Starting phenix.real_space_refine on Mon Jul 28 19:39:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rx2_24722/07_2025/7rx2_24722.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rx2_24722/07_2025/7rx2_24722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rx2_24722/07_2025/7rx2_24722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rx2_24722/07_2025/7rx2_24722.map" model { file = "/net/cci-nas-00/data/ceres_data/7rx2_24722/07_2025/7rx2_24722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rx2_24722/07_2025/7rx2_24722.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLU:plan': 8, 'ARG:plan': 3, 'ASP:plan': 2} 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: {'GLU:plan': 8, 'ARG:plan': 3, 'ASP:plan': 2} 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: 7.12, per 1000 atoms: 0.69 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: 2.82 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.07 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: 2.89 Time building geometry restraints manager: 3.20 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: 0.04 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: 4.140 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: 0.260 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.180 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 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:14.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.060 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.050 0.003 TRP A 155 HIS 0.006 0.002 HIS B 619 PHE 0.017 0.002 PHE B 61 TYR 0.014 0.003 TYR A 352 ARG 0.010 0.001 ARG B 170 Details of bonding type rmsd hydrogen bonds : bond 0.26029 ( 644) hydrogen bonds : angle 9.70080 ( 1884) covalent geometry : bond 0.00960 (10616) covalent geometry : angle 1.07907 (14344) *********************** 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 : 1.083 Fit side-chains REVERT: B 74 ARG cc_start: 0.7520 (tpp-160) cc_final: 0.7311 (ttm-80) REVERT: B 192 MET cc_start: 0.8460 (mtt) cc_final: 0.8116 (mtp) REVERT: B 257 LYS cc_start: 0.6986 (mtpt) cc_final: 0.6620 (mmmm) REVERT: B 289 LEU cc_start: 0.8441 (tt) cc_final: 0.8119 (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: 0.7197 (ttp80) REVERT: B 647 ARG cc_start: 0.8051 (ttp80) cc_final: 0.7833 (ttm110) REVERT: B 704 ARG cc_start: 0.7062 (ttm170) cc_final: 0.6819 (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: 0.8136 (mtp) REVERT: A 257 LYS cc_start: 0.7000 (mtpt) cc_final: 0.6727 (mmmm) REVERT: A 258 GLU cc_start: 0.7438 (tp30) cc_final: 0.7223 (tp30) REVERT: A 289 LEU cc_start: 0.8418 (tt) cc_final: 0.8163 (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: 1.5435 time to fit residues: 245.8360 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 : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 GLN B 113 HIS B 148 ASN B 150 GLN B 370 ASN B 499 ASN B 539 ASN B 639 ASN A 102 GLN A 113 HIS A 148 ASN A 150 GLN A 370 ASN A 499 ASN ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.131806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.101610 restraints weight = 11625.055| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.54 r_work: 0.2962 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1746 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= 0.118 Angle : 0.520 5.471 14344 Z= 0.283 Chirality : 0.040 0.148 1570 Planarity : 0.005 0.044 1768 Dihedral : 16.961 104.880 1696 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.32 % Allowed : 11.15 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.23), residues: 1210 helix: 0.39 (0.17), residues: 838 sheet: -0.72 (0.79), residues: 44 loop : -2.28 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 155 HIS 0.003 0.001 HIS A 130 PHE 0.010 0.001 PHE A 61 TYR 0.011 0.001 TYR B 180 ARG 0.004 0.000 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.04904 ( 644) hydrogen bonds : angle 4.51906 ( 1884) covalent geometry : bond 0.00238 (10616) covalent geometry : angle 0.52033 (14344) *********************** 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 142 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 1.064 Fit side-chains