Starting phenix.real_space_refine on Fri Feb 14 21:00:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rx2_24722/02_2025/7rx2_24722.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rx2_24722/02_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_24722/02_2025/7rx2_24722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rx2_24722/02_2025/7rx2_24722.map" model { file = "/net/cci-nas-00/data/ceres_data/7rx2_24722/02_2025/7rx2_24722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rx2_24722/02_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-5592/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: 6.68, per 1000 atoms: 0.64 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: 2.43 Conformation dependent library (CDL) restraints added in 1.2 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: 0.87 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: 3.29 Time building geometry restraints manager: 2.85 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 727 or resid 1502 or (resid 1504 and (name C01 \ or name C02 or name C03 or name C1 or name C19 or name C2 or name C20 or name C2 \ 1 or name C22 or name C23 or name C24 or name C25 or name C26 or name C3 or name \ C4 or name C5 or name C6 or name C7 or name C8 or name O01 or name O02 or name \ O03 or name O04 or name O11)) or (resid 1505 and (name C01 or name C02 or name C \ 03 or name C1 or name C19 or name C2 or name C20 or name C21 or name C22 or name \ C23 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name O \ 01 or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or na \ me O14 or name P )) or resid 1506 or (resid 1507 and (name C01 or name C02 or na \ me C03 or name C06 or name C19 or name C2 or name C20 or name C21 or name C22 or \ name C23 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name O01 or name O02 or name O03 or name O04 or name O11 or name O12 o \ r name O13 or name O14 or name P )) or resid 1508 or (resid 1509 and (name C01 o \ r name C02 or name C03 or name C1 or name C19 or name C2 or name C20 or name C21 \ or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or \ name O01 or name O02 or name O03 or name O04 or name O11 or name O12 or name O1 \ 3 or name O14 or name P )))) selection = (chain 'B' and (resid 11 through 727 or resid 802 or (resid 804 and (name C01 or \ name C02 or name C03 or name C1 or name C19 or name C2 or name C20 or name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name O01 or name O02 or name O0 \ 3 or name O04 or name O11)) or (resid 805 and (name C01 or name C02 or name C03 \ or name C1 or name C19 or name C2 or name C20 or name C21 or name C22 or name C2 \ 3 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name O01 \ or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or name \ O14 or name P )) or (resid 806 and (name C01 or name C02 or name C03 or name C1 \ or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C \ 3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O01 \ or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or name \ O14 or name P )) or (resid 807 and (name C01 or name C02 or name C03 or name C06 \ or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name \ C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O01 \ or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or name \ O14 or name P )) or resid 808 through 809)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.510 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: 0.300 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 25.370 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 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:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.300 ------------------------------------------------------------------------------- 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= 0.616 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 *********************** 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 : 1.108 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: 1.6019 time to fit residues: 254.9422 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 : 1.138 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.101618 restraints weight = 11625.596| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.54 r_work: 0.2963 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.00 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= 0.152 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 *********************** 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 : 1.227 Fit side-chains REVERT: B 74 ARG cc_start: 0.8022 (tpp-160) cc_final: 0.7760 (ttm-80) REVERT: B 599 