Starting phenix.real_space_refine on Sat Aug 23 16:03:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ut7_42532/08_2025/8ut7_42532.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ut7_42532/08_2025/8ut7_42532.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 { model { file = "/net/cci-nas-00/data/ceres_data/8ut7_42532/08_2025/8ut7_42532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ut7_42532/08_2025/8ut7_42532.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ut7_42532/08_2025/8ut7_42532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ut7_42532/08_2025/8ut7_42532.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 8094 2.51 5 N 2314 2.21 5 O 2584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13046 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 630 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'TRANS': 125} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 126 Planarities with less than four sites: {'UNK:plan-1': 126} Unresolved non-hydrogen planarities: 126 Chain: "H" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 535 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'TRANS': 106} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 107 Planarities with less than four sites: {'UNK:plan-1': 107} Unresolved non-hydrogen planarities: 107 Chain: "A" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3851 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 467} Chain breaks: 1 Chain: "C" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3851 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 467} Chain breaks: 1 Chain: "E" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3843 Classifications: {'peptide': 486} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 466} Chain breaks: 1 Chain: "B" 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: "D" 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: "F" 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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 2.74, per 1000 atoms: 0.21 Number of scatterers: 13046 At special positions: 0 Unit cell: (116, 91.35, 140.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2584 8.00 N 2314 7.00 C 8094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.02 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.04 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.02 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.02 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=1.17 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS E 466 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.04 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.02 Simple disulfide: pdb=" SG CYS E 473 " - pdb=" SG CYS E 477 " distance=2.89 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 601 " - " ASN A 38 " " NAG A 602 " - " ASN A 63 " " NAG A 603 " - " ASN A 133 " " NAG A 604 " - " ASN A 246 " " NAG A 605 " - " ASN A 285 " " NAG A 606 " - " ASN A 483 " " NAG B 1 " - " ASN A 165 " " NAG C 601 " - " ASN C 38 " " NAG C 602 " - " ASN C 63 " " NAG C 603 " - " ASN C 133 " " NAG C 604 " - " ASN C 246 " " NAG C 605 " - " ASN C 285 " " NAG C 606 " - " ASN C 483 " " NAG D 1 " - " ASN C 165 " " NAG E 601 " - " ASN E 38 " " NAG E 602 " - " ASN E 63 " " NAG E 603 " - " ASN E 133 " " NAG E 604 " - " ASN E 246 " " NAG E 605 " - " ASN E 285 " " NAG E 606 " - " ASN E 483 " " NAG F 1 " - " ASN E 165 " Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 336.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3176 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 41 sheets defined 28.6% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 108 through 113 Processing helix chain 'H' and resid 30 through 32 No H-bonds generated for 'chain 'H' and resid 30 through 32' Processing helix chain 'H' and resid 80 through 84 removed outlier: 3.903A pdb=" N UNK H 84 " --> pdb=" O UNK H 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 4.831A pdb=" N GLY A 78 " --> pdb=" O GLN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 404 through 456 Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 491 through 500 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.847A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLY C 78 " --> pdb=" O GLN C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 367 through 385 Processing helix chain 'C' and resid 404 through 456 Processing helix chain 'C' and resid 474 through 483 Processing helix chain 'C' and resid 491 through 500 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 3.737A pdb=" N ASP E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLY E 78 " --> pdb=" O GLN E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 116 Processing helix chain 'E' and resid 187 through 196 removed outlier: 3.633A pdb=" N GLN E 191 " --> pdb=" O THR E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 385 Processing helix chain 'E' and resid 404 through 456 Processing helix chain 'E' and resid 474 through 483 Processing helix chain 'E' and resid 491 through 500 Processing sheet with id=AA1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.007A pdb=" N UNK G 33 " --> pdb=" O UNK G 99 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N UNK G 38 " --> pdb=" O UNK G 47 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N UNK G 47 " --> pdb=" O UNK G 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.843A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 366 removed outlier: 4.456A pdb=" N TYR A 351 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA8, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA9, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AB1, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.017A pdb=" N ILE A 51 " --> pdb=" O GLY A 275 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.628A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N PHE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 100 through 101 removed outlier: 4.969A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.729A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB6, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.623A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB8, first strand: chain 'A' and resid 281 through 283 removed outlier: 4.278A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 361 through 366 removed outlier: 4.469A pdb=" N TYR C 351 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AC2, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC3, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC4, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.012A pdb=" N ILE C 51 " --> pdb=" O GLY C 275 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.667A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N PHE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 100 through 101 removed outlier: 7.094A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 100 through 101 removed outlier: 7.094A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC9, first strand: chain 'C' and resid 136 through 140 removed outlier: 4.477A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD2, first strand: chain 'C' and resid 286 through 288 removed outlier: 4.309A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS C 305 " --> pdb=" O ASN C 389 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 361 through 365 Processing sheet with id=AD4, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AD5, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD6, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD7, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.729A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 100 through 101 removed outlier: 4.918A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 100 through 101 removed outlier: 7.708A pdb=" N ILE E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AE2, first strand: chain 'E' and resid 136 through 140 removed outlier: 4.607A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AE4, first strand: chain 'E' and resid 281 through 283 removed outlier: 4.344A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 303 through 304 613 hydrogen bonds defined for protein. 1638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.06 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 4497 1.37 - 1.51: 3755 1.51 - 1.66: 4957 1.66 - 1.80: 43 1.80 - 1.95: 29 Bond restraints: 13281 Sorted by residual: bond pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " ideal model delta sigma weight residual 1.808 1.946 -0.138 3.30e-02 9.18e+02 1.76e+01 bond pdb=" N CYS E 477 " pdb=" CA CYS E 477 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.21e-02 6.83e+03 7.77e+00 bond pdb=" N ASP E 474 " pdb=" CA ASP E 474 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.27e-02 6.20e+03 7.39e+00 bond pdb=" N CYS C 277 " pdb=" CA CYS C 277 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.29e-02 6.01e+03 7.00e+00 bond pdb=" N ASN C 278 " pdb=" CA ASN C 278 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.23e-02 6.61e+03 6.88e+00 ... (remaining 13276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 17258 2.54 - 5.07: 