REVERT: B 74 ARG cc_start: 0.8022 (tpp-160) cc_final: 0.7759 (ttm-80) REVERT: B 599 ASN cc_start: 0.6885 (t0) cc_final: 0.6670 (t0) REVERT: B 641 ARG cc_start: 0.7910 (ttp80) cc_final: 0.7420 (ttp80) REVERT: B 642 ARG cc_start: 0.7608 (ttp-170) cc_final: 0.7392 (ttm170) REVERT: B 647 ARG cc_start: 0.8184 (ttp80) cc_final: 0.7856 (ttm110) REVERT: B 704 ARG cc_start: 0.7397 (ttm170) cc_final: 0.6804 (mtt-85) REVERT: B 708 ARG cc_start: 0.7388 (tpp-160) cc_final: 0.6985 (ttm-80) REVERT: B 725 LYS cc_start: 0.7615 (tmtt) cc_final: 0.7341 (tmtp) REVERT: A 70 LYS cc_start: 0.8212 (tmmt) cc_final: 0.7389 (mppt) REVERT: A 200 SER cc_start: 0.8169 (m) cc_final: 0.7933 (m) REVERT: A 257 LYS cc_start: 0.7026 (mtpt) cc_final: 0.6802 (mmmm) REVERT: A 438 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.6286 (mp10) REVERT: A 626 TYR cc_start: 0.8702 (t80) cc_final: 0.8409 (t80) REVERT: A 641 ARG cc_start: 0.7873 (ttp80) cc_final: 0.7341 (ttp80) REVERT: A 704 ARG cc_start: 0.7364 (ttm170) cc_final: 0.6990 (mtm-85) REVERT: A 708 ARG cc_start: 0.7554 (tpp-160) cc_final: 0.7316 (ttm-80) outliers start: 14 outliers final: 6 residues processed: 135 average time/residue: 1.3026 time to fit residues: 188.6327 Evaluate side-chains 114 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 438 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.127181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.095538 restraints weight = 11719.096| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.60 r_work: 0.2864 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10616 Z= 0.272 Angle : 0.654 9.954 14344 Z= 0.349 Chirality : 0.048 0.189 1570 Planarity : 0.005 0.041 1768 Dihedral : 16.647 104.274 1696 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.02 % Allowed : 12.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.24), residues: 1210 helix: 1.22 (0.17), residues: 832 sheet: -0.85 (0.72), residues: 48 loop : -2.34 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 155 HIS 0.009 0.002 HIS A 619 PHE 0.025 0.002 PHE B 61 TYR 0.017 0.003 TYR B 212 ARG 0.004 0.001 ARG A 170 Details of bonding type rmsd hydrogen bonds : bond 0.06103 ( 644) hydrogen bonds : angle 4.50185 ( 1884) covalent geometry : bond 0.00638 (10616) covalent geometry : angle 0.65427 (14344) *********************** 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 143 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 1.247 Fit side-chains REVERT: B 74 ARG cc_start: 0.8057 (tpp-160) cc_final: 0.7773 (ttm-80) REVERT: B 129 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6768 (ptt180) REVERT: B 289 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8283 (tp) REVERT: B 438 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.6099 (mp10) REVERT: B 641 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7637 (ttt90) REVERT: B 647 ARG cc_start: 0.8400 (ttp80) cc_final: 0.7955 (ttm110) REVERT: B 704 ARG cc_start: 0.7464 (ttm170) cc_final: 0.7081 (mtm-85) REVERT: B 708 ARG cc_start: 0.7379 (tpp-160) cc_final: 0.7080 (ttm-80) REVERT: A 257 LYS cc_start: 0.7122 (mtpt) cc_final: 0.6832 (mmmm) REVERT: A 258 GLU cc_start: 0.7841 (tp30) cc_final: 0.7639 (tp30) REVERT: A 289 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8291 (tp) REVERT: A 438 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.6049 (mp10) REVERT: A 641 ARG cc_start: 0.7995 (ttp80) cc_final: 0.7534 (ttt90) REVERT: A 704 ARG cc_start: 0.7272 (ttm170) cc_final: 0.6437 (mtt-85) REVERT: A 707 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7797 (mtt) REVERT: A 708 ARG cc_start: 0.7459 (tpp-160) cc_final: 0.7114 (ttm-80) outliers start: 32 outliers final: 24 residues processed: 125 average time/residue: 1.4698 time to fit residues: 196.2090 Evaluate side-chains 134 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 147 THR 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.130109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.099758 restraints weight = 11610.754| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.55 r_work: 0.2935 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2201 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= 0.120 Angle : 0.466 6.260 14344 Z= 0.254 Chirality : 0.039 0.145 1570 Planarity : 0.003 0.036 1768 Dihedral : 15.167 95.362 1696 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.80 % Allowed : 14.56 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.26), residues: 1210 helix: 2.03 (0.18), residues: 840 sheet: -0.76 (0.73), residues: 48 loop : -2.14 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 155 HIS 0.004 0.001 HIS A 130 PHE 0.015 0.001 PHE B 61 TYR 0.010 0.001 TYR B 180 ARG 0.002 0.000 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.04477 ( 644) hydrogen bonds : angle 4.08692 ( 1884) covalent geometry : bond 0.00260 (10616) covalent geometry : angle 0.46552 (14344) *********************** 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 135 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 1.105 Fit side-chains REVERT: B 74 ARG cc_start: 0.7912 (tpp-160) cc_final: 0.7684 (ttm-80) REVERT: B 150 GLN cc_start: 0.7871 (tt0) cc_final: 0.7239 (tp40) REVERT: B 257 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6644 (mptt) REVERT: B 289 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8351 (tp) REVERT: B 438 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.6035 (mp10) REVERT: B 641 ARG cc_start: 0.7961 (ttp80) cc_final: 0.7499 (ttt90) REVERT: B 647 ARG cc_start: 0.8302 (ttp80) cc_final: 0.7916 (ttm110) REVERT: B 704 ARG cc_start: 0.7448 (ttm170) cc_final: 0.6686 (mtt-85) REVERT: B 708 ARG cc_start: 0.7447 (tpp-160) cc_final: 0.7120 (ttm-80) REVERT: A 70 LYS cc_start: 0.8227 (tmmt) cc_final: 0.7362 (mppt) REVERT: A 257 LYS cc_start: 0.7101 (mtpt) cc_final: 0.6583 (mppt) REVERT: A 641 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7537 (ttp80) REVERT: A 704 ARG cc_start: 0.7291 (ttm170) cc_final: 0.6938 (mtm-85) REVERT: A 708 ARG cc_start: 0.7510 (tpp-160) cc_final: 0.7265 (ttm-80) outliers start: 19 outliers final: 12 residues processed: 123 average time/residue: 1.4600 time to fit residues: 191.7089 Evaluate side-chains 126 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 321 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 89 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 112 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.128735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.098657 restraints weight = 11546.019| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.52 r_work: 0.2873 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10616 Z= 0.234 Angle : 0.596 9.104 14344 Z= 0.319 Chirality : 0.046 0.164 1570 Planarity : 0.004 0.036 1768 Dihedral : 15.530 97.241 1696 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.69 % Allowed : 14.65 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.25), residues: 1210 helix: 1.94 (0.18), residues: 832 sheet: -0.71 (0.72), residues: 48 loop : -2.28 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 227 HIS 0.007 0.001 HIS B 619 PHE 0.023 0.002 PHE A 61 TYR 0.016 0.002 TYR A 212 ARG 0.003 0.001 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.05527 ( 644) hydrogen bonds : angle 4.27935 ( 1884) covalent geometry : bond 0.00549 (10616) covalent geometry : angle 0.59605 (14344) *********************** 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 145 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 106 time to evaluate : 1.220 Fit side-chains REVERT: B 74 ARG cc_start: 0.7999 (tpp-160) cc_final: 0.7766 (ttm-80) REVERT: B 129 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6893 (ptt180) REVERT: B 438 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.6006 (mp10) REVERT: B 641 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7646 (ttt90) REVERT: B 647 ARG cc_start: 0.8359 (ttp80) cc_final: 0.7958 (ttm110) REVERT: B 704 ARG cc_start: 0.7463 (ttm170) cc_final: 0.6684 (mtt-85) REVERT: B 707 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7617 (mpp) REVERT: B 708 ARG cc_start: 0.7400 (tpp-160) cc_final: 0.7126 (ttm-80) REVERT: A 129 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6940 (ptm160) REVERT: A 257 LYS cc_start: 0.7079 (mtpt) cc_final: 0.6635 (mptt) REVERT: A 452 LYS cc_start: 0.5883 (OUTLIER) cc_final: 0.5272 (tttm) REVERT: A 641 