ASN cc_start: 0.6884 (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: 0.7609 (ttp-170) cc_final: 0.7394 (ttm170) REVERT: B 647 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7857 (ttm110) REVERT: B 704 ARG cc_start: 0.7396 (ttm170) cc_final: 0.6803 (mtt-85) REVERT: B 708 ARG cc_start: 0.7387 (tpp-160) cc_final: 0.6984 (ttm-80) REVERT: B 725 LYS cc_start: 0.7616 (tmtt) cc_final: 0.7342 (tmtp) REVERT: A 70 LYS cc_start: 0.8212 (tmmt) cc_final: 0.7389 (mppt) REVERT: A 200 SER cc_start: 0.8170 (m) cc_final: 0.7934 (m) REVERT: A 257 LYS cc_start: 0.7025 (mtpt) cc_final: 0.6802 (mmmm) REVERT: A 438 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.6287 (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: 0.7362 (ttm170) cc_final: 0.6988 (mtm-85) REVERT: A 708 ARG cc_start: 0.7551 (tpp-160) cc_final: 0.7313 (ttm-80) outliers start: 14 outliers final: 6 residues processed: 135 average time/residue: 1.3737 time to fit residues: 199.2772 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 : 1.193 ------------------------------------------------------------------------------- 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: 0.5980 chunk 4 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.127479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.095814 restraints weight = 11718.168| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.61 r_work: 0.2868 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 10616 Z= 0.358 Angle : 0.620 9.280 14344 Z= 0.332 Chirality : 0.046 0.175 1570 Planarity : 0.004 0.039 1768 Dihedral : 16.418 102.545 1696 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.93 % Allowed : 12.48 % 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: 0.44 (0.25), residues: 1210 helix: 1.32 (0.17), residues: 834 sheet: -0.90 (0.72), residues: 48 loop : -2.26 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 155 HIS 0.008 0.002 HIS A 619 PHE 0.023 0.002 PHE B 61 TYR 0.016 0.002 TYR B 212 ARG 0.003 0.001 ARG A 170 *********************** 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 140 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 1.236 Fit side-chains REVERT: B 74 ARG cc_start: 0.8058 (tpp-160) cc_final: 0.7769 (ttm-80) REVERT: B 289 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8288 (tp) REVERT: B 438 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.6088 (mp10) REVERT: B 641 ARG cc_start: 0.8040 (ttp80) cc_final: 0.7610 (ttt90) REVERT: B 647 ARG cc_start: 0.8402 (ttp80) cc_final: 0.7941 (ttm110) REVERT: B 704 ARG cc_start: 0.7454 (ttm170) cc_final: 0.6675 (mtt-85) REVERT: B 708 ARG cc_start: 0.7405 (tpp-160) cc_final: 0.7119 (ttm-80) REVERT: A 257 LYS cc_start: 0.7090 (mtpt) cc_final: 0.6741 (mmmm) REVERT: A 289 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8304 (tp) REVERT: A 438 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.6090 (mp10) REVERT: A 641 ARG cc_start: 0.7997 (ttp80) cc_final: 0.7526 (ttt90) REVERT: A 704 ARG cc_start: 0.7297 (ttm170) cc_final: 0.6453 (mtt-85) REVERT: A 708 ARG cc_start: 0.7506 (tpp-160) cc_final: 0.7173 (ttm-80) outliers start: 31 outliers final: 22 residues processed: 123 average time/residue: 1.4897 time to fit residues: 195.8076 Evaluate side-chains 128 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 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 393 VAL Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 111 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.131254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.100136 restraints weight = 11521.192| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.56 r_work: 0.2917 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10616 Z= 0.213 Angle : 0.499 7.133 14344 Z= 0.272 Chirality : 0.041 0.151 1570 Planarity : 0.004 0.037 1768 Dihedral : 15.281 95.615 1696 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.17 % Allowed : 14.37 % Favored : 83.46 % 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: 1.23 (0.25), residues: 1210 helix: 1.97 (0.18), residues: 840 sheet: -0.83 (0.73), residues: 48 loop : -2.14 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 227 HIS 0.004 0.001 HIS A 619 PHE 0.017 0.001 PHE B 61 TYR 0.010 0.001 TYR A 589 ARG 0.002 0.000 ARG B 21 *********************** 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 139 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.189 Fit side-chains REVERT: B 74 ARG cc_start: 0.7968 (tpp-160) cc_final: 0.7726 (ttm-80) REVERT: B 129 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6794 (ptt180) REVERT: B 289 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8387 (tp) REVERT: B 438 