Starting phenix.real_space_refine on Sat Oct 24 05:12:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j03_61047/10_2026/9j03_61047.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j03_61047/10_2026/9j03_61047.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/9j03_61047/10_2026/9j03_61047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j03_61047/10_2026/9j03_61047.map" model { file = "/net/cci-nas-00/data/ceres_data/9j03_61047/10_2026/9j03_61047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j03_61047/10_2026/9j03_61047.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.035 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 74 5.16 5 C 7964 2.51 5 N 1974 2.21 5 O 2396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12412 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1133 Classifications: {'peptide': 140} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 133} Chain: "D" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1133 Classifications: {'peptide': 140} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 133} Chain: "B" Number of atoms: 4803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4803 Classifications: {'peptide': 601} Link IDs: {'PTRANS': 20, 'TRANS': 580} Chain: "A" Number of atoms: 4803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4803 Classifications: {'peptide': 601} Link IDs: {'PTRANS': 20, 'TRANS': 580} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 102 Unusual residues: {'2IL': 3, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'2IL:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 73 Unusual residues: {'2IL': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'2IL:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {'GP4': 1, 'NAG': 2, 'X6Z': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 88 Unusual residues: {'2IL': 1, 'GP4': 1, 'NAG': 2, 'X6Z': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'2IL:plan-1': 1} Unresolved non-hydrogen planarities: 1 Restraints were copied for chains: F, I, P Time building chain proxies: 3.21, per 1000 atoms: 0.26 Number of scatterers: 12412 At special positions: 0 Unit cell: (155.184, 97.52, 110.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 4 15.00 O 2396 8.00 N 1974 7.00 C 7964 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 51 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 105 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 51 " distance=2.03 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS D 95 " - pdb=" SG CYS D 105 " distance=2.03 Simple disulfide: pdb=" SG CYS B 29 " - pdb=" SG CYS B 40 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 306 " distance=2.02 Simple disulfide: pdb=" SG CYS B 583 " - pdb=" SG CYS B 609 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 627 " distance=2.03 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 40 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 306 " distance=2.02 Simple disulfide: pdb=" SG CYS A 583 " - pdb=" SG CYS A 609 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 627 " distance=2.03 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=6, symmetry=0 Links applied ALPHA1- OXT " GP4 A 701 " - " X6Z A 702 " " GP4 B 701 " - " X6Z B 702 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " NAG H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " NAG P 3 " NAG-ASN " NAG A 704 " - " ASN A 205 " " NAG A 705 " - " ASN A 497 " " NAG B 703 " - " ASN B 205 " " NAG B 704 " - " ASN B 497 " " NAG C 204 " - " ASN C 114 " " NAG D 201 " - " ASN D 114 " " NAG E 1 " - " ASN C 26 " " NAG F 1 " - " ASN D 26 " " NAG G 1 " - " ASN B 526 " " NAG H 1 " - " ASN A 575 " " NAG I 1 " - " ASN A 526 " " NAG P 1 " - " ASN B 575 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 567.4 milliseconds 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2836 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 28 sheets defined 5.8% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 239 through 250 Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.637A pdb=" N ASN B 282 " --> pdb=" O GLY B 279 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 283 " --> pdb=" O LEU B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 279 through 283' Processing helix chain 'B' and resid 392 through 397 removed outlier: 3.971A pdb=" N PHE B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 595 removed outlier: 3.544A pdb=" N LEU B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 239 through 250 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.636A pdb=" N ASN A 282 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 283 " --> pdb=" O LEU A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 283' Processing helix chain 'A' and resid 392 through 397 removed outlier: 3.970A pdb=" N PHE A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 595 removed outlier: 3.543A pdb=" N LEU A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 22 through 27 removed outlier: 3.559A pdb=" N VAL C 24 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ILE C 32 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN C 26 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA C 30 " --> pdb=" O ASN C 26 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N MET C 145 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N SER C 139 " --> pdb=" O MET C 145 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE C 147 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE C 80 " --> pdb=" O PRO C 88 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL C 82 " --> pdb=" O ASN C 86 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ASN