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7605 (ttt90) REVERT: A 704 ARG cc_start: 0.7280 (ttm170) cc_final: 0.6435 (mtt-85) REVERT: A 708 ARG cc_start: 0.7475 (tpp-160) cc_final: 0.7198 (ttm-80) REVERT: A 725 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7276 (tmtp) outliers start: 39 outliers final: 23 residues processed: 131 average time/residue: 1.3813 time to fit residues: 193.7606 Evaluate side-chains 136 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 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 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 129 ARG Chi-restraints excluded: chain A residue 147 THR 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 321 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 725 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 19 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.129442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.099232 restraints weight = 11550.694| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.53 r_work: 0.2890 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10616 Z= 0.186 Angle : 0.540 7.824 14344 Z= 0.292 Chirality : 0.043 0.158 1570 Planarity : 0.004 0.036 1768 Dihedral : 15.249 96.189 1696 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.12 % Allowed : 15.78 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1210 helix: 2.07 (0.18), residues: 834 sheet: -0.48 (0.76), residues: 48 loop : -2.22 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 227 HIS 0.005 0.001 HIS B 619 PHE 0.019 0.001 PHE A 61 TYR 0.012 0.002 TYR A 212 ARG 0.002 0.000 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.05112 ( 644) hydrogen bonds : angle 4.19730 ( 1884) covalent geometry : bond 0.00429 (10616) covalent geometry : angle 0.53959 (14344) *********************** 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 142 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 1.070 Fit side-chains REVERT: B 74 ARG cc_start: 0.7945 (tpp-160) cc_final: 0.7739 (ttm-80) REVERT: B 257 LYS cc_start: 0.7047 (mtpp) cc_final: 0.6285 (mppt) REVERT: B 438 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.5966 (mp10) REVERT: B 641 ARG cc_start: 0.8000 (ttp80) cc_final: 0.7547 (ttt90) REVERT: B 647 ARG cc_start: 0.8346 (ttp80) cc_final: 0.7941 (ttm110) REVERT: B 704 ARG cc_start: 0.7450 (ttm170) cc_final: 0.6670 (mtt-85) REVERT: B 707 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7617 (mpp) REVERT: B 708 ARG cc_start: 0.7388 (tpp-160) cc_final: 0.7121 (ttm-80) REVERT: A 70 LYS cc_start: 0.8284 (tmmt) cc_final: 0.7378 (mppt) REVERT: A 94 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7518 (mm-30) REVERT: A 129 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6926 (ptm160) REVERT: A 452 LYS cc_start: 0.5897 (OUTLIER) cc_final: 0.5289 (tttm) REVERT: A 641 ARG cc_start: 0.7973 (ttp80) cc_final: 0.7569 (ttt90) REVERT: A 704 ARG cc_start: 0.7301 (ttm170) cc_final: 0.6473 (mtt-85) REVERT: A 708 ARG cc_start: 0.7475 (tpp-160) cc_final: 0.7124 (ttm-80) REVERT: A 725 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7295 (tmtp) outliers start: 33 outliers final: 22 residues processed: 129 average time/residue: 1.4530 time to fit residues: 200.2944 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 : 1.050 ------------------------------------------------------------------------------- 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 393 VAL Chi-restraints excluded: chain B residue 438 GLN 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 61 PHE Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 147 THR 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 321 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 725 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.131053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.099591 restraints weight = 11681.958| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.60 r_work: 0.2932 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2418 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= 0.122 Angle : 0.458 6.035 14344 Z= 0.249 Chirality : 0.039 0.143 1570 Planarity : 0.003 0.034 1768 Dihedral : 14.557 93.723 1696 