Starting phenix.real_space_refine on Sun Dec 29 13:45:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rx2_24722/12_2024/7rx2_24722.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rx2_24722/12_2024/7rx2_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_24722/12_2024/7rx2_24722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rx2_24722/12_2024/7rx2_24722.map" model { file = "/net/cci-nas-00/data/ceres_data/7rx2_24722/12_2024/7rx2_24722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rx2_24722/12_2024/7rx2_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10390 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 4969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4969 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 30, 'TRANS': 584} Chain breaks: 4 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 4969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4969 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 30, 'TRANS': 584} Chain breaks: 4 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "B" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 217 Unusual residues: {' CA': 2, 'PGW': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PGW:plan-3': 5} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 217 Unusual residues: {' CA': 2, 'PGW': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PGW:plan-3': 5} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 7.35, per 1000 atoms: 0.71 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: 2.89 Conformation dependent library (CDL) restraints added in 1.0 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: 0.95 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: 3.08 Time building geometry restraints manager: 3.23 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: 0.00 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: 3.560 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: 0.310 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.400 Find NCS groups from input model: 0.480 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:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.280 ------------------------------------------------------------------------------- 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 : 1.106 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: 1.6390 time to fit residues: 260.8191 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 : 1.269 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 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 : 1.172 Fit side-chains REVERT: B 74 ARG cc_start: 0.7409 (tpp-160) cc_final: 0.7193 (ttm-80) REVERT: B 192 MET cc_start: 0.8358 (mtt) cc_final: 0.8147 (mtp) REVERT: B 599 ASN cc_start: 0.6854 (t0) cc_final: 0.6643 (t0) REVERT: B 641 ARG cc_start: 0.7290 (ttp80) cc_final: 0.6873 (ttp80) REVERT: B 704 ARG cc_start: 0.7057 (ttm170) cc_final: 0.6609 (mtt-85) REVERT: B 708 ARG cc_start: 0.7101 (tpp-160) cc_final: 0.6781 (ttm-80) REVERT: B 725 LYS cc_start: 0.7606 (tmtt) cc_final: 0.7376 (tmtp) REVERT: A 70 LYS cc_start: 0.7993 (tmmt) cc_final: 0.7314 (mppt) REVERT: A 200 SER cc_start: 0.8127 (m) cc_final: 0.7913 (m) REVERT: A 438 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.6512 (mp10) REVERT: A 626 TYR cc_start: 0.8282 (t80) cc_final: 0.8022 (t80) REVERT: A 641 ARG cc_start: 0.7263 (ttp80) cc_final: 0.6810 (ttp80) REVERT: A 704 ARG cc_start: 0.7009 (ttm170) cc_final: 0.6761 (mtm-85) outliers start: 14 outliers final: 6 residues processed: 135 average time/residue: 1.4032 time to fit residues: 203.1059 Evaluate side-chains 113 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 34 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 0.0020 chunk 110 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 0.0670 overall best weight: 2.6132 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10616 Z= 0.336 Angle : 0.606 9.022 14344 Z= 0.325 Chirality : 0.046 0.169 1570 Planarity : 0.004 0.039 1768 Dihedral : 16.357 102.181 1696 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.93 % Allowed : 12.57 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.49 (0.25), residues: 1210 helix: 1.36 (0.18), residues: 834 sheet: -0.90 (0.73), residues: 48 loop : -2.25 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 155 HIS 0.007 0.002 HIS B 619 PHE 0.022 0.002 PHE B 61 TYR 0.016 0.002 TYR A 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 : 1.259 Fit side-chains REVERT: B 74 ARG cc_start: 0.7412 (tpp-160) cc_final: 0.7155 (ttm-80) REVERT: B 289 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8366 (tp) REVERT: B 322 PHE cc_start: 0.7292 (m-80) cc_final: 0.7089 (m-10) REVERT: B 438 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.6299 (mp10) REVERT: B 641 ARG cc_start: 0.7388 (ttp80) cc_final: 0.7056 (ttt90) REVERT: B 704 ARG cc_start: 0.7120 (ttm170) cc_final: 0.6509 (mtt-85) REVERT: B 708 ARG cc_start: 0.7142 (tpp-160) cc_final: 0.6874 (ttm-80) REVERT: A 289 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8377 (tp) REVERT: A 438 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.6322 (mp10) REVERT: A 641 ARG cc_start: 0.7376 (ttp80) cc_final: 0.6982 (ttt90) outliers start: 31 outliers final: 22 residues processed: 123 average time/residue: 1.4881 time to fit residues: 195.6208 Evaluate side-chains 127 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 83 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 98 optimal weight: 6.