C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 49 Processing sheet with id=AA3, first strand: chain 'D' and resid 22 through 27 removed outlier: 3.558A pdb=" N VAL D 24 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ILE D 32 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN D 26 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA D 30 " --> pdb=" O ASN D 26 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N MET D 145 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N SER D 139 " --> pdb=" O MET D 145 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE D 147 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE D 80 " --> pdb=" O PRO D 88 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL D 82 " --> pdb=" O ASN D 86 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ASN D 86 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 45 through 49 Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 33 removed outlier: 6.410A pdb=" N THR B 37 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER B 62 " --> pdb=" O CYS B 40 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU B 59 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 107 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 93 removed outlier: 3.553A pdb=" N ILE B 93 " --> pdb=" O SER B 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 179 through 181 removed outlier: 7.094A pdb=" N LEU B 180 " --> pdb=" O ASP B 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 189 through 190 removed outlier: 3.577A pdb=" N ILE B 190 " --> pdb=" O PHE B 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 234 removed outlier: 6.478A pdb=" N LEU B 231 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N GLY B 261 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU B 233 " --> pdb=" O GLY B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 315 through 316 removed outlier: 6.624A pdb=" N LEU B 315 " --> pdb=" O VAL B 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 412 through 413 removed outlier: 6.904A pdb=" N ILE B 412 " --> pdb=" O LYS B 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 451 through 453 removed outlier: 6.605A pdb=" N LEU B 452 " --> pdb=" O LYS B 477 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU B 476 " --> pdb=" O ASP B 502 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 501 " --> pdb=" O VAL B 524 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 460 through 461 Processing sheet with id=AB5, first strand: chain 'B' and resid 487 through 488 Processing sheet with id=AB6, first strand: chain 'B' and resid 534 through 535 Processing sheet with id=AB7, first strand: chain 'B' and resid 548 through 550 removed outlier: 6.609A pdb=" N LEU B 549 " --> pdb=" O ASN B 575 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 30 through 33 removed outlier: 6.409A pdb=" N THR A 37 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A 62 " --> pdb=" O CYS A 40 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU A 59 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU A 107 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 92 through 93 removed outlier: 3.553A pdb=" N ILE A 93 " --> pdb=" O SER A 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 179 through 181 removed outlier: 7.094A pdb=" N LEU A 180 " --> pdb=" O ASP A 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 189 through 190 removed outlier: 3.578A pdb=" N ILE A 190 " --> pdb=" O PHE A 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 231 through 234 removed outlier: 6.478A pdb=" N LEU A 231 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N GLY A 261 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU A 233 " --> pdb=" O GLY A 261 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 315 through 316 removed outlier: 6.624A pdb=" N LEU A 315 " --> pdb=" O VAL A 338 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'A' and resid 412 through 413 removed outlier: 6.905A pdb=" N ILE A 412 " --> pdb=" O LYS A 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 451 through 453 removed outlier: 6.604A pdb=" N LEU A 452 " --> pdb=" O LYS A 477 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU A 476 " --> pdb=" O ASP A 502 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 501 " --> pdb=" O VAL A 524 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 460 through 461 Processing sheet with id=AC8, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AC9, first strand: chain 'A' and resid 534 through 535 Processing sheet with id=AD1, first strand: chain 'A' and resid 548 through 550 removed outlier: 6.609A pdb=" N LEU A 549 " --> pdb=" O ASN A 575 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 142 hydrogen bonds defined for protein. 354 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.57 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3823 1.34 - 1.46: 2845 1.46 - 1.58: 5868 1.58 - 1.71: 20 1.71 - 1.83: 102 Bond restraints: 12658 Sorted by residual: bond pdb=" C15 2IL C 201 " pdb=" O4 2IL C 201 " ideal model delta sigma weight residual 1.208 1.409 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C15 2IL D 202 " pdb=" O4 2IL D 202 " ideal model delta sigma weight residual 1.208 1.409 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C15 2IL C 202 " pdb=" O4 2IL C 202 " ideal model delta sigma weight residual 1.208 1.406 -0.198 2.00e-02 2.50e+03 9.76e+01 bond pdb=" C15 2IL D 203 " pdb=" O4 2IL D 203 " ideal model delta sigma weight residual 1.208 1.405 -0.197 2.00e-02 2.50e+03 9.71e+01 bond pdb=" C15 2IL C 203 " pdb=" O4 2IL C 203 " ideal model delta sigma weight residual 