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.6091 (mp10) REVERT: B 641 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7553 (ttt90) REVERT: B 647 ARG cc_start: 0.8344 (ttp80) cc_final: 0.7970 (ttm110) REVERT: B 704 ARG cc_start: 0.7465 (ttm170) cc_final: 0.6708 (mtt-85) REVERT: B 708 ARG cc_start: 0.7441 (tpp-160) cc_final: 0.7088 (ttm-80) REVERT: A 70 LYS cc_start: 0.8223 (tmmt) cc_final: 0.7376 (mppt) REVERT: A 192 MET cc_start: 0.8793 (mtt) cc_final: 0.8585 (mtt) REVERT: A 257 LYS cc_start: 0.7020 (mtpt) cc_final: 0.6574 (mppt) REVERT: A 641 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7550 (ttt90) REVERT: A 704 ARG cc_start: 0.7305 (ttm170) cc_final: 0.6509 (mtt-85) REVERT: A 708 ARG cc_start: 0.7542 (tpp-160) cc_final: 0.7295 (ttm-80) outliers start: 23 outliers final: 16 residues processed: 127 average time/residue: 1.5040 time to fit residues: 204.0331 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 : 1.123 ------------------------------------------------------------------------------- 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 137 ASP 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 353 GLU Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 147 THR 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: 0.5980 chunk 96 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.132285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.101479 restraints weight = 11443.319| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.54 r_work: 0.2912 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2257 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= 0.212 Angle : 0.498 7.099 14344 Z= 0.270 Chirality : 0.041 0.148 1570 Planarity : 0.004 0.034 1768 Dihedral : 14.828 93.655 1696 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.12 % Allowed : 14.46 % Favored : 82.42 % 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: 1.50 (0.26), residues: 1210 helix: 2.19 (0.18), residues: 840 sheet: -0.62 (0.72), residues: 48 loop : -2.16 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 227 HIS 0.005 0.001 HIS B 619 PHE 0.018 0.001 PHE B 61 TYR 0.011 0.001 TYR A 212 ARG 0.003 0.000 ARG B 21 *********************** 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 148 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 1.191 Fit side-chains REVERT: B 74 ARG cc_start: 0.7958 (tpp-160) cc_final: 0.7742 (ttm-80) REVERT: B 129 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6873 (ptt180) REVERT: B 150 GLN cc_start: 0.7847 (tt0) cc_final: 0.7258 (tp40) REVERT: B 257 LYS cc_start: 0.7111 (mtpp) cc_final: 0.6417 (mptt) REVERT: B 438 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.6011 (mp10) REVERT: B 641 ARG cc_start: 0.7995 (ttp80) cc_final: 0.7553 (ttt90) REVERT: B 647 ARG cc_start: 0.8343 (ttp80) cc_final: 0.7971 (ttm110) REVERT: B 704 ARG cc_start: 0.7466 (ttm170) cc_final: 0.6733 (mtt-85) REVERT: B 707 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7569 (mpp) REVERT: B 708 ARG cc_start: 0.7470 (tpp-160) cc_final: 0.7154 (ttm-80) REVERT: A 70 LYS cc_start: 0.8266 (tmmt) cc_final: 0.7396 (mppt) REVERT: A 129 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6869 (ptm160) REVERT: A 150 GLN cc_start: 0.7839 (tt0) cc_final: 0.7240 (tp40) REVERT: A 192 MET cc_start: 0.8782 (mtt) cc_final: 0.8571 (mtt) REVERT: A 641 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7576 (ttt90) REVERT: A 704 ARG cc_start: 0.7310 (ttm170) cc_final: 0.6973 (mtm-85) REVERT: A 708 ARG cc_start: 0.7537 (tpp-160) cc_final: 0.7307 (ttm-80) REVERT: A 725 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7282 (tmtp) outliers start: 33 outliers final: 23 residues processed: 135 average time/residue: 1.4347 time to fit residues: 207.1061 Evaluate side-chains 143 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 137 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 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 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: 5.9990 chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 B 595 HIS ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 HIS A 595 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.129572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.099485 restraints weight = 11514.268| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.52 r_work: 0.2878 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10616 Z= 0.367 Angle : 0.615 9.019 14344 Z= 0.329 Chirality : 0.047 0.181 1570 Planarity : 0.004 0.036 1768 Dihedral : 15.516 97.077 1696 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.88 % Allowed : 14.27 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.15 (0.25), residues: 1210 helix: 1.95 (0.18), residues: 832 sheet: -0.44 (0.75), residues: 48 loop : -2.30 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 227 HIS 0.008 0.001 HIS A 619 PHE 0.022 0.002 PHE A 61 TYR 0.017 0.002 TYR B 432 ARG 0.003 0.001 ARG B 21 *********************** 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 151 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 1.084 Fit side-chains REVERT: B 74 ARG cc_start: 0.7976 (tpp-160) cc_final: 0.7756 (ttm-80) REVERT: B 102 GLN cc_start: 0.7694 (pt0) cc_final: 0.7477 (pp30) REVERT: B 129 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6881 (ptt180) REVERT: B 257 LYS cc_start: 0.7104 (mtpp) cc_final: 0.6316 (mppt) REVERT: B 438 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.5991 (mp10) REVERT: B 641 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7691 (ttt90) REVERT: B 647 ARG cc_start: 0.8357 (ttp80) cc_final: 0.7971 (ttm110) REVERT: B 704 ARG cc_start: 0.7413 (ttm170) cc_final: 0.6638 (mtt-85) REVERT: B 707 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7598 (mpp) REVERT: B 708 ARG cc_start: 0.7426 (tpp-160) cc_final: 0.7147 (ttm-80) REVERT: A 41 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8096 (tm) REVERT: A 70 LYS cc_start: 0.8277 (tmmt) cc_final: 0.7431 (mppt) REVERT: A 94 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7514 (mm-30) REVERT: A 102 GLN cc_start: 0.7686 (pp30) cc_final: 0.7484 (pp30) REVERT: A 129 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6994 (ptm160) REVERT: A 192 MET cc_start: 0.8799 (mtt) cc_final: 0.8553 (mtt) REVERT: A 641 ARG cc_start: 0.8051 (ttp80) cc_final: 0.7662 (ttt90) REVERT: A 704 ARG cc_start: 0.7300 (ttm170) cc_final: 0.6505 (mtt-85) REVERT: A 708 ARG cc_start: 0.7498 (tpp-160) cc_final: 0.7188 (ttm-80) REVERT: A 725 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7318 (tmtp) outliers start: 41 outliers final: 26 residues processed: 134 average time/residue: 1.3918 time to fit residues: 199.8499 Evaluate side-chains 140 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 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 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 41 LEU 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 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 590 MET Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 725 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 90 optimal weight: 0.3980 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 HIS ** 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 = 0.3507 r_free = 0.3507 target = 0.131553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.100114 restraints weight = 11696.652| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.60 r_work: 0.2926 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2512 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= 0.148 Angle : 0.441 5.396 14344 Z= 0.241 Chirality : 0.038 0.140 1570 Planarity : 0.003 0.034 1768 Dihedral : 14.514 92.298 1696 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.08 % Allowed : 16.16 % Favored : 81.76 % 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: 1.77 (0.26), residues: 1210 helix: 2.41 (0.18), residues: 840 sheet: -0.29 (0.75), residues: 48 loop : -2.11 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 227 HIS 0.003 0.000 HIS A 619 PHE 0.013 0.001 PHE B 61 TYR 0.010 0.001 TYR A 180 ARG 0.001 0.000 ARG A 229 *********************** 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 138 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.156 Fit side-chains REVERT: B 74 ARG cc_start: 0.7922 (tpp-160) cc_final: 0.7720 (ttm-80) REVERT: B 94 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7525 (mm-30) REVERT: B 102 GLN cc_start: 0.7717 (pt0) cc_final: 0.7501 (pp30) REVERT: B 129 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6837 (ptt180) REVERT: B 150 GLN cc_start: 0.7801 (tt0) cc_final: 0.7153 (tm-30) REVERT: B 257 LYS cc_start: 0.6970 (mtpp) cc_final: 0.6281 (mptt) REVERT: B 641 ARG cc_start: 0.7942 (ttp80) cc_final: 0.7484 (ttt90) REVERT: B 647 ARG cc_start: 0.8301 (ttp80) cc_final: 0.7947 (ttm110) REVERT: B 704 ARG cc_start: 0.7426 (ttm170) cc_final: 0.7088 (mtm-85) REVERT: B 708 ARG cc_start: 0.7417 (tpp-160) cc_final: 0.7114 (ttm-80) REVERT: A 70 LYS cc_start: 0.8222 (tmmt) cc_final: 0.7364 (mppt) REVERT: A 94 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7514 (mm-30) REVERT: A 129 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.6864 (ptm160) REVERT: A 150 GLN cc_start: 0.7787 (tt0) cc_final: 0.7144 (tm-30) REVERT: A 192 MET cc_start: 0.8782 (mtt) cc_final: 0.8578 (mtp) REVERT: A 641 ARG