaluate side-chains 126 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 117 optimal weight: 0.4980 chunk 114 optimal weight: 0.0070 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 30 optimal weight: 0.0020 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 overall best weight: 0.4206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 283 GLN B 355 GLN ** B 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN A 283 GLN ** A 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.135073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.104068 restraints weight = 11701.653| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.60 r_work: 0.2990 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10616 Z= 0.083 Angle : 0.398 4.822 14344 Z= 0.218 Chirality : 0.037 0.132 1570 Planarity : 0.003 0.033 1768 Dihedral : 10.593 77.175 1598 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.42 % Allowed : 16.26 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.26), residues: 1210 helix: 2.60 (0.18), residues: 830 sheet: -0.33 (0.72), residues: 48 loop : -2.15 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 651 TYR 0.009 0.001 TYR A 180 PHE 0.013 0.001 PHE A 61 TRP 0.015 0.001 TRP A 155 HIS 0.003 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00171 / 0.08 (10616) covalent geometry : angle 0.39785 / 0.22 (14344) hydrogen bonds : bond 0.03615 / 2.37 ( 644) hydrogen bonds : angle 3.75749 / 2.61 ( 1884) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.396 Fit side-chains REVERT: B 74 ARG cc_start: 0.7893 (tpp-160) cc_final: 0.7675 (ttm-80) REVERT: B 94 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7424 (mt-10) REVERT: B 150 GLN cc_start: 0.7798 (tt0) cc_final: 0.7154 (tm-30) REVERT: B 257 LYS cc_start: 0.7096 (mtpp) cc_final: 0.6427 (mptt) REVERT: B 641 ARG cc_start: 0.7931 (ttp80) cc_final: 0.7498 (ttt90) REVERT: B 647 ARG cc_start: 0.8220 (ttp80) cc_final: 0.7844 (ttm110) REVERT: B 704 ARG cc_start: 0.7434 (ttm170) cc_final: 0.6663 (mtt-85) REVERT: A 129 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.6630 (ptm160) REVERT: A 150 GLN cc_start: 0.7810 (tt0) cc_final: 0.7173 (tm-30) REVERT: A 200 SER cc_start: 0.8200 (m) cc_final: 0.7991 (m) REVERT: A 641 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7532 (ttp80) REVERT: A 704 ARG cc_start: 0.7263 (ttm170) cc_final: 0.6919 (mtm-85) outliers start: 15 outliers final: 9 residues processed: 133 average time/residue: 0.5043 time to fit residues: 71.9385 Evaluate side-chains 127 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 16 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 0.0870 chunk 103 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.127539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.097145 restraints weight = 11856.329| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.55 r_work: 0.2871 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10616 Z= 0.229 Angle : 0.578 7.907 14344 Z= 0.310 Chirality : 0.045 0.157 1570 Planarity : 0.004 0.033 1768 Dihedral : 11.472 77.568 1598 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.40 % Allowed : 15.50 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.25), residues: 1210 helix: 2.26 (0.18), residues: 834 sheet: -0.39 (0.73), residues: 48 loop : -2.16 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 21 TYR 0.016 0.002 TYR B 212 PHE 0.023 0.002 PHE A 61 TRP 0.016 0.002 TRP A 227 HIS 0.008 0.002 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (10616) covalent geometry : angle 0.57789 / 0.31 (14344) hydrogen bonds : bond 0.05414 / 3.55 ( 644) hydrogen bonds : angle 4.17071 / 2.90 ( 1884) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.350 Fit side-chains REVERT: B 74 ARG cc_start: 0.8010 (tpp-160) cc_final: 0.7778 (ttm-80) REVERT: B 257 LYS cc_start: 0.7048 (mtpp) cc_final: 0.6353 (mptt) REVERT: B 438 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.5982 (mp10) REVERT: B 641 ARG cc_start: 0.8042 (ttp80) cc_final: 0.7658 (ttt90) REVERT: B 647 ARG cc_start: 0.8365 (ttp80) cc_final: 0.7936 (ttm110) REVERT: B 704 ARG cc_start: 0.7434 (ttm170) cc_final: 0.6663 (mtt-85) REVERT: A 438 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.5857 (mp10) REVERT: A 452 LYS cc_start: 0.5907 (OUTLIER) cc_final: 0.5306 (tttm) REVERT: A 641 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7612 (ttt90) REVERT: A 704 ARG cc_start: 0.7264 (ttm170) cc_final: 0.6943 (mtm-85) outliers start: 36 outliers final: 27 residues processed: 133 average time/residue: 0.5970 time to fit residues: 84.7941 Evaluate side-chains 140 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 725 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 55 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.130122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.100003 restraints weight = 