1.208 1.404 -0.196 2.00e-02 2.50e+03 9.60e+01 ... (remaining 12653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 16374 2.55 - 5.11: 567 5.11 - 7.66: 104 7.66 - 10.22: 29 10.22 - 12.77: 6 Bond angle restraints: 17080 Sorted by residual: angle pdb=" N GLU A 563 " pdb=" CA GLU A 563 " pdb=" C GLU A 563 " ideal model delta sigma weight residual 113.30 100.53 12.77 1.34e+00 5.57e-01 9.09e+01 angle pdb=" N GLU B 563 " pdb=" CA GLU B 563 " pdb=" C GLU B 563 " ideal model delta sigma weight residual 113.30 100.53 12.77 1.34e+00 5.57e-01 9.08e+01 angle pdb=" N GLN B 562 " pdb=" CA GLN B 562 " pdb=" C GLN B 562 " ideal model delta sigma weight residual 110.70 101.43 9.27 1.55e+00 4.16e-01 3.58e+01 angle pdb=" N GLN A 562 " pdb=" CA GLN A 562 " pdb=" C GLN A 562 " ideal model delta sigma weight residual 110.70 101.43 9.27 1.55e+00 4.16e-01 3.58e+01 angle pdb=" N ASN A 265 " pdb=" CA ASN A 265 " pdb=" C ASN A 265 " ideal model delta sigma weight residual 112.54 119.65 -7.11 1.22e+00 6.72e-01 3.40e+01 ... (remaining 17075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.13: 7398 23.13 - 46.26: 509 46.26 - 69.39: 91 69.39 - 92.53: 40 92.53 - 115.66: 10 Dihedral angle restraints: 8048 sinusoidal: 3688 harmonic: 4360 Sorted by residual: dihedral pdb=" CB CYS C 37 " pdb=" SG CYS C 37 " pdb=" SG CYS C 148 " pdb=" CB CYS C 148 " ideal model delta sinusoidal sigma weight residual -86.00 -32.54 -53.46 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CB CYS D 37 " pdb=" SG CYS D 37 " pdb=" SG CYS D 148 " pdb=" CB CYS D 148 " ideal model delta sinusoidal sigma weight residual -86.00 -32.55 -53.45 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CA ASP A 273 " pdb=" C ASP A 273 " pdb=" N LYS A 274 " pdb=" CA LYS A 274 " ideal model delta harmonic sigma weight residual -180.00 -152.69 -27.31 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 8045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.256: 1958 0.256 - 0.513: 38 0.513 - 0.769: 2 0.769 - 1.026: 0 1.026 - 1.282: 2 Chirality restraints: 2000 Sorted by residual: chirality pdb=" C1 NAG H 3 " pdb=" O4 NAG H 2 " pdb=" C2 NAG H 3 " pdb=" O5 NAG H 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.12 -1.28 2.00e-02 2.50e+03 4.11e+03 chirality pdb=" C1 NAG P 3 " pdb=" O4 NAG P 2 " pdb=" C2 NAG P 3 " pdb=" O5 NAG P 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.12 -1.28 2.00e-02 2.50e+03 4.09e+03 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-02 2.50e+03 1.41e+03 ... (remaining 1997 not shown) Planarity restraints: 2142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C15 2IL C 202 " 0.101 2.00e-02 2.50e+03 5.85e-02 3.42e+01 pdb=" C16 2IL C 202 " -0.032 2.00e-02 2.50e+03 pdb=" O3 2IL C 202 " -0.035 2.00e-02 2.50e+03 pdb=" O4 2IL C 202 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 2IL D 203 " -0.101 2.00e-02 2.50e+03 5.84e-02 3.42e+01 pdb=" C16 2IL D 203 " 0.032 2.00e-02 2.50e+03 pdb=" O3 2IL D 203 " 0.035 2.00e-02 2.50e+03 pdb=" O4 2IL D 203 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 2IL A 703 " -0.101 2.00e-02 2.50e+03 5.81e-02 3.38e+01 pdb=" C16 2IL A 703 " 0.031 2.00e-02 2.50e+03 pdb=" O3 2IL A 703 " 0.035 2.00e-02 2.50e+03 pdb=" O4 2IL A 703 " 0.035 2.00e-02 2.50e+03 ... (remaining 2139 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 265 2.66 - 3.22: 11370 3.22 - 3.78: 17061 3.78 - 4.34: 25553 4.34 - 4.90: 41720 Nonbonded interactions: 95969 Sorted by model distance: nonbonded pdb=" O GLY D 123 " pdb=" OG SER A 416 " model vdw 2.105 3.040 nonbonded pdb=" CD2 HIS B 458 " pdb=" CD2 HIS A 458 " model vdw 2.200 3.480 nonbonded pdb=" OD1 ASP B 405 " pdb=" OG SER B 407 " model vdw 2.217 3.040 nonbonded pdb=" OD1 ASP A 405 " pdb=" OG SER A 407 " model vdw 2.218 3.040 nonbonded pdb=" O SER C 127 " pdb=" OH TYR C 131 " model vdw 2.234 3.040 ... (remaining 95964 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 27 through 702 or resid 704)) selection = (chain 'B' and (resid 27 through 702 or resid 704)) } ncs_group { reference = (chain 'C' and (resid 19 through 158 or (resid 202 through 203 and (name C1 or n \ ame C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name C \ 22 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 C9 or name O2 or name O3 or name O4 \ )))) selection = (chain 'D' and (resid 19 through 158 or (resid 202 through 203 and (name C1 or n \ ame C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name C \ 22 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 C9 or name O2 or name O3 or name O4 \ )))) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.950 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: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.000 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 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:7.