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.65 % Allowed : 16.35 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.26), residues: 1210 helix: 2.38 (0.18), residues: 840 sheet: -0.33 (0.76), residues: 48 loop : -2.14 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 227 HIS 0.004 0.001 HIS B 130 PHE 0.015 0.001 PHE A 61 TYR 0.009 0.001 TYR A 180 ARG 0.001 0.000 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.04361 ( 644) hydrogen bonds : angle 3.99310 ( 1884) covalent geometry : bond 0.00267 (10616) covalent geometry : angle 0.45761 (14344) *********************** 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 144 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 1.073 Fit side-chains REVERT: B 74 ARG cc_start: 0.7913 (tpp-160) cc_final: 0.7709 (ttm-80) REVERT: B 94 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7538 (mm-30) REVERT: B 129 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6914 (ptt180) REVERT: B 150 GLN cc_start: 0.7809 (tt0) cc_final: 0.7173 (tm-30) REVERT: B 257 LYS cc_start: 0.7003 (mtpp) cc_final: 0.6250 (mppt) REVERT: B 641 ARG cc_start: 0.7973 (ttp80) cc_final: 0.7513 (ttt90) REVERT: B 647 ARG cc_start: 0.8309 (ttp80) cc_final: 0.7925 (ttm110) REVERT: B 704 ARG cc_start: 0.7424 (ttm170) cc_final: 0.6646 (mtt-85) REVERT: B 708 ARG cc_start: 0.7439 (tpp-160) cc_final: 0.7119 (ttm-80) REVERT: A 70 LYS cc_start: 0.8210 (tmmt) cc_final: 0.7357 (mppt) REVERT: A 94 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7512 (mm-30) REVERT: A 129 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6865 (ptm160) REVERT: A 150 GLN cc_start: 0.7804 (tt0) cc_final: 0.7156 (tm-30) REVERT: A 641 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7495 (ttt90) REVERT: A 704 ARG cc_start: 0.7285 (ttm170) cc_final: 0.6943 (mtm-85) REVERT: A 708 ARG cc_start: 0.7543 (tpp-160) cc_final: 0.7330 (ttm-80) outliers start: 28 outliers final: 17 residues processed: 135 average time/residue: 1.4266 time to fit residues: 205.8968 Evaluate side-chains 134 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 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 129 ARG Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 270 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 702 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 117 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.0370 chunk 83 optimal weight: 0.0870 chunk 112 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.8242 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.129643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.099340 restraints weight = 11559.430| |-----------------------------------------------------------------------------| 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: 0.8473 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10616 Z= 0.171 Angle : 0.517 7.067 14344 Z= 0.279 Chirality : 0.042 0.149 1570 Planarity : 0.004 0.034 1768 Dihedral : 14.803 95.190 1696 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.74 % Allowed : 16.54 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.26), residues: 1210 helix: 2.31 (0.18), residues: 838 sheet: -0.25 (0.77), residues: 48 loop : -2.19 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 712 HIS 0.005 0.001 HIS B 619 PHE 0.019 0.001 PHE B 61 TYR 0.013 0.002 TYR A 432 ARG 0.002 0.000 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.04918 ( 644) hydrogen bonds : angle 4.09907 ( 1884) covalent geometry : bond 0.00391 (10616) covalent geometry : angle 0.51732 (14344) *********************** 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 142 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 1.132 Fit side-chains REVERT: B 74 ARG cc_start: 0.7967 (tpp-160) cc_final: 0.7745 (ttm-80) REVERT: B 94 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7543 (mm-30) REVERT: B 129 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6878 (ptt180) REVERT: B 257 LYS cc_start: 0.6953 (mtpp) cc_final: 0.6213 (mppt) REVERT: B 641 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7585 (ttt90) REVERT: B 647 ARG cc_start: 0.8323 (ttp80) cc_final: 0.7937 (ttm110) REVERT: B 704 ARG cc_start: 0.7403 (ttm170) cc_final: 0.6632 (mtt-85) REVERT: B 707 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7593 (mpp) REVERT: B 708 ARG cc_start: 0.7382 (tpp-160) cc_final: 0.7145 (ttm-80) REVERT: A 70 LYS cc_start: 0.8254 (tmmt) cc_final: 0.7384 (mppt) REVERT: A 94 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7538 (mm-30) REVERT: A 129 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6928 (ptm160) REVERT: A 452 LYS cc_start: 0.5840 (OUTLIER) cc_final: 0.5298 (tttm) REVERT: A 641 ARG cc_start: 0.7992 (ttp80) cc_final: 0.7543 (ttt90) REVERT: A 704 ARG cc_start: 0.7320 (ttm170) cc_final: 0.6528 (mtt-85) REVERT: A 708 ARG cc_start: 0.7505 (tpp-160) cc_final: 0.7272 (ttm-80) outliers start: 29 outliers final: 20 residues processed: 132 average time/residue: 1.7915 time to fit residues: 255.5797 Evaluate side-chains 137 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 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 707 MET Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 147 THR 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 393 VAL Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 725 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.132816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.102008 restraints weight = 11557.993| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.55 r_work: 0.2918 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2425 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= 0.147 Angle : 0.488 6.250 14344 Z= 0.265 Chirality : 0.041 0.147 1570 Planarity : 0.003 0.034 1768 Dihedral : 14.659 94.829 1696 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.46 % Allowed : 16.82 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.26), residues: 1210 helix: 2.41 (0.18), residues: 836 sheet: -0.12 (0.77), residues: 48 loop : -2.20 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 712 HIS 0.004 0.001 HIS B 619 PHE 0.018 0.001 PHE B 61 TYR 0.012 0.001 TYR A 432 ARG 0.002 0.000 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.04687 ( 644) hydrogen bonds : angle 4.04507 ( 1884) covalent geometry : bond 0.00331 (10616) covalent geometry : angle 0.48815 (14344) *********************** 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 137 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 1.601 Fit side-chains REVERT: B 74 ARG cc_start: 0.7954 (tpp-160) cc_final: 0.7746 (ttm-80) REVERT: B 94 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7561 (mm-30) REVERT: B 129 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6877 (ptt180) REVERT: B 150 GLN cc_start: 0.7802 (tt0) cc_final: 0.7234 (tm-30) REVERT: B 641 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7598 (ttt90) REVERT: B 647 ARG cc_start: 0.8327 (ttp80) cc_final: 0.7961 (ttm110) REVERT: B 704 ARG cc_start: 0.7412 (ttm170) cc_final: 0.7092 (mtm-85) REVERT: B 707 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7581 (mpp) REVERT: B 708 ARG cc_start: 0.7401 (tpp-160) cc_final: 0.7087 (ttm-80) REVERT: A 70 LYS cc_start: 0.8242 (tmmt) cc_final: 0.7397 (mppt) REVERT: A 94 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7522 (mm-30) REVERT: A 129 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.6934 (ptm160) REVERT: A 150 GLN cc_start: 0.7796 (tt0) cc_final: 0.7223 (tm-30) REVERT: A 452 LYS cc_start: 0.5856 (OUTLIER) cc_final: 0.5316 (tttm) REVERT: A 641 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7568 (ttt90) REVERT: A 704 ARG cc_start: 0.7361 (ttm170) cc_final: 0.7029 (mtm-85) REVERT: A 708 ARG cc_start: 0.7548 (tpp-160) cc_final: 0.7329 (ttm-80) outliers start: 26 outliers final: 20 residues processed: 129 average time/residue: 2.1685 time to fit residues: 301.7821 Evaluate side-chains 135 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 1.564 ------------------------------------------------------------------------------- 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 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 707 MET Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 147 THR 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 452 LYS Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 725 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 