11571.225| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.54 r_work: 0.2901 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10616 Z= 0.153 Angle : 0.490 6.575 14344 Z= 0.267 Chirality : 0.041 0.149 1570 Planarity : 0.003 0.033 1768 Dihedral : 11.179 77.119 1598 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.93 % Allowed : 16.45 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.26), residues: 1210 helix: 2.34 (0.18), residues: 838 sheet: -0.35 (0.76), residues: 48 loop : -2.18 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 21 TYR 0.011 0.002 TYR A 212 PHE 0.017 0.001 PHE A 61 TRP 0.015 0.002 TRP A 227 HIS 0.004 0.001 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (10616) covalent geometry : angle 0.49045 / 0.27 (14344) hydrogen bonds : bond 0.04759 / 3.12 ( 644) hydrogen bonds : angle 4.04692 / 2.81 ( 1884) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.259 Fit side-chains REVERT: B 74 ARG cc_start: 0.7958 (tpp-160) cc_final: 0.7742 (ttm-80) REVERT: B 391 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7577 (mmt-90) REVERT: B 641 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7532 (ttt90) REVERT: B 647 ARG cc_start: 0.8327 (ttp80) cc_final: 0.7935 (ttm110) REVERT: B 704 ARG cc_start: 0.7430 (ttm170) cc_final: 0.6660 (mtt-85) REVERT: A 94 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7524 (mm-30) REVERT: A 150 GLN cc_start: 0.7817 (tt0) cc_final: 0.7215 (tp40) REVERT: A 641 ARG cc_start: 0.7974 (ttp80) cc_final: 0.7512 (ttt90) REVERT: A 704 ARG cc_start: 0.7259 (ttm170) cc_final: 0.6937 (mtm-85) outliers start: 31 outliers final: 21 residues processed: 130 average time/residue: 0.5335 time to fit residues: 74.5372 Evaluate side-chains 133 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 391 ARG Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 725 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 111 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS B 595 HIS ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN A 595 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.127797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.097739 restraints weight = 11689.943| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.53 r_work: 0.2871 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10616 Z= 0.269 Angle : 0.623 8.830 14344 Z= 0.333 Chirality : 0.047 0.171 1570 Planarity : 0.004 0.035 1768 Dihedral : 12.016 78.173 1598 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.21 % Allowed : 16.45 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.25), residues: 1210 helix: 1.96 (0.18), residues: 830 sheet: -0.14 (0.79), residues: 48 loop : -2.37 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 237 TYR 0.018 0.002 TYR A 432 PHE 0.026 0.002 PHE B 61 TRP 0.016 0.002 TRP A 227 HIS 0.008 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.27 (10616) covalent geometry : angle 0.62278 / 0.33 (14344) hydrogen bonds : bond 0.05780 / 3.80 ( 644) hydrogen bonds : angle 4.32500 / 3.00 ( 1884) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.342 Fit side-chains REVERT: B 74 ARG cc_start: 0.8006 (tpp-160) cc_final: 0.7773 (ttm-80) REVERT: B 94 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7529 (mm-30) REVERT: B 257 LYS cc_start: 0.6962 (mtpp) cc_final: 0.6272 (mptt) REVERT: B 641 ARG cc_start: 0.8059 (ttp80) cc_final: 0.7695 (ttt90) REVERT: B 647 ARG cc_start: 0.8375 (ttp80) cc_final: 0.7978 (ttm110) REVERT: B 704 ARG cc_start: 0.7426 (ttm170) cc_final: 0.6655 (mtt-85) REVERT: A 94 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7523 (mm-30) REVERT: A 257 LYS cc_start: 0.7042 (mtpt) cc_final: 0.6534 (mptt) REVERT: A 452 LYS cc_start: 0.5844 (OUTLIER) cc_final: 0.5307 (tttm) REVERT: A 641 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7661 (ttt90) REVERT: A 704 ARG cc_start: 0.7291 (ttm170) cc_final: 0.6526 (mtt-85) outliers start: 34 outliers final: 26 residues processed: 132 average time/residue: 0.5300 time to fit residues: 74.9797 Evaluate side-chains 134 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 725 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.130544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.100637 restraints weight = 11550.693| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.53 r_work: 0.2898 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10616 Z= 0.152 Angle : 0.495 6.473 14344 Z= 0.270 Chirality : 0.041 0.152 1570 Planarity : 0.004 0.035 1768 Dihedral : 11.469 78.068 1598 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.65 % Allowed : 17.11 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.26), residues: 1210 helix: 2.27 (0.18), residues: 836 sheet: -0.12 (0.81), residues: 48 loop : -2.23 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 21 TYR 0.012 0.001 TYR A 432 PHE 0.017 0.001 PHE A 61 TRP 0.017 0.002 TRP A 227 HIS 0.004 0.001 