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 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 0.201 12702 Z= 0.516 Angle : 1.510 41.228 17180 Z= 0.672 Chirality : 0.086 1.282 2000 Planarity : 0.006 0.118 2130 Dihedral : 16.711 115.656 5170 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.08 % Favored : 87.92 % Rotamer: Outliers : 0.07 % Allowed : 4.93 % Favored : 94.99 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.12 (0.17), residues: 1474 helix: -4.46 (0.25), residues: 82 sheet: -3.09 (0.24), residues: 362 loop : -3.69 (0.15), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 196 TYR 0.017 0.002 TYR D 75 PHE 0.015 0.002 PHE B 330 TRP 0.007 0.001 TRP A 593 HIS 0.004 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00991 / 0.50 (12658) covalent geometry : angle 1.15051 / 0.59 (17080) SS BOND : bond 0.00364 / 0.22 ( 14) SS BOND : angle 2.60260 / 1.65 ( 28) hydrogen bonds : bond 0.20746 / 14.01 ( 142) hydrogen bonds : angle 9.01302 / 6.37 ( 354) glycosidic custom : bond 0.02745 / 1.38 ( 2) glycosidic custom : angle 3.20499 / 1.82 ( 6) Misc. bond : bond 0.03955 / 1.84 ( 6) link_BETA1-4 : bond 0.06475 / 3.44 ( 10) link_BETA1-4 : angle 21.62794 / 13.95 ( 30) link_NAG-ASN : bond 0.02427 / 1.47 ( 12) link_NAG-ASN : angle 7.93589 / 4.49 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.533 Fit side-chains REVERT: C 40 MET cc_start: 0.5831 (pmm) cc_final: 0.5620 (pmt) REVERT: C 85 MET cc_start: 0.7929 (mtm) cc_final: 0.7637 (mtp) REVERT: D 40 MET cc_start: 0.5737 (pmm) cc_final: 0.5450 (pmt) REVERT: D 85 MET cc_start: 0.7923 (mtm) cc_final: 0.7668 (mtp) REVERT: B 39 GLN cc_start: 0.7746 (pp30) cc_final: 0.7448 (pp30) REVERT: B 274 LYS cc_start: 0.8206 (mtmt) cc_final: 0.7970 (mmtt) REVERT: A 213 ASN cc_start: 0.4428 (m-40) cc_final: 0.4127 (m-40) REVERT: A 273 ASP cc_start: 0.7314 (p0) cc_final: 0.7091 (m-30) REVERT: A 274 LYS cc_start: 0.8072 (mtmt) cc_final: 0.7732 (mmtm) outliers start: 1 outliers final: 1 residues processed: 210 average time/residue: 0.5657 time to fit residues: 129.0551 Evaluate side-chains 98 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 337 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 19 GLN C 49 ASN C 83 ASN C 86 ASN D 19 GLN D 49 ASN D 83 ASN D 86 ASN ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 309 ASN B 339 ASN B 361 ASN B 510 GLN B 530 ASN A 219 GLN A 268 ASN A 309 ASN A 339 ASN A 361 ASN A 365 ASN A 510 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.181518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.156588 restraints weight = 18858.619| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 2.95 r_work: 0.4273 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12702 Z= 0.162 Angle : 0.881 23.324 17180 Z= 0.403 Chirality : 0.053 0.537 2000 Planarity : 0.004 0.042 2130 Dihedral : 14.051 91.456 2276 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 2.47 % Allowed : 13.35 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.48 (0.18), residues: 1474 helix: -3.36 (0.40), residues: 82 sheet: -2.73 (0.25), residues: 376 loop : -3.25 (0.16), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 460 TYR 0.024 0.002 TYR A 328 PHE 0.028 0.002 PHE B 75 TRP 0.008 0.001 TRP B 593 HIS 0.007 0.001 HIS B 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (12658) covalent geometry : angle 0.79021 / 0.38 (17080) SS BOND : bond 0.00186 / 0.11 ( 14) SS BOND : angle 1.07582 / 0.67 ( 28) hydrogen bonds : bond 0.03647 / 2.37 ( 142) hydrogen bonds : angle 6.77277 / 4.85 ( 354) glycosidic custom : bond 0.00158 / 0.08 ( 2) glycosidic custom : angle 3.00790 / 1.59 ( 6) Misc. bond : bond 0.00185 / 0.10 ( 6) link_BETA1-4 : bond 0.01944 / 0.86 ( 10) link_BETA1-4 : angle 5.21027 / 3.94 ( 30) link_NAG-ASN : bond 0.01225 / 0.75 ( 12) link_NAG-ASN : angle 7.02603 / 3.88 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: C 40 MET cc_start: 0.5671 (pmm) cc_final: 0.4763 (pp-130) REVERT: C 85 MET cc_start: 0.8239 (mtm) cc_final: 0.8004 (mtp) REVERT: C 130 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7927 (ttpt) REVERT: D 40 MET cc_start: 0.5518 (pmm) cc_final: 0.5252 (pmt) REVERT: D 85 MET cc_start: 0.8237 (mtm) cc_final: 0.8002 (mtp) REVERT: D 130 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8139 (ttpt) REVERT: B 39 GLN cc_start: 0.7281 (pp30) cc_final: 0.6783 (pp30) REVERT: B 219 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7844 (tm-30) REVERT: B 243 MET cc_start: 0.6062 (ttt) cc_final: 0.5583 (ttp) REVERT: B 272 PHE cc_start: 0.7920 (t80) cc_final: 0.7619 (t80) REVERT: B 557 MET cc_start: 0.7700 (mmt) cc_final: 0.7296 (mmt) REVERT: A 243 MET cc_start: 0.6165 (ttt) cc_final: 0.5723 (ttm) REVERT: A 274 LYS cc_start: 0.8440 (mtmt) cc_final: 0.7990 (mmtt) REVERT: A 557 MET cc_start: 0.7623 (mmt) cc_final: 0.7296 (mmt) outliers start: 34 outliers final: 3 residues processed: 145 average time/residue: 0.5223 time to fit residues: 83.0999 Evaluate side-chains 92 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 281 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: [97, 85, 118, 34, 1, 50, 111, 55, 18, 71, 133] chunk 97 optimal weight: 0.6980 chunk 85 optimal weight: 0.0970 chunk 118 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 55 optimal weight: 0.0370 chunk 18 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 62 HIS D 83 ASN ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN B 339 ASN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN B 579 ASN A 339 ASN ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.182650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.157700 restraints weight = 18994.880| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 2.95 r_work: 0.4286 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12702 Z= 0.128 Angle : 0.795 22.894 17180 Z= 0.364 Chirality : 0.049 0.410 2000 Planarity : 0.004 0.042 2130 Dihedral : 12.705 81.276 2274 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 2.54 % Allowed : 14.15 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.96 (0.19), residues: 1474 helix: -2.09 (0.56), residues: 80 sheet: -2.37 (0.26), residues: 358 loop : -2.98 (0.17), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 196 TYR 0.017 0.001 TYR A 551 PHE 0.025 0.001 PHE B 75 TRP 0.004 0.001 TRP B 593 HIS 0.006 0.001 HIS B 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (12658) covalent geometry : angle 0.70829 / 0.34 (17080) SS BOND : bond 0.00187 / 0.11 ( 14) SS BOND : angle 0.86982 / 0.51 ( 