Starting phenix.real_space_refine on Wed Mar 4 03:51:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rx2_24722/03_2026/7rx2_24722.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rx2_24722/03_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_24722/03_2026/7rx2_24722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rx2_24722/03_2026/7rx2_24722.map" model { file = "/net/cci-nas-00/data/ceres_data/7rx2_24722/03_2026/7rx2_24722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rx2_24722/03_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-5986/lib/python3.9/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: 161 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: 161 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: 2.38, per 1000 atoms: 0.23 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: 0.88 Conformation dependent library (CDL) restraints added in 569.4 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: 0.19 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: 1.49 Time building geometry restraints manager: 1.16 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: 5968 27.61 - 55.22: 288 55.22 - 82.82: 80 82.82 - 110.43: 14 110.43 - 138.04: 10 Dihedral angle restraints: 6360 sinusoidal: 2738 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 6357 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: 0.02 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: 5.610 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: 0.090 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.520 Find NCS groups from input model: 0.220 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: 0.000 Load rotamer database and sin/cos tables:8.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 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 : 18.455 138.040 4008 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 covalent geometry : bond 0.00960 (10616) covalent geometry : angle 1.07907 (14344) hydrogen bonds : bond 0.26029 ( 644) hydrogen bonds : angle 9.70080 ( 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 : 0.412 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: 0.7490 time to fit residues: 118.7758 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 : 0.289 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 539 ASN A 639 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.132273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.102136 restraints weight = 11649.134| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.54 r_work: 0.2956 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10616 Z= 0.120 Angle : 0.525 5.604 14344 Z= 0.286 Chirality : 0.040 0.147 1570 Planarity : 0.005 0.044 1768 Dihedral : 17.090 105.523 1696 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.51 % Allowed : 11.25 % Favored : 87.24 % 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: -0.62 (0.23), residues: 1210 helix: 0.38 (0.17), residues: 836 sheet: -0.72 (0.80), residues: 44 loop : -2.31 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 170 TYR 0.011 0.001 TYR B 589 PHE 0.011 0.001 PHE A 61 TRP 0.021 0.002 TRP B 155 HIS 0.003 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00244 (10616) covalent geometry : angle 0.52539 (14344) hydrogen bonds : bond 0.04976 ( 644) hydrogen bonds : angle 4.55306 ( 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: 16 poor density : 125 time to evaluate : 0.376 Fit side-chains REVERT: B 74 ARG cc_start: 0.8030 (tpp-160) cc_final: 0.7766 (ttm-80) REVERT: B 599 ASN cc_start: 0.6901 (t0) cc_final: 0.6686 (t0) REVERT: B 641 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7390 (ttp80) REVERT: B 642 ARG cc_start: 0.7601 (ttp-170) cc_final: 0.7388 (ttm170) REVERT: B 647 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7865 (ttm110) REVERT: B 704 ARG cc_start: 0.7393 (ttm170) cc_final: 0.6804 (mtt-85) REVERT: B 708 ARG cc_start: 0.7349 (tpp-160) cc_final: 0.6939 (ttm-80) REVERT: B 725 LYS cc_start: 0.7636 (tmtt) cc_final: 0.7365 (tmtp) REVERT: A 200 SER cc_start: 0.8183 (m) cc_final: 0.7946 (m) REVERT: A 257 LYS cc_start: 0.7023 (mtpt) cc_final: 0.6797 (mmmm) REVERT: A 438 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.6312 (mp10) REVERT: A 626 TYR cc_start: 0.8708 (t80) cc_final: 0.8410 (t80) REVERT: A 641 ARG cc_start: 0.7875 (ttp80) cc_final: 0.7263 (ttp80) REVERT: A 704 ARG cc_start: 0.7354 (ttm170) cc_final: 0.6984 (mtm-85) REVERT: A 708 ARG cc_start: 0.7534 (tpp-160) cc_final: 0.7270 (ttm-80) outliers start: 16 outliers final: 8 residues processed: 133 average time/residue: 0.6546 time to fit residues: 92.7602 Evaluate side-chains 115 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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: 9.9990 chunk 11 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.126935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.095173 restraints weight = 11711.728| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.61 r_work: 0.2854 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 10616 Z= 0.297 Angle : 0.681 10.297 14344 Z= 0.362 Chirality : 0.049 0.196 1570 Planarity : 0.005 0.041 1768 Dihedral : 16.858 105.763 1696 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.12 % Allowed : 12.29 % Favored : 84.59 % 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: 0.19 (0.24), residues: 1210 helix: 1.16 (0.17), residues: 830 sheet: -0.85 (0.72), residues: 48 loop : -2.41 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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 0.008 0.002 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00699 (10616) covalent geometry : angle 0.68081 (14344) hydrogen bonds : bond 0.06253 ( 644) hydrogen bonds : angle 4.55812 ( 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 145 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.416 Fit side-chains REVERT: B 74 ARG cc_start: 0.8073 (tpp-160) cc_final: 0.7792 (ttm-80) REVERT: B 89 ARG cc_start: 0.8124 (mtp85) cc_final: 0.7909 (ttt90) REVERT: B 129 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6783 (ptt180) REVERT: B 289 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8287 (tp) REVERT: B 438 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.6078 (mp10) REVERT: B 641 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7637 (ttt90) REVERT: B 647 ARG cc_start: 0.8427 (ttp80) cc_final: 0.7954 (ttm110) REVERT: B 704 ARG cc_start: 0.7470 (ttm170) cc_final: 0.6657 (mtt-85) REVERT: B 708 ARG cc_start: 0.7379 (tpp-160) cc_final: 0.7074 (ttm-80) REVERT: B 725 LYS cc_start: 0.7812 (tmtt) cc_final: 0.7598 (tmtp) REVERT: A 257 LYS cc_start: 0.7155 (mtpt) cc_final: 0.6852 (mmmm) REVERT: A 289 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8291 (tp) REVERT: A 438 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.6027 (mp10) REVERT: A 641 ARG cc_start: 0.7997 (ttp80) cc_final: 0.7540 (ttt90) REVERT: A 704 ARG cc_start: 0.7275 (ttm170) cc_final: 0.6470 (mtt-85) REVERT: A 707 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7801 (mtt) REVERT: A 708 ARG cc_start: 0.7417 (tpp-160) cc_final: 0.7105 (ttm-80) outliers start: 33 outliers final: 24 residues processed: 126 average time/residue: 0.7416 time to fit residues: 99.0578 Evaluate side-chains 135 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 41 LEU 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: 9.9990 chunk 108 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.131996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.100447 restraints weight = 11602.157| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.61 r_work: 0.2927 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10616 Z= 0.112 Angle : 0.456 5.896 14344 Z= 0.249 Chirality : 0.039 0.143 1570 Planarity : 0.003 0.036 1768 Dihedral : 15.083 95.277 1696 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.80 % Allowed : 14.27 % Favored : 83.93 % 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: 1.31 (0.26), residues: 1210 helix: 2.03 (0.18), residues: 840 sheet: -0.70 (0.74), residues: 48 loop : -2.15 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 651 TYR 0.010 0.001 TYR A 180 PHE 0.014 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 covalent geometry : bond 0.00236 (10616) covalent geometry : angle 0.45586 (14344) hydrogen bonds : bond 0.04354 ( 644) hydrogen bonds : angle 4.07137 ( 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 141 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.434 Fit side-chains REVERT: B 74 ARG cc_start: 0.7931 (tpp-160) cc_final: 0.7704 (ttm-80) REVERT: B 150 GLN cc_start: 0.7877 (tt0) cc_final: 0.7234 (tp40) REVERT: B 257 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6619 (mptt) REVERT: B 641 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7439 (ttt90) REVERT: B 647 ARG cc_start: 0.8294 (ttp80) cc_final: 0.7899 (ttm110) REVERT: B 704 ARG cc_start: 0.7441 (ttm170) cc_final: 0.6681 (mtt-85) REVERT: B 708 ARG cc_start: 0.7457 (tpp-160) cc_final: 0.7134 (ttm-80) REVERT: A 257 LYS cc_start: 0.7121 (mtpt) cc_final: 0.6830 (mmmm) REVERT: A 641 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7518 (ttp80) REVERT: A 704 ARG cc_start: 0.7293 (ttm170) cc_final: 0.6936 (mtm-85) REVERT: A 708 ARG cc_start: 0.7499 (tpp-160) cc_final: 0.7260 (ttm-80) outliers start: 19 outliers final: 10 residues processed: 129 average time/residue: 0.7129 time to fit residues: 97.7746 Evaluate side-chains 124 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 257 LYS 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 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 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: 4.9990 chunk 114 optimal weight: 0.2980 chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 595 HIS ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.098127 restraints weight = 11577.724| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.53 r_work: 0.2871 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10616 Z= 0.232 Angle : 0.599 9.232 14344 Z= 0.320 Chirality : 0.046 0.169 1570 Planarity : 0.004 0.036 1768 Dihedral : 15.531 97.520 1696 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.21 % Allowed : 14.93 % Favored : 81.85 % 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: 1.10 (0.25), residues: 1210 helix: 1.92 (0.18), residues: 832 sheet: -0.62 (0.74), residues: 48 loop : -2.31 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 21 TYR 0.016 0.002 TYR B 212 PHE 0.023 0.002 PHE B 61 TRP 0.018 0.002 TRP A 227 HIS 0.007 0.001 HIS B 619 Details of bonding type rmsd covalent geometry : bond 0.00542 (10616) covalent geometry : angle 0.59880 (14344) hydrogen bonds : bond 0.05581 ( 644) hydrogen bonds : angle 4.29172 ( 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 141 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.413 Fit side-chains REVERT: B 74 ARG cc_start: 0.8000 (tpp-160) cc_final: 0.7766 (ttm-80) REVERT: B 641 ARG cc_start: 0.8041 (ttp80) cc_final: 0.7656 (ttt90) REVERT: B 647 ARG cc_start: 0.8367 (ttp80) cc_final: 0.7958 (ttm110) REVERT: B 704 ARG cc_start: 0.7467 (ttm170) cc_final: 0.6687 (mtt-85) REVERT: B 707 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7642 (mpp) REVERT: B 708 ARG cc_start: 0.7400 (tpp-160) cc_final: 0.7128 (ttm-80) REVERT: A 438 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.5868 (mp10) REVERT: A 452 LYS cc_start: 0.5880 (OUTLIER) cc_final: 0.5265 (tttm) REVERT: A 641 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7609 (ttt90) REVERT: A 704 ARG cc_start: 0.7297 (ttm170) cc_final: 0.6457 (mtt-85) REVERT: A 708 ARG cc_start: 0.7471 (tpp-160) cc_final: 0.7171 (ttm-80) REVERT: A 725 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7279 (tmtp) outliers start: 34 outliers final: 23 residues processed: 129 average time/residue: 0.7038 time to fit residues: 96.5016 Evaluate side-chains 133 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 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 B residue 707 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.128357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.098111 restraints weight = 11681.980| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.54 r_work: 0.2866 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10616 Z= 0.234 Angle : 0.598 8.984 14344 Z= 0.320 Chirality : 0.046 0.171 1570 Planarity : 0.004 0.037 1768 Dihedral : 15.555 97.869 1696 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.59 % Allowed : 15.50 % Favored : 80.91 % 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: 1.07 (0.25), residues: 1210 helix: 1.89 (0.18), residues: 832 sheet: -0.38 (0.78), residues: 48 loop : -2.33 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 21 TYR 0.015 0.002 TYR A 212 PHE 0.023 0.002 PHE A 61 TRP 0.018 0.002 TRP A 227 HIS 0.007 0.001 HIS B 619 Details of bonding type rmsd covalent geometry : bond 0.00545 (10616) covalent geometry : angle 0.59767 (14344) hydrogen bonds : bond 0.05535 ( 644) hydrogen bonds : angle 4.32256 ( 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 144 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 0.388 Fit side-chains REVERT: B 74 ARG cc_start: 0.7984 (tpp-160) cc_final: 0.7761 (ttm-80) REVERT: B 257 LYS cc_start: 0.6966 (mtpp) cc_final: 0.6260 (mptt) REVERT: B 641 ARG cc_start: 0.8046 (ttp80) cc_final: 0.7668 (ttt90) REVERT: B 647 ARG cc_start: 