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10616 Z= 0.142 Angle : 0.442 5.720 14344 Z= 0.242 Chirality : 0.038 0.139 1570 Planarity : 0.003 0.035 1768 Dihedral : 14.812 92.753 1696 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.98 % Allowed : 14.37 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.26), residues: 1210 helix: 2.17 (0.18), residues: 840 sheet: -0.74 (0.72), residues: 48 loop : -2.07 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 155 HIS 0.003 0.001 HIS A 130 PHE 0.014 0.001 PHE B 61 TYR 0.009 0.001 TYR B 180 ARG 0.002 0.000 ARG A 708 *********************** 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 138 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.471 Fit side-chains REVERT: B 129 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6621 (ptt180) REVERT: B 150 GLN cc_start: 0.7470 (tt0) cc_final: 0.7147 (tp40) REVERT: B 192 MET cc_start: 0.8329 (mtt) cc_final: 0.8100 (mtp) REVERT: B 257 LYS cc_start: 0.7037 (OUTLIER) cc_final: 0.6790 (mptt) REVERT: B 438 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.6246 (mp10) REVERT: B 641 ARG cc_start: 0.7265 (ttp80) cc_final: 0.6857 (ttt90) REVERT: B 704 ARG cc_start: 0.7099 (ttm170) cc_final: 0.6509 (mtt-85) REVERT: B 708 ARG cc_start: 0.7166 (tpp-160) cc_final: 0.6950 (ttm-80) REVERT: A 70 LYS cc_start: 0.7980 (tmmt) cc_final: 0.7284 (mppt) REVERT: A 150 GLN cc_start: 0.7467 (tt0) cc_final: 0.7142 (tp40) REVERT: A 257 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6676 (mptt) REVERT: A 641 ARG cc_start: 0.7281 (ttp80) cc_final: 0.6933 (ttp80) outliers start: 21 outliers final: 10 residues processed: 126 average time/residue: 1.5087 time to fit residues: 203.4302 Evaluate side-chains 124 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 595 HIS ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10616 Z= 0.377 Angle : 0.617 9.032 14344 Z= 0.328 Chirality : 0.047 0.168 1570 Planarity : 0.004 0.036 1768 Dihedral : 15.537 97.105 1696 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.69 % Allowed : 14.46 % 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: 1.14 (0.25), residues: 1210 helix: 1.95 (0.18), residues: 832 sheet: -0.56 (0.73), residues: 48 loop : -2.27 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 227 HIS 0.008 0.002 HIS B 619 PHE 0.023 0.002 PHE B 61 TYR 0.017 0.002 TYR B 212 ARG 0.004 0.001 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 144 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 105 time to evaluate : 1.254 Fit side-chains REVERT: B 129 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6677 (ptt180) REVERT: B 192 MET cc_start: 0.8359 (mtt) cc_final: 0.8095 (mtt) REVERT: B 438 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.6246 (mp10) REVERT: B 641 ARG cc_start: 0.7408 (ttp80) cc_final: 0.7110 (ttt90) REVERT: B 704 ARG cc_start: 0.7114 (ttm170) cc_final: 0.6499 (mtt-85) REVERT: B 707 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.6804 (mpp) REVERT: B 708 ARG cc_start: 0.7117 (tpp-160) cc_final: 0.6876 (ttm-80) REVERT: A 129 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6781 (ptm160) REVERT: A 257 LYS cc_start: 0.6965 (OUTLIER) cc_final: 0.6676 (mppt) REVERT: A 438 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.6107 (mp10) REVERT: A 641 ARG cc_start: 0.7403 (ttp80) cc_final: 0.7079 (ttt90) REVERT: A 725 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7247 (tmtp) outliers start: 39 outliers final: 26 residues processed: 130 average time/residue: 1.4563 time to fit residues: 203.1349 Evaluate side-chains 138 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 62 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 257 LYS 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 438 GLN Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 725 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 69 optimal weight: 0.0670 chunk 29 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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= 0.139 Angle : 0.438 5.646 14344 Z= 0.240 Chirality : 0.038 0.138 1570 Planarity : 0.003 0.033 1768 Dihedral : 14.533 92.118 1696 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.27 % Allowed : 16.26 % Favored : 81.47 % 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: 1.71 (0.26), residues: 1210 helix: 2.43 (0.18), residues: 830 sheet: -0.43 (0.75), residues: 48 loop : -2.19 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 712 HIS 0.004 0.001 HIS A 130 PHE 0.013 0.001 PHE B 61 TYR 0.010 0.001 TYR B 180 ARG 0.002 0.000 ARG A 651 *********************** 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 138 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.093 Fit side-chains REVERT: B 129 