8 optimal weight: 0.0170 chunk 102 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- 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 ** B 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN A 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.134212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.103746 restraints weight = 11545.710| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.55 r_work: 0.2940 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2656 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= 0.098 Angle : 0.421 4.568 14344 Z= 0.230 Chirality : 0.038 0.134 1570 Planarity : 0.003 0.034 1768 Dihedral : 13.820 91.378 1696 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.36 % Allowed : 16.92 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.26), residues: 1210 helix: 2.70 (0.18), residues: 828 sheet: 0.02 (0.77), residues: 48 loop : -2.11 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 712 HIS 0.003 0.001 HIS A 619 PHE 0.012 0.001 PHE B 61 TYR 0.008 0.001 TYR A 180 ARG 0.001 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 644) hydrogen bonds : angle 3.85052 ( 1884) covalent geometry : bond 0.00209 (10616) covalent geometry : angle 0.42124 (14344) ********************** 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 148 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 1.074 Fit side-chains REVERT: B 74 ARG cc_start: 0.7937 (tpp-160) cc_final: 0.7729 (ttm-80) REVERT: B 94 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7555 (mm-30) REVERT: B 129 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6953 (ptt180) REVERT: B 150 GLN cc_start: 0.7810 (tt0) cc_final: 0.7236 (tm-30) REVERT: B 641 ARG cc_start: 0.7971 (ttp80) cc_final: 0.7579 (ttt90) REVERT: B 647 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7888 (ttm110) REVERT: B 704 ARG cc_start: 0.7422 (ttm170) cc_final: 0.7095 (mtm-85) REVERT: B 708 ARG cc_start: 0.7477 (tpp-160) cc_final: 0.7205 (ttm-80) REVERT: A 70 LYS cc_start: 0.8184 (tmmt) cc_final: 0.7374 (mppt) REVERT: A 94 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7539 (mm-30) REVERT: A 129 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6795 (ptm160) REVERT: A 150 GLN cc_start: 0.7837 (tt0) cc_final: 0.7221 (tm-30) REVERT: A 452 LYS cc_start: 0.5850 (OUTLIER) cc_final: 0.5311 (tttm) REVERT: A 641 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7571 (ttt90) REVERT: A 704 ARG cc_start: 0.7337 (ttm170) cc_final: 0.6997 (mtm-85) outliers start: 25 outliers final: 16 residues processed: 137 average time/residue: 1.4443 time to fit residues: 213.1264 Evaluate side-chains 135 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 129 ARG 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 46 VAL Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 147 THR 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 452 LYS Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 725 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 93 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.131414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.100211 restraints weight = 11475.152| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.58 r_work: 0.2919 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2570 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= 0.135 Angle : 0.468 5.516 14344 Z= 0.253 Chirality : 0.040 0.142 1570 Planarity : 0.003 0.033 1768 Dihedral : 14.053 91.822 1696 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.27 % Allowed : 17.11 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.26), residues: 1210 helix: 2.63 (0.18), residues: 830 sheet: -0.04 (0.78), residues: 48 loop : -2.11 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 227 HIS 0.004 0.001 HIS B 619 PHE 0.017 0.001 PHE B 61 TYR 0.010 0.001 TYR B 432 ARG 0.002 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.04460 ( 644) hydrogen bonds : angle 3.93436 ( 1884) covalent geometry : bond 0.00302 (10616) covalent geometry : angle 0.46781 (14344) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8184.65 seconds wall clock time: 144 minutes 23.58 seconds (8663.58 seconds total)