0.8365 (ttp80) cc_final: 0.7968 (ttm110) REVERT: B 704 ARG cc_start: 0.7434 (ttm170) cc_final: 0.6654 (mtt-85) REVERT: B 707 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7600 (mpp) REVERT: B 708 ARG cc_start: 0.7425 (tpp-160) cc_final: 0.7143 (ttm-80) REVERT: A 94 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7531 (mm-30) REVERT: A 289 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8283 (tp) REVERT: A 438 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.5869 (mp10) REVERT: A 452 LYS cc_start: 0.5859 (OUTLIER) cc_final: 0.5273 (tttm) REVERT: A 641 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7622 (ttt90) REVERT: A 704 ARG cc_start: 0.7327 (ttm170) cc_final: 0.6497 (mtt-85) REVERT: A 708 ARG cc_start: 0.7408 (tpp-160) cc_final: 0.7102 (ttm-80) REVERT: A 725 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7328 (tmtp) outliers start: 38 outliers final: 21 residues processed: 128 average time/residue: 0.6315 time to fit residues: 86.2511 Evaluate side-chains 132 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 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 393 VAL Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 707 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 289 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE 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 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: 0.7980 chunk 94 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 0.0470 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.2680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.130206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.098735 restraints weight = 11506.021| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.59 r_work: 0.2903 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10616 Z= 0.132 Angle : 0.477 6.492 14344 Z= 0.259 Chirality : 0.040 0.147 1570 Planarity : 0.003 0.035 1768 Dihedral : 14.872 96.339 1696 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.27 % Allowed : 17.20 % Favored : 80.53 % 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: 1.59 (0.26), residues: 1210 helix: 2.28 (0.18), residues: 838 sheet: -0.28 (0.79), residues: 48 loop : -2.21 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 21 TYR 0.009 0.001 TYR A 180 PHE 0.016 0.001 PHE A 61 TRP 0.017 0.002 TRP B 712 HIS 0.004 0.001 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00291 (10616) covalent geometry : angle 0.47714 (14344) hydrogen bonds : bond 0.04586 ( 644) hydrogen bonds : angle 4.07115 ( 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 134 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.398 Fit side-chains REVERT: B 74 ARG cc_start: 0.7961 (tpp-160) cc_final: 0.7743 (ttm-80) REVERT: B 150 GLN cc_start: 0.7767 (tt0) cc_final: 0.7140 (tm-30) REVERT: B 257 LYS cc_start: 0.6990 (mtpp) cc_final: 0.6305 (mptt) REVERT: B 641 ARG cc_start: 0.7977 (ttp80) cc_final: 0.7524 (ttt90) REVERT: B 647 ARG cc_start: 0.8319 (ttp80) cc_final: 0.7930 (ttm110) REVERT: B 704 ARG cc_start: 0.7437 (ttm170) cc_final: 0.7101 (mtm-85) REVERT: B 708 ARG cc_start: 0.7375 (tpp-160) cc_final: 0.7146 (ttm-80) REVERT: A 94 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7512 (mm-30) REVERT: A 150 GLN cc_start: 0.7765 (tt0) cc_final: 0.7126 (tm-30) REVERT: A 641 ARG cc_start: 0.7982 (ttp80) cc_final: 0.7524 (ttt90) REVERT: A 704 ARG cc_start: 0.7362 (ttm170) cc_final: 0.6582 (mtt-85) REVERT: A 708 ARG cc_start: 0.7499 (tpp-160) cc_final: 0.7173 (ttm-80) outliers start: 24 outliers final: 15 residues processed: 126 average time/residue: 0.6514 time to fit residues: 87.5382 Evaluate side-chains 125 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 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 A residue 31 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 111 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 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 = 0.3483 r_free = 0.3483 target = 0.129206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.099026 restraints weight = 11571.052| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.54 r_work: 0.2880 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10616 Z= 0.209 Angle : 0.566 8.325 14344 Z= 0.303 Chirality : 0.044 0.163 1570 Planarity : 0.004 0.035 1768 Dihedral : 15.240 98.182 1696 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.55 % Allowed : 16.92 % Favored : 80.53 % 