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6703 (ptt180) REVERT: B 150 GLN cc_start: 0.7421 (tt0) cc_final: 0.7100 (tp40) REVERT: B 192 MET cc_start: 0.8314 (mtt) cc_final: 0.8092 (mtp) REVERT: B 257 LYS cc_start: 0.7057 (mtpp) cc_final: 0.6462 (mptt) REVERT: B 641 ARG cc_start: 0.7272 (ttp80) cc_final: 0.6896 (ttt90) REVERT: B 704 ARG cc_start: 0.7097 (ttm170) cc_final: 0.6511 (mtt-85) REVERT: B 708 ARG cc_start: 0.7143 (tpp-160) cc_final: 0.6920 (ttm-80) REVERT: A 41 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8118 (tm) REVERT: A 129 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6575 (ptm160) REVERT: A 150 GLN cc_start: 0.7407 (tt0) cc_final: 0.7123 (tp40) REVERT: A 257 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6644 (mptt) REVERT: A 641 ARG cc_start: 0.7290 (ttp80) cc_final: 0.6900 (ttt90) outliers start: 24 outliers final: 12 residues processed: 126 average time/residue: 1.4525 time to fit residues: 195.8487 Evaluate side-chains 128 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 1.319 ------------------------------------------------------------------------------- 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 270 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 257 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 117 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 71 optimal weight: 0.0270 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2525 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= 0.172 Angle : 0.459 5.809 14344 Z= 0.249 Chirality : 0.039 0.141 1570 Planarity : 0.003 0.032 1768 Dihedral : 14.283 90.324 1696 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.80 % Allowed : 16.82 % 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: 1.83 (0.26), residues: 1210 helix: 2.53 (0.18), residues: 830 sheet: -0.33 (0.76), residues: 48 loop : -2.20 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 712 HIS 0.004 0.001 HIS B 619 PHE 0.015 0.001 PHE A 61 TYR 0.010 0.001 TYR B 212 ARG 0.002 0.000 ARG A 708 *********************** 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 133 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 1.360 Fit side-chains REVERT: B 129 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6738 (ptt180) REVERT: B 192 MET cc_start: 0.8317 (mtt) cc_final: 0.8102 (mtp) REVERT: B 257 LYS cc_start: 0.7056 (mtpp) cc_final: 0.6432 (mptt) REVERT: B 641 ARG cc_start: 0.7301 (ttp80) cc_final: 0.7000 (ttt90) REVERT: B 704 ARG cc_start: 0.7069 (ttm170) cc_final: 0.6448 (mtt-85) REVERT: B 708 ARG cc_start: 0.7158 (tpp-160) cc_final: 0.6948 (ttm-80) REVERT: A 41 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8109 (tm) REVERT: A 129 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6570 (ptm160) REVERT: A 150 GLN cc_start: 0.7433 (tt0) cc_final: 0.7159 (tp40) REVERT: A 257 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6667 (mptt) REVERT: A 641 ARG cc_start: 0.7327 (ttp80) cc_final: 0.6934 (ttt90) outliers start: 19 outliers final: 13 residues processed: 125 average time/residue: 1.5225 time to fit residues: 203.0406 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 : 1.335 ------------------------------------------------------------------------------- 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 270 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain 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 137 ASP Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 257 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10616 Z= 0.231 Angle : 0.502 6.389 14344 Z= 0.272 Chirality : 0.041 0.146 1570 Planarity : 0.004 0.032 1768 Dihedral : 14.576 90.839 1696 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.74 % Allowed : 15.97 % Favored : 81.29 % 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: 1.71 (0.26), residues: 1210 helix: 2.44 (0.18), residues: 828 sheet: -0.20 (0.78), residues: 48 loop : -2.22 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 712 HIS 0.005 0.001 HIS B 619 PHE 0.017 0.001 PHE A 61 TYR 0.012 0.002 TYR B 212 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 139 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 1.263 Fit side-chains REVERT: B 129 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6685 (ptt180) REVERT: B 150 GLN cc_start: 0.7440 (tt0) cc_final: 0.7163 (tm-30) REVERT: B 192 MET cc_start: 0.8327 (mtt) cc_final: 0.8074 (mtt) REVERT: B 641 ARG cc_start: 0.7345 (ttp80) cc_final: 0.7058 (ttt90) REVERT: B 704 ARG cc_start: 0.7051 (ttm170) cc_final: 0.6442 (mtt-85) REVERT: B 707 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6754 (mpp) REVERT: B 708 ARG cc_start: 0.7124 (tpp-160) cc_final: 0.6884 (ttm-80) REVERT: A 41 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8111 (tm) REVERT: A 129 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6734 (ptm160) REVERT: A 257 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6664 (mptt) REVERT: A 641 ARG cc_start: 0.7326 (ttp80) cc_final: 0.6979 (ttt90) outliers start: 29 outliers final: 18 residues processed: 129 average time/residue: 1.4252 time to fit residues: 197.2748 Evaluate side-chains 131 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 62 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 257 LYS Chi-restraints excluded: chain A residue 270 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2535 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= 0.194 Angle : 0.471 6.027 14344 Z= 0.256 Chirality : 0.040 0.144 1570 Planarity : 0.003 0.032 1768 Dihedral : 14.340 89.574 1696 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.55 % Allowed : 16.07 % 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: 1.81 (0.26), residues: 1210 helix: 2.52 (0.18), residues: 828 sheet: -0.16 (0.79), residues: 48 loop : -2.19 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 712 HIS 0.004 0.001 HIS A 619 PHE 0.016 0.001 PHE A 61 TYR 0.011 0.001 TYR A 432 ARG 0.002 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 137 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.974 Fit side-chains REVERT: B 129 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6707 (ptt180) REVERT: B 150 GLN cc_start: 0.7460 (tt0) cc_final: 0.7195 (tm-30) REVERT: B 192 MET cc_start: 0.8313 (mtt) cc_final: 0.8061 (mtt) REVERT: B 641 ARG cc_start: 0.7336 (ttp80) cc_final: 0.7036 (ttt90) REVERT: B 704 ARG cc_start: 0.7055 (ttm170) cc_final: 0.6434 (mtt-85) REVERT: B 708 ARG cc_start: 0.7118 (tpp-160) cc_final: 0.6891 (ttm-80) REVERT: A 41 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8094 (tm) REVERT: A 129 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6745 (ptm160) REVERT: A 150 GLN cc_start: 0.7390 (tt0) cc_final: 0.7144 (tm-30) REVERT: A 257 LYS cc_start: 0.6862 (OUTLIER) cc_final: 0.6649 (mptt) REVERT: A 641 ARG cc_start: 0.7325 (ttp80) cc_final: 0.6956 (ttt90) outliers start: 27 outliers final: 17 residues processed: 128 average time/residue: 1.3622 time to fit residues: 186.4919 Evaluate side-chains 132 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain 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 257 LYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 353 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2578 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= 0.184 Angle : 0.462 5.447 14344 Z= 0.251 Chirality : 0.040 0.142 1570 Planarity : 0.003 0.032 1768 Dihedral : 14.139 88.644 1696 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.27 % Allowed : 16.54 % Favored : 81.19 % 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: 1.88 (0.26), residues: 1210 helix: 2.55 (0.18), residues: 830 sheet: -0.09 (0.80), residues: 48 loop : -2.14 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 712 HIS 0.004 0.001 HIS B 619 PHE 0.015 0.001 PHE A 61 TYR 0.011 0.001 TYR B 432 ARG 0.002 0.000 ARG B 21 ********************** 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 135 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 1.199 Fit side-chains REVERT: B 129 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6761 (ptt180) REVERT: B 150 GLN cc_start: 0.7456 (tt0) cc_final: 0.7185 (tm-30) REVERT: B 192 MET cc_start: 0.8310 (mtt) cc_final: 0.8061 (mtt) REVERT: B 641 ARG cc_start: 0.7328 (ttp80) cc_final: 0.7027 (ttt90) REVERT: B 704 ARG cc_start: 0.7078 (ttm170) cc_final: 0.6462 (mtt-85) REVERT: B 708 ARG cc_start: 0.7115 (tpp-160) cc_final: 0.6912 (ttm-80) REVERT: A 41 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8092 (tm) REVERT: A 129 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6785 (ptm160) REVERT: A 150 GLN cc_start: 0.7391 (tt0) cc_final: 0.7147 (tm-30) REVERT: A 641 ARG cc_start: 0.7321 (ttp80) cc_final: 0.7011 (ttt90) REVERT: A 725 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7166 (tmtm) outliers start: 24 outliers final: 19 residues processed: 126 average time/residue: 1.4691 time to fit residues: 197.7775 Evaluate side-chains 134 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain 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 62 VAL Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 725 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 99 optimal weight: 0.0670 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.130445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.100147 restraints weight = 11504.777| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.54 r_work: 0.2911 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2578 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= 0.196 Angle : 0.473 5.991 14344 Z= 0.256 Chirality : 0.040 0.144 1570 Planarity : 0.003 0.032 1768 Dihedral : 14.155 89.950 1696 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.46 % Allowed : 16.64 % 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: 1.84 (0.26), residues: 1210 helix: 2.52 (0.18), residues: 830 sheet: -0.11 (0.80), residues: 48 loop : -2.16 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 712 HIS 0.004 0.001 HIS B 619 PHE 0.017 0.001 PHE B 61 TYR 0.011 0.001 TYR A 432 ARG 0.002 0.000 ARG B 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3997.06 seconds wall clock time: 72 minutes 53.63 seconds (4373.63 seconds total)