28) hydrogen bonds : bond 0.03165 / 2.08 ( 142) hydrogen bonds : angle 6.34397 / 4.52 ( 354) glycosidic custom : bond 0.00288 / 0.15 ( 2) glycosidic custom : angle 2.26654 / 1.21 ( 6) Misc. bond : bond 0.00021 / 0.01 ( 6) link_BETA1-4 : bond 0.01818 / 0.81 ( 10) link_BETA1-4 : angle 4.46961 / 3.44 ( 30) link_NAG-ASN : bond 0.01042 / 0.63 ( 12) link_NAG-ASN : angle 6.71995 / 3.76 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 0.473 Fit side-chains REVERT: C 40 MET cc_start: 0.5571 (pmm) cc_final: 0.5180 (pmt) REVERT: C 85 MET cc_start: 0.8296 (mtm) cc_final: 0.8087 (mtp) REVERT: D 40 MET cc_start: 0.5368 (pmm) cc_final: 0.5099 (pmt) REVERT: D 85 MET cc_start: 0.8265 (mtm) cc_final: 0.8041 (mtp) REVERT: B 39 GLN cc_start: 0.7354 (pp30) cc_final: 0.6783 (pp30) REVERT: B 243 MET cc_start: 0.6120 (ttt) cc_final: 0.5711 (ttp) REVERT: B 388 LYS cc_start: 0.7909 (tptt) cc_final: 0.7668 (mmtp) REVERT: B 437 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7443 (ttp) REVERT: B 466 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.7126 (tp) REVERT: B 557 MET cc_start: 0.7636 (mmt) cc_final: 0.7155 (mmt) REVERT: B 579 ASN cc_start: 0.4409 (OUTLIER) cc_final: 0.4142 (p0) REVERT: A 213 ASN cc_start: 0.4400 (m-40) cc_final: 0.4137 (m-40) REVERT: A 243 MET cc_start: 0.6224 (ttt) cc_final: 0.5804 (ttm) REVERT: A 274 LYS cc_start: 0.8493 (mtmt) cc_final: 0.8112 (mmtm) REVERT: A 557 MET cc_start: 0.7572 (mmt) cc_final: 0.7154 (mmt) outliers start: 35 outliers final: 9 residues processed: 122 average time/residue: 0.5065 time to fit residues: 68.0124 Evaluate side-chains 91 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 579 ASN Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 514 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: [118, 1, 130, 74, 135, 99, 47, 132, 85, 92, 96] chunk 118 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 130 optimal weight: 0.3980 chunk 74 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 49 ASN B 51 ASN ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 ASN A 51 ASN A 339 ASN A 562 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.182277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.156866 restraints weight = 18780.470| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 2.99 r_work: 0.4266 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12702 Z= 0.134 Angle : 0.781 22.403 17180 Z= 0.358 Chirality : 0.050 0.418 2000 Planarity : 0.004 0.040 2130 Dihedral : 11.584 83.093 2274 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 2.76 % Allowed : 15.38 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.76 (0.20), residues: 1474 helix: -1.65 (0.62), residues: 80 sheet: -2.20 (0.26), residues: 358 loop : -2.88 (0.17), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 234 TYR 0.021 0.001 TYR A 551 PHE 0.027 0.001 PHE B 75 TRP 0.004 0.001 TRP B 593 HIS 0.005 0.001 HIS B 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (12658) covalent geometry : angle 0.69524 / 0.34 (17080) SS BOND : bond 0.00223 / 0.13 ( 14) SS BOND : angle 1.89877 / 1.09 ( 28) hydrogen bonds : bond 0.03003 / 1.99 ( 142) hydrogen bonds : angle 6.10814 / 4.34 ( 354) glycosidic custom : bond 0.00273 / 0.14 ( 2) glycosidic custom : angle 2.29543 / 1.22 ( 6) Misc. bond : bond 0.00026 / 0.01 ( 6) link_BETA1-4 : bond 0.01657 / 0.74 ( 10) link_BETA1-4 : angle 4.10470 / 3.14 ( 30) link_NAG-ASN : bond 0.01011 / 0.60 ( 12) link_NAG-ASN : angle 6.65638 / 3.72 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 91 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: C 40 MET cc_start: 0.5454 (pmm) cc_final: 0.5064 (pmt) REVERT: C 85 MET cc_start: 0.8291 (mtm) cc_final: 0.8033 (mtp) REVERT: D 40 MET cc_start: 0.5302 (pmm) cc_final: 0.5043 (pmt) REVERT: D 85 MET cc_start: 0.8281 (mtm) cc_final: 0.8033 (mtp) REVERT: B 39 GLN cc_start: 0.7346 (pp30) cc_final: 0.6743 (pp30) REVERT: B 557 MET cc_start: 0.7649 (mmt) cc_final: 0.7194 (mmt) REVERT: A 213 ASN cc_start: 0.4475 (m-40) cc_final: 0.4206 (m-40) REVERT: A 243 MET cc_start: 0.6233 (ttt) cc_final: 0.5810 (ttm) REVERT: A 274 LYS cc_start: 0.8530 (mtmt) cc_final: 0.8172 (mttm) REVERT: A 557 MET cc_start: 0.7610 (mmt) cc_final: 0.7210 (mmt) outliers start: 38 outliers final: 13 residues processed: 120 average time/residue: 0.5343 time to fit residues: 70.4967 Evaluate side-chains 94 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 596 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: [31, 73, 33, 98, 21, 106, 104, 79, 52, 22, 100] chunk 31 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 chunk 104 optimal weight: 0.4980 chunk 79 optimal weight: 0.0970 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 100 optimal weight: 0.0270 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 GLN A 339 ASN A 361 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.183434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.158669 restraints weight = 18923.878| |-----------------------------------------------------------------------------| r_work (start): 0.4415 rms_B_bonded: 2.97 r_work: 0.4297 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12702 Z= 0.114 Angle : 0.741 22.105 17180 Z= 0.341 Chirality : 0.049 0.414 2000 Planarity : 0.003 0.036 2130 Dihedral : 11.015 89.342 2274 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.32 % Allowed : 16.55 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.57 (0.20), residues: 1474 helix: -1.60 (0.62), residues: 80 sheet: -2.04 (0.26), residues: 362 loop : -2.74 (0.17), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 234 TYR 0.023 0.001 TYR B 551 PHE 0.029 0.001 PHE A 75 TRP 0.004 0.000 