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: 1.40 (0.25), residues: 1210 helix: 2.16 (0.18), residues: 832 sheet: -0.28 (0.80), residues: 48 loop : -2.27 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 21 TYR 0.014 0.002 TYR B 212 PHE 0.023 0.002 PHE B 61 TRP 0.017 0.002 TRP A 227 HIS 0.006 0.001 HIS B 619 Details of bonding type rmsd covalent geometry : bond 0.00486 (10616) covalent geometry : angle 0.56642 (14344) hydrogen bonds : bond 0.05318 ( 644) hydrogen bonds : angle 4.22397 ( 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 136 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.445 Fit side-chains REVERT: B 74 ARG cc_start: 0.7965 (tpp-160) cc_final: 0.7764 (ttm-80) REVERT: B 94 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7475 (mm-30) REVERT: B 257 LYS cc_start: 0.6974 (mtpp) cc_final: 0.6295 (mptt) REVERT: B 438 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.5849 (mp10) REVERT: B 641 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7623 (ttt90) REVERT: B 647 ARG cc_start: 0.8367 (ttp80) cc_final: 0.7956 (ttm110) REVERT: B 704 ARG cc_start: 0.7433 (ttm170) cc_final: 0.7110 (mtm-85) REVERT: B 708 ARG cc_start: 0.7427 (tpp-160) cc_final: 0.7166 (ttm-80) REVERT: A 94 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7521 (mm-30) REVERT: A 438 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.5879 (mp10) REVERT: A 452 LYS cc_start: 0.5899 (OUTLIER) cc_final: 0.5356 (tttm) REVERT: A 641 ARG cc_start: 0.8000 (ttp80) cc_final: 0.7576 (ttt90) REVERT: A 704 ARG cc_start: 0.7333 (ttm170) cc_final: 0.6586 (mtt-85) REVERT: A 708 ARG cc_start: 0.7437 (tpp-160) cc_final: 0.7092 (ttm-80) outliers start: 27 outliers final: 20 residues processed: 128 average time/residue: 0.6595 time to fit residues: 89.8931 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 : 0.406 ------------------------------------------------------------------------------- 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 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 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 311 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 452 LYS 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: 5.9990 chunk 2 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 120 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3487 r_free = 0.3487 target = 0.129760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.099487 restraints weight = 11528.163| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.54 r_work: 0.2895 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2429 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= 0.147 Angle : 0.494 6.692 14344 Z= 0.267 Chirality : 0.041 0.149 1570 Planarity : 0.003 0.035 1768 Dihedral : 14.892 96.611 1696 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.36 % Allowed : 17.49 % Favored : 80.15 % 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: 1.61 (0.26), residues: 1210 helix: 2.31 (0.18), residues: 838 sheet: -0.25 (0.80), residues: 48 loop : -2.22 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 21 TYR 0.010 0.001 TYR B 212 PHE 0.017 0.001 PHE B 61 TRP 0.017 0.002 TRP B 227 HIS 0.004 0.001 HIS B 619 Details of bonding type rmsd covalent geometry : bond 0.00332 (10616) covalent geometry : angle 0.49393 (14344) hydrogen bonds : bond 0.04737 ( 644) hydrogen bonds : angle 4.09277 ( 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 134 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.459 Fit side-chains REVERT: B 74 ARG cc_start: 0.7953 (tpp-160) cc_final: 0.7751 (ttm-80) REVERT: B 94 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7486 (mm-30) REVERT: B 150 GLN cc_start: 0.7771 (tt0) cc_final: 0.7176 (tm-30) REVERT: B 257 LYS cc_start: 0.6923 (mtpp) cc_final: 0.6252 (mptt) REVERT: B 641 ARG cc_start: 0.7970 (ttp80) cc_final: 0.7529 (ttt90) REVERT: B 647 ARG cc_start: 0.8327 (ttp80) cc_final: 0.7936 (ttm110) REVERT: B 704 ARG cc_start: 0.7408 (ttm170) cc_final: 0.7080 (mtm-85) REVERT: B 708 ARG cc_start: 0.7387 (tpp-160) cc_final: 0.7165 (ttm-80) REVERT: A 70 LYS cc_start: 0.8337 (ttpp) cc_final: 0.7466 (mppt) REVERT: A 94 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7501 (mm-30) REVERT: A 150 GLN cc_start: 0.7779 (tt0) cc_final: 0.7173 (tm-30) REVERT: A 641 ARG cc_start: 0.7961 (ttp80) cc_final: 0.7513 (ttt90) REVERT: A 704 ARG cc_start: 0.7352 (ttm170) cc_final: 0.6599 (mtt-85) REVERT: A 708 ARG cc_start: 0.7498 (tpp-160) cc_final: 0.7170 (ttm-80) outliers start: 25 outliers final: 20 residues processed: 126 average time/residue: 0.7093 time to fit residues: 95.0567 Evaluate side-chains 129 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 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 590 MET Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 311 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 725 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 111 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.131436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.100653 restraints weight = 11477.777| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.57 r_work: 0.2926 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10616 Z= 0.117 Angle : 0.450 5.642 14344 Z= 0.244 Chirality : 0.039 0.139 1570 Planarity : 0.003 0.035 1768 Dihedral : 14.256 94.376 1696 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.08 % Allowed : 17.86 % Favored : 80.06 % 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: 1.86 (0.26), residues: 1210 helix: 2.55 (0.18), residues: 830 sheet: -0.19 (0.79), residues: 48 loop : -2.19 (0.35), residues: 332 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 0.015 0.001 PHE B 61 TRP 0.018 0.002 TRP A 227 HIS 0.004 0.001 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00257 (10616) covalent geometry : angle 0.44994 (14344) hydrogen bonds : bond 0.04273 ( 644) hydrogen bonds : angle 3.94397 ( 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: 22 poor density : 114 time to evaluate : 0.422 Fit side-chains REVERT: B 41 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8105 (tm) REVERT: B 94 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7524 (mm-30) REVERT: B 150 GLN cc_start: 0.7812 (tt0) cc_final: 0.7227 (tm-30) REVERT: B 438 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.5819 (mp10) REVERT: B 641 ARG cc_start: 0.7967 (ttp80) cc_final: 0.7586 (ttt90) REVERT: B 647 ARG cc_start: 0.8300 (ttp80) cc_final: 0.7915 (ttm110) REVERT: B 704 ARG cc_start: 0.7431 (ttm170) cc_final: 0.7116 (mtm-85) REVERT: B 708 ARG cc_start: 0.7452 (tpp-160) cc_final: 0.7078 (ttm-80) REVERT: A 70 LYS cc_start: 0.8322 (ttpp) cc_final: 0.7465 (mppt) REVERT: A 94 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7508 (mm-30) REVERT: A 150 GLN cc_start: 0.7806 (tt0) cc_final: 0.7220 (tm-30) REVERT: A 641 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7584 (ttt90) REVERT: A 704 ARG cc_start: 0.7367 (ttm170) cc_final: 0.6969 (mtm-85) outliers start: 22 outliers final: 18 residues processed: 125 average time/residue: 0.6407 time to fit residues: 85.5903 Evaluate side-chains 132 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 41 LEU 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 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 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 243 VAL Chi-restraints excluded: chain A residue 270 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 113 optimal weight: 0.0050 chunk 26 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 90 optimal weight: 0.0970 chunk 95 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 52 optimal weight: 0.0270 chunk 88 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.3852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN A 355 GLN ** A 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.135710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.104973 restraints weight = 11561.406| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.58 r_work: 0.3006 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10616 Z= 0.080 Angle : 0.393 4.380 14344 Z= 0.213 Chirality : 0.037 0.141 1570 Planarity : 0.003 0.035 1768 Dihedral : 13.150 89.466 1696 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.13 % Allowed : 18.90 % Favored : 79.96 % 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: 2.37 (0.27), residues: 1210 helix: 2.87 (0.19), residues: 838 sheet: -0.02 (0.77), residues: 48 loop : -1.89 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 21 TYR 0.008 0.001 TYR B 180 PHE 0.013 0.001 PHE B 61 TRP 0.018 0.002 TRP A 227 HIS 0.003 0.001 HIS A 619 Details of bonding type rmsd covalent geometry : bond 0.00168 (10616) covalent geometry : angle 0.39253 (14344) hydrogen bonds : bond 0.03483 ( 644) hydrogen bonds : angle 3.70339 ( 1884) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3623.27 seconds wall clock time: 62 minutes 28.07 seconds (3748.07 seconds total)