cc_start: 0.7960 (ttp80) cc_final: 0.7490 (ttt90) REVERT: A 704 ARG cc_start: 0.7322 (ttm170) cc_final: 0.6977 (mtm-85) REVERT: A 708 ARG cc_start: 0.7530 (tpp-160) cc_final: 0.7317 (ttm-80) outliers start: 22 outliers final: 17 residues processed: 128 average time/residue: 1.4953 time to fit residues: 204.1212 Evaluate side-chains 133 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain 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 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 353 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 117 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.1980 chunk 83 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 91 optimal weight: 0.1980 chunk 74 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.131776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.100462 restraints weight = 11580.517| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.59 r_work: 0.2923 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2558 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= 0.162 Angle : 0.450 5.641 14344 Z= 0.244 Chirality : 0.039 0.139 1570 Planarity : 0.003 0.033 1768 Dihedral : 14.144 90.412 1696 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.17 % Allowed : 16.45 % Favored : 81.38 % 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: 1.90 (0.26), residues: 1210 helix: 2.57 (0.18), residues: 830 sheet: -0.16 (0.76), residues: 48 loop : -2.14 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 712 HIS 0.004 0.001 HIS B 619 PHE 0.015 0.001 PHE B 61 TYR 0.009 0.001 TYR A 432 ARG 0.002 0.000 ARG B 21 *********************** 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 137 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 1.127 Fit side-chains REVERT: B 74 ARG cc_start: 0.7953 (tpp-160) cc_final: 0.7737 (ttm-80) REVERT: B 94 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7530 (mm-30) REVERT: B 102 GLN cc_start: 0.7729 (pt0) cc_final: 0.7475 (pp30) REVERT: B 129 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6875 (ptt180) REVERT: B 150 GLN cc_start: 0.7819 (tt0) cc_final: 0.7213 (tm-30) REVERT: B 641 ARG cc_start: 0.7974 (ttp80) cc_final: 0.7592 (ttt90) REVERT: B 647 ARG cc_start: 0.8290 (ttp80) cc_final: 0.7919 (ttm110) REVERT: B 704 ARG cc_start: 0.7422 (ttm170) cc_final: 0.7091 (mtm-85) REVERT: B 707 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7586 (mpp) REVERT: B 708 ARG cc_start: 0.7452 (tpp-160) cc_final: 0.7154 (ttm-80) REVERT: A 70 LYS cc_start: 0.8196 (tmmt) cc_final: 0.7366 (mppt) REVERT: A 94 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7497 (mm-30) REVERT: A 129 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.6859 (ptm160) REVERT: A 150 GLN cc_start: 0.7826 (tt0) cc_final: 0.7203 (tm-30) REVERT: A 641 ARG cc_start: 0.7967 (ttp80) cc_final: 0.7568 (ttt90) REVERT: A 704 ARG cc_start: 0.7328 (ttm170) cc_final: 0.6982 (mtm-85) outliers start: 23 outliers final: 13 residues processed: 128 average time/residue: 1.4812 time to fit residues: 202.7363 Evaluate side-chains 129 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 129 ARG 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3462 r_free = 0.3462 target = 0.128025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.096750 restraints weight = 11765.310| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.56 r_work: 0.2907 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10616 Z= 0.310 Angle : 0.565 7.458 14344 Z= 0.302 Chirality : 0.044 0.155 1570 Planarity : 0.004 0.033 1768 Dihedral : 15.031 94.229 1696 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.74 % Allowed : 16.35 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.57 (0.25), residues: 1210 helix: 2.27 (0.18), residues: 834 sheet: -0.12 (0.79), residues: 48 loop : -2.19 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 227 HIS 0.006 0.001 HIS A 619 PHE 0.023 0.002 PHE B 61 TYR 0.015 0.002 TYR B 432 ARG 0.003 0.000 ARG A 21 *********************** 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 138 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 1.133 Fit side-chains REVERT: B 74 ARG cc_start: 0.7980 (tpp-160) cc_final: 0.7772 (ttm-80) REVERT: B 94 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7543 (mm-30) REVERT: B 102 GLN cc_start: 0.7723 (pt0) cc_final: 0.7493 (pp30) REVERT: B 129 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6907 (ptt180) REVERT: B 257 LYS cc_start: 0.6996 (mtpp) cc_final: 0.6321 (mptt) REVERT: B 641 ARG cc_start: 0.8056 (ttp80) cc_final: 0.7662 (ttt90) REVERT: B 647 ARG cc_start: 0.8363 (ttp80) cc_final: 0.8004 (ttm110) REVERT: B 704 ARG cc_start: 0.7413 (ttm170) cc_final: 0.6646 (mtt-85) REVERT: B 708 ARG cc_start: 0.7420 (tpp-160) cc_final: 0.7167 (ttm-80) REVERT: A 41 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8091 (tm) REVERT: A 70 LYS cc_start: 0.8277 (tmmt) cc_final: 0.7457 (mppt) REVERT: A 94 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7553 (mm-30) REVERT: A 129 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.6995 (ptm160) REVERT: A 641 ARG cc_start: 0.8055 (ttp80) cc_final: 0.7655 (ttt90) REVERT: A 704 ARG cc_start: 0.7329 (ttm170) cc_final: 0.7014 (mtm-85) outliers start: 29 outliers final: 20 residues processed: 129 average time/residue: 1.3907 time to fit residues: 192.3100 Evaluate side-chains 132 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 393 VAL 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 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 325 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE 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: 2.9990 chunk 22 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 8 optimal weight: 0.0870 chunk 102 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 HIS ** 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 = 0.3526 r_free = 0.3526 target = 0.133039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.101954 restraints weight = 11596.860| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.59 r_work: 0.2941 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2660 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= 0.136 Angle : 0.428 4.693 14344 Z= 0.234 Chirality : 0.038 0.139 1570 Planarity : 0.003 0.034 1768 Dihedral : 14.024 90.237 1696 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.80 % Allowed : 17.49 % 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: 1.97 (0.26), residues: 1210 helix: 2.62 (0.18), residues: 830 sheet: -0.01 (0.79), residues: 48 loop : -2.12 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 712 HIS 0.003 0.001 HIS A 619 PHE 0.010 0.001 PHE A 61 TYR 0.009 0.001 TYR A 86 ARG 0.002 0.000 ARG A 708 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 1.164 Fit side-chains REVERT: B 74 ARG cc_start: 0.7931 (tpp-160) cc_final: 0.7722 (ttm-80) REVERT: B 94 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7532 (mm-30) REVERT: B 129 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6980 (ptt180) REVERT: B 150 GLN cc_start: 0.7851 (tt0) cc_final: 0.7241 (tm-30) REVERT: B 641 ARG cc_start: 0.7964 (ttp80) cc_final: 0.7562 (ttt90) REVERT: B 647 ARG cc_start: 0.8266 (ttp80) cc_final: 0.7894 (ttm110) REVERT: B 704 ARG cc_start: 0.7426 (ttm170) cc_final: 0.7097 (mtm-85) REVERT: B 708 ARG cc_start: 0.7441 (tpp-160) cc_final: 0.7160 (ttm-80) REVERT: A 41 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8096 (tm) REVERT: A 70 LYS cc_start: 0.8191 (tmmt) cc_final: 0.7370 (mppt) REVERT: A 94 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7519 (mm-30) REVERT: A 129 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.6871 (ptm160) REVERT: A 150 GLN cc_start: 0.7802 (tt0) cc_final: 0.7210 (tm-30) REVERT: A 641 ARG cc_start: 0.7949 (ttp80) cc_final: 0.7557 (ttt90) REVERT: A 704 ARG cc_start: 0.7331 (ttm170) cc_final: 0.7009 (mtm-85) outliers start: 19 outliers final: 14 residues processed: 128 average time/residue: 1.4709 time to fit residues: 200.9190 Evaluate side-chains 131 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 137 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 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 129 ARG 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 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: 6.9990 chunk 80 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 99 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 = 0.131340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.100088 restraints weight = 11488.763| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.58 r_work: 0.2913 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2579 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= 0.194 Angle : 0.471 5.713 14344 Z= 0.255 Chirality : 0.040 0.143 1570 Planarity : 0.003 0.033 1768 Dihedral : 14.164 90.571 1696 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.89 % Allowed : 17.49 % 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: 1.92 (0.26), residues: 1210 helix: 2.59 (0.18), residues: 830 sheet: -0.03 (0.80), residues: 48 loop : -2.16 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 712 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 708 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7360.83 seconds wall clock time: 131 minutes 0.25 seconds (7860.25 seconds total)