TRP B 593 HIS 0.004 0.001 HIS B 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (12658) covalent geometry : angle 0.66023 / 0.32 (17080) SS BOND : bond 0.00275 / 0.17 ( 14) SS BOND : angle 1.35855 / 0.78 ( 28) hydrogen bonds : bond 0.02746 / 1.79 ( 142) hydrogen bonds : angle 5.83984 / 4.14 ( 354) glycosidic custom : bond 0.00352 / 0.18 ( 2) glycosidic custom : angle 2.03472 / 1.08 ( 6) Misc. bond : bond 0.00023 / 0.01 ( 6) link_BETA1-4 : bond 0.01389 / 0.62 ( 10) link_BETA1-4 : angle 3.59756 / 2.75 ( 30) link_NAG-ASN : bond 0.00970 / 0.58 ( 12) link_NAG-ASN : angle 6.51094 / 3.65 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 0.570 Fit side-chains REVERT: C 40 MET cc_start: 0.5407 (pmm) cc_final: 0.5023 (pmt) REVERT: D 40 MET cc_start: 0.5364 (pmm) cc_final: 0.5088 (pmt) REVERT: D 85 MET cc_start: 0.8295 (mtm) cc_final: 0.8042 (mtp) REVERT: D 128 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7491 (mmpt) REVERT: B 39 GLN cc_start: 0.7424 (pp30) cc_final: 0.6793 (pp30) REVERT: B 243 MET cc_start: 0.6165 (ttt) cc_final: 0.5810 (ttp) REVERT: B 557 MET cc_start: 0.7559 (mmt) cc_final: 0.7127 (mmt) REVERT: A 213 ASN cc_start: 0.4527 (m-40) cc_final: 0.4269 (m-40) REVERT: A 243 MET cc_start: 0.6253 (ttt) cc_final: 0.5841 (ttm) REVERT: A 274 LYS cc_start: 0.8548 (mtmt) cc_final: 0.8167 (mttm) REVERT: A 371 ASP cc_start: 0.7961 (t70) cc_final: 0.7689 (t70) REVERT: A 557 MET cc_start: 0.7640 (mmt) cc_final: 0.7243 (mmt) outliers start: 32 outliers final: 9 residues processed: 117 average time/residue: 0.5472 time to fit residues: 70.3532 Evaluate side-chains 90 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 514 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: [49, 47, 20, 29, 12, 45, 63, 85, 18, 111, 104] chunk 49 optimal weight: 4.9990 chunk 47 optimal weight: 0.0970 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN B 339 ASN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 64 ASN A 219 GLN A 339 ASN A 361 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.179043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.153574 restraints weight = 18810.184| |-----------------------------------------------------------------------------| r_work (start): 0.4341 rms_B_bonded: 2.97 r_work: 0.4225 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12702 Z= 0.193 Angle : 0.837 22.075 17180 Z= 0.387 Chirality : 0.052 0.452 2000 Planarity : 0.004 0.038 2130 Dihedral : 10.920 86.896 2274 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 2.39 % Allowed : 17.13 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.20), residues: 1474 helix: -1.83 (0.59), residues: 82 sheet: -2.15 (0.25), residues: 380 loop : -2.72 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 234 TYR 0.024 0.002 TYR B 551 PHE 0.024 0.002 PHE A 75 TRP 0.006 0.001 TRP A 332 HIS 0.006 0.001 HIS C 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (12658) covalent geometry : angle 0.75763 / 0.37 (17080) SS BOND : bond 0.00441 / 0.28 ( 14) SS BOND : angle 1.41486 / 0.84 ( 28) hydrogen bonds : bond 0.03159 / 2.05 ( 142) hydrogen bonds : angle 6.04674 / 4.29 ( 354) glycosidic custom : bond 0.00188 / 0.09 ( 2) glycosidic custom : angle 2.78287 / 1.47 ( 6) Misc. bond : bond 0.00054 / 0.03 ( 6) link_BETA1-4 : bond 0.01680 / 0.75 ( 10) link_BETA1-4 : angle 4.04611 / 3.10 ( 30) link_NAG-ASN : bond 0.01020 / 0.61 ( 12) link_NAG-ASN : angle 6.76345 / 3.76 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 0.487 Fit side-chains REVERT: C 40 MET cc_start: 0.5427 (pmm) cc_final: 0.5077 (pmt) REVERT: D 40 MET cc_start: 0.5391 (pmm) cc_final: 0.4984 (pmt) REVERT: D 85 MET cc_start: 0.8372 (mtm) cc_final: 0.8090 (mtp) REVERT: D 128 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7515 (mmpt) REVERT: D 144 GLU cc_start: 0.7840 (tp30) cc_final: 0.7627 (mm-30) REVERT: B 39 GLN cc_start: 0.7419 (pp30) cc_final: 0.6735 (pp30) REVERT: B 243 MET cc_start: 0.6135 (ttt) cc_final: 0.5786 (ttp) REVERT: B 557 MET cc_start: 0.7586 (mmt) cc_final: 0.7169 (mmt) REVERT: A 213 ASN cc_start: 0.4717 (m-40) cc_final: 0.4437 (m-40) REVERT: A 243 MET cc_start: 0.6256 (ttt) cc_final: 0.5838 (ttm) REVERT: A 274 LYS cc_start: 0.8687 (mtmt) cc_final: 0.8264 (mmtm) REVERT: A 371 ASP cc_start: 0.8076 (t70) cc_final: 0.7735 (t70) REVERT: A 557 MET cc_start: 0.7652 (mmt) cc_final: 0.7262 (mmt) outliers start: 33 outliers final: 10 residues processed: 110 average time/residue: 0.5205 time to fit residues: 63.0041 Evaluate side-chains 87 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 514 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: [58, 22, 86, 7, 120, 88, 53, 45, 26, 114, 32] chunk 58 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN B 334 HIS B 339 ASN B 365 ASN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN A 334 HIS A 339 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.175925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.150445 restraints weight = 18950.921| |-----------------------------------------------------------------------------| r_work (start): 0.4305 rms_B_bonded: 2.97 r_work: 0.4187 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12702 Z= 0.250 Angle : 0.908 22.047 17180 Z= 0.419 Chirality : 0.054 0.459 2000 Planarity : 0.004 0.045 2130 Dihedral : 11.097 81.959 2274 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 2.76 % Allowed : 18.07 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.87 (0.19), residues: 1474 helix: -2.50 (0.50), residues: 96 sheet: -2.36 (0.24), residues: 382 loop : -2.82 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 289 TYR 0.026 0.002 TYR B 551 PHE 0.029 0.002 PHE B 75 