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (10616) covalent geometry : angle 0.49505 / 0.27 (14344) hydrogen bonds : bond 0.04793 / 3.14 ( 644) hydrogen bonds : angle 4.11409 / 2.86 ( 1884) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.252 Fit side-chains REVERT: B 74 ARG cc_start: 0.7965 (tpp-160) cc_final: 0.7746 (ttm-80) REVERT: B 94 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7536 (mm-30) REVERT: B 150 GLN cc_start: 0.7751 (tt0) cc_final: 0.7177 (tm-30) REVERT: B 641 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7549 (ttt90) REVERT: B 647 ARG cc_start: 0.8315 (ttp80) cc_final: 0.7948 (ttm110) REVERT: B 704 ARG cc_start: 0.7400 (ttm170) cc_final: 0.6626 (mtt-85) REVERT: A 94 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7499 (mm-30) REVERT: A 150 GLN cc_start: 0.7762 (tt0) cc_final: 0.7147 (tm-30) REVERT: A 452 LYS cc_start: 0.5910 (OUTLIER) cc_final: 0.5362 (tttm) REVERT: A 641 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7514 (ttt90) REVERT: A 704 ARG cc_start: 0.7305 (ttm170) cc_final: 0.6527 (mtt-85) outliers start: 28 outliers final: 25 residues processed: 124 average time/residue: 0.5266 time to fit residues: 69.7820 Evaluate side-chains 133 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 725 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 111 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 113 optimal weight: 0.0370 overall best weight: 1.1660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.130880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.100947 restraints weight = 11529.614| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.53 r_work: 0.2921 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10616 Z= 0.126 Angle : 0.457 5.823 14344 Z= 0.250 Chirality : 0.039 0.143 1570 Planarity : 0.003 0.034 1768 Dihedral : 10.987 77.316 1598 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.55 % Allowed : 17.20 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.26), residues: 1210 helix: 2.46 (0.18), residues: 840 sheet: -0.14 (0.80), residues: 48 loop : -2.15 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 708 TYR 0.011 0.001 TYR B 432 PHE 0.015 0.001 PHE A 61 TRP 0.017 0.002 TRP A 227 HIS 0.004 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (10616) covalent geometry : angle 0.45747 / 0.25 (14344) hydrogen bonds : bond 0.04417 / 2.90 ( 644) hydrogen bonds : angle 3.97833 / 2.76 ( 1884) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.248 Fit side-chains REVERT: B 74 ARG cc_start: 0.7934 (tpp-160) cc_final: 0.7721 (ttm-80) REVERT: B 94 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7542 (mm-30) REVERT: B 150 GLN cc_start: 0.7808 (tt0) cc_final: 0.7236 (tm-30) REVERT: B 391 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7516 (mmt-90) REVERT: B 641 ARG cc_start: 0.7973 (ttp80) cc_final: 0.7580 (ttt90) REVERT: B 647 ARG cc_start: 0.8300 (ttp80) cc_final: 0.7920 (ttm110) REVERT: B 704 ARG cc_start: 0.7396 (ttm170) cc_final: 0.7071 (mtm-85) REVERT: A 70 LYS cc_start: 0.8320 (ttpp) cc_final: 0.7456 (mppt) REVERT: A 94 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7527 (mm-30) REVERT: A 150 GLN cc_start: 0.7827 (tt0) cc_final: 0.7225 (tm-30) REVERT: A 452 LYS cc_start: 0.5899 (OUTLIER) cc_final: 0.5361 (tttm) REVERT: A 641 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7502 (ttt90) REVERT: A 704 ARG cc_start: 0.7321 (ttm170) cc_final: 0.7001 (mtm-85) outliers start: 27 outliers final: 21 residues processed: 126 average time/residue: 0.5552 time to fit residues: 74.8081 Evaluate side-chains 132 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 391 ARG Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 725 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 113 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.128919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.098657 restraints weight = 11642.155| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.55 r_work: 0.2894 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10616 Z= 0.150 Angle : 0.486 6.049 14344 Z= 0.264 Chirality : 0.041 0.146 1570 Planarity : 0.003 0.034 1768 Dihedral : 11.049 77.030 1598 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.55 % Allowed : 17.20 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.26), residues: 1210 helix: 2.46 (0.18), residues: 838 sheet: -0.09 (0.80), residues: 48 loop : -2.15 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 708 TYR 0.012 0.001 TYR A 432 PHE 0.016 0.001 PHE B 61 TRP 0.017 0.002 TRP A 227 HIS 0.005 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (10616) covalent geometry : angle 0.48579 / 0.26 (14344) hydrogen bonds : bond 0.04702 / 3.08 ( 644) hydrogen bonds : angle 4.03293 / 2.80 ( 1884) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3066.81 seconds wall clock time: 52 minutes 59.51 seconds (3179.51 seconds total)