TRP 0.004 0.001 TRP B 332 HIS 0.007 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.25 (12658) covalent geometry : angle 0.82846 / 0.40 (17080) SS BOND : bond 0.00328 / 0.20 ( 14) SS BOND : angle 1.36908 / 0.83 ( 28) hydrogen bonds : bond 0.03392 / 2.23 ( 142) hydrogen bonds : angle 6.28537 / 4.46 ( 354) glycosidic custom : bond 0.00101 / 0.05 ( 2) glycosidic custom : angle 3.19514 / 1.70 ( 6) Misc. bond : bond 0.00065 / 0.04 ( 6) link_BETA1-4 : bond 0.01947 / 0.87 ( 10) link_BETA1-4 : angle 4.39596 / 3.40 ( 30) link_NAG-ASN : bond 0.01096 / 0.66 ( 12) link_NAG-ASN : angle 6.98143 / 3.87 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 77 time to evaluate : 0.398 Fit side-chains REVERT: D 40 MET cc_start: 0.5479 (pmm) cc_final: 0.5172 (pmt) REVERT: D 85 MET cc_start: 0.8385 (mtm) cc_final: 0.8061 (mtp) REVERT: D 128 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7450 (mmpt) REVERT: B 39 GLN cc_start: 0.7504 (pp30) cc_final: 0.6845 (pp30) REVERT: B 243 MET cc_start: 0.6197 (ttt) cc_final: 0.5818 (ttp) REVERT: B 557 MET cc_start: 0.7637 (mmt) cc_final: 0.7335 (mmm) REVERT: A 213 ASN cc_start: 0.5010 (m-40) cc_final: 0.4606 (m-40) REVERT: A 243 MET cc_start: 0.6348 (ttt) cc_final: 0.5902 (ttm) REVERT: A 274 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8488 (mttm) REVERT: A 557 MET cc_start: 0.7701 (mmt) cc_final: 0.7278 (mmt) outliers start: 38 outliers final: 15 residues processed: 111 average time/residue: 0.5052 time to fit residues: 61.9483 Evaluate side-chains 86 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 594 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: [53, 32, 126, 39, 15, 18, 1, 119, 46, 114, 135] chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN B 334 HIS B 339 ASN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN A 334 HIS A 339 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.173799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.148428 restraints weight = 18945.085| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 2.97 r_work: 0.4165 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 12702 Z= 0.295 Angle : 0.961 22.207 17180 Z= 0.446 Chirality : 0.056 0.465 2000 Planarity : 0.005 0.048 2130 Dihedral : 11.256 79.372 2274 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.42 % Favored : 87.58 % Rotamer: Outliers : 2.54 % Allowed : 19.16 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.19), residues: 1474 helix: -2.58 (0.49), residues: 96 sheet: -2.44 (0.24), residues: 382 loop : -2.93 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 234 TYR 0.025 0.002 TYR B 551 PHE 0.025 0.003 PHE B 533 TRP 0.008 0.001 TRP A 593 HIS 0.010 0.002 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.29 (12658) covalent geometry : angle 0.88089 / 0.43 (17080) SS BOND : bond 0.00630 / 0.38 ( 14) SS BOND : angle 1.54648 / 0.94 ( 28) hydrogen bonds : bond 0.03558 / 2.35 ( 142) hydrogen bonds : angle 6.43755 / 4.57 ( 354) glycosidic custom : bond 0.00160 / 0.08 ( 2) glycosidic custom : angle 3.40853 / 1.82 ( 6) Misc. bond : bond 0.00073 / 0.04 ( 6) link_BETA1-4 : bond 0.02068 / 0.93 ( 10) link_BETA1-4 : angle 4.62070 / 3.56 ( 30) link_NAG-ASN : bond 0.01143 / 0.68 ( 12) link_NAG-ASN : angle 7.11128 / 3.93 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 74 time to evaluate : 0.492 Fit side-chains REVERT: C 143 GLU cc_start: 0.8058 (mp0) cc_final: 0.7569 (mp0) REVERT: D 40 MET cc_start: 0.5632 (pmm) cc_final: 0.5326 (pmt) REVERT: D 85 MET cc_start: 0.8386 (mtm) cc_final: 0.8067 (mtp) REVERT: D 128 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7625 (mmpt) REVERT: B 39 GLN cc_start: 0.7525 (pp30) cc_final: 0.6860 (pp30) REVERT: B 201 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7360 (mtt) REVERT: B 243 MET cc_start: 0.6373 (ttt) cc_final: 0.5948 (ttp) REVERT: B 557 MET cc_start: 0.7661 (mmt) cc_final: 0.7323 (mmm) REVERT: A 243 MET cc_start: 0.6439 (ttt) cc_final: 0.6144 (ttp) REVERT: A 274 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8324 (mmtm) REVERT: A 557 MET cc_start: 0.7679 (mmt) cc_final: 0.7269 (mmt) outliers start: 35 outliers final: 15 residues processed: 105 average time/residue: 0.5152 time to fit residues: 59.6697 Evaluate side-chains 87 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 604 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: [109, 95, 3, 114, 55, 58, 98, 91, 102, 10, 22] chunk 109 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 114 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 HIS B 339 ASN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN B 530 ASN A 334 HIS A 339 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.179454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.154224 restraints weight = 18812.540| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 2.96 r_work: 0.4237 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12702 Z= 0.135 Angle : 0.791 22.074 17180 Z= 0.363 Chirality : 0.050 0.419 2000 Planarity : 0.004 0.049 2130 Dihedral : 10.846 76.750 2274 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 1.52 % Allowed : 20.25 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.68 (0.19), residues: 1474 helix: -2.37 (0.50), residues: 96 sheet: -2.09 (0.26), residues: 366 loop : -2.76 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 234 TYR 0.023 0.001 TYR B 551 PHE 0.013 0.001 PHE A 330 TRP 0.004 0.001 TRP B 593 HIS 0.008 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (12658) covalent geometry : angle 0.71082 / 0.34 (17080) SS BOND : bond 0.00327 / 0.19 ( 14) SS BOND : angle 1.14339 / 0.68 ( 28) hydrogen bonds : bond 0.02793 / 1.83 ( 142) hydrogen bonds : angle 6.00176 / 4.24 ( 354) glycosidic custom : bond 0.00255 / 0.13 ( 2) glycosidic custom : angle 2.52997 / 1.34 ( 6) Misc. bond : bond 0.00038 / 0.02 ( 6) link_BETA1-4 : bond 0.01507 / 0.67 ( 10) link_BETA1-4 : angle 3.67545 / 2.84 ( 30) link_NAG-ASN : bond 0.01072 / 0.65 ( 12) link_NAG-ASN : angle 6.72908 / 3.76 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.484 Fit side-chains REVERT: D 85 MET cc_start: 0.8397 (mtm) cc_final: 0.8107 (mtp) REVERT: B 39 GLN cc_start: 0.7405 (pp30) cc_final: 0.6762 (pp30) REVERT: B 201 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7073 (mtt) REVERT: B 388 LYS cc_start: 0.8052 (mmtt) cc_final: 0.7683 (mmtt) REVERT: B 557 MET cc_start: 0.7593 (mmt) cc_final: 0.7170 (mmt) REVERT: A 201 MET cc_start: 0.7811 (mmm) cc_final: 0.6728 (mtt) REVERT: A 243 MET cc_start: 0.6233 (ttt) cc_final: 0.5955 (ttp) REVERT: A 274 LYS cc_start: 0.8693 (mtmt) cc_final: 0.8304 (mmtm) REVERT: A 557 MET cc_start: 0.7628 (mmt) cc_final: 0.7199 (mmt) outliers start: 21 outliers final: 8 residues processed: 104 average time/residue: 0.5574 time to fit residues: 63.4181 Evaluate side-chains 85 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 514 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: [96, 17, 144, 76, 63, 114, 116, 45, 129, 97, 69] chunk 96 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN B 334 HIS B 339 ASN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 530 ASN A 334 HIS A 339 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.178309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.153123 restraints weight = 18880.649| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 2.97 r_work: 0.4224 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12702 Z= 0.161 Angle : 0.823 22.033 17180 Z= 0.378 Chirality : 0.051 0.434 2000 Planarity : 0.005 0.080 2130 Dihedral : 10.700 76.884 2274 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 1.23 % Allowed : 20.97 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.20), residues: 1474 helix: -2.24 (0.51), residues: 96 sheet: -2.09 (0.25), residues: 386 loop : -2.69 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 196 TYR 0.028 0.002 TYR B 551 PHE 0.028 0.002 PHE A 75 TRP 0.002 0.000 TRP B 332 HIS 0.009 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (12658) covalent geometry : angle 0.74543 / 0.36 (17080) SS BOND : bond 0.00318 / 0.18 ( 14) SS BOND : angle 1.28802 / 0.75 ( 28) hydrogen bonds : bond 0.02919 / 1.91 ( 142) hydrogen bonds : angle 6.01202 / 4.25 ( 354) glycosidic custom : bond 0.00273 / 0.14 ( 2) glycosidic custom : angle 2.71802 / 1.44 ( 6) Misc. bond : bond 0.00046 / 0.02 ( 6) link_BETA1-4 : bond 0.01514 / 0.68 ( 10) link_BETA1-4 : angle 3.70664 / 2.84 ( 30) link_NAG-ASN : bond 0.01040 / 0.62 ( 12) link_NAG-ASN : angle 6.73980 / 3.75 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.620 Fit side-chains REVERT: D 85 MET cc_start: 0.8381 (mtm) cc_final: 0.8071 (mtp) REVERT: B 39 GLN cc_start: 0.7443 (pp30) cc_final: 0.6816 (pp30) REVERT: B 201 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7125 (mtt) REVERT: B 243 MET cc_start: 0.6216 (ttt) cc_final: 0.5886 (ttp) REVERT: B 388 LYS cc_start: 0.8080 (mmtt) cc_final: 0.7695 (mmtt) REVERT: B 557 MET cc_start: 0.7606 (mmt) cc_final: 0.7146 (mmt) REVERT: A 201 MET cc_start: 0.7717 (mmm) cc_final: 0.6900 (mtt) REVERT: A 243 MET cc_start: 0.6356 (ttt) cc_final: 0.6014 (ttp) REVERT: A 274 LYS cc_start: 0.8662 (mtmt) cc_final: 0.8268 (mmtm) REVERT: A 388 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7929 (mmtt) REVERT: A 557 MET cc_start: 0.7640 (mmt) cc_final: 0.7202 (mmt) outliers start: 17 outliers final: 10 residues processed: 96 average time/residue: 0.5603 time to fit residues: 59.1708 Evaluate side-chains 88 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 334 HIS Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 514 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: [29, 89, 19, 34, 60, 121, 56, 110, 24, 85, 79] chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 HIS B 339 ASN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 HIS A 339 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.179313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.154197 restraints weight = 18828.512| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 2.97 r_work: 0.4236 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12702 Z= 0.144 Angle : 0.801 22.034 17180 Z= 0.368 Chirality : 0.050 0.429 2000 Planarity : 0.004 0.073 2130 Dihedral : 10.600 77.063 2274 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 1.31 % Allowed : 20.97 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.56 (0.20), residues: 1474 helix: -2.20 (0.51), residues: 96 sheet: -2.03 (0.26), residues: 372 loop : -2.68 (0.17), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 196 TYR 0.026 0.002 TYR B 551 PHE 0.027 0.001 PHE A 75 TRP 0.002 0.000 TRP B 332 HIS 0.021 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (12658) covalent geometry : angle 0.72333 / 0.35 (17080) SS BOND : bond 0.00313 / 0.18 ( 14) SS BOND : angle 1.20182 / 0.69 ( 28) hydrogen bonds : bond 0.02843 / 1.85 ( 142) hydrogen bonds : angle 5.96539 / 4.21 ( 354) glycosidic custom : bond 0.00293 / 0.15 ( 2) glycosidic custom : angle 2.58323 / 1.37 ( 6) Misc. bond : bond 0.00041 / 0.02 ( 6) link_BETA1-4 : bond 0.01452 / 0.65 ( 10) link_BETA1-4 : angle 3.59348 / 2.77 ( 30) link_NAG-ASN : bond 0.01043 / 0.63 ( 12) link_NAG-ASN : angle 6.68782 / 3.73 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3589.52 seconds wall clock time: 62 minutes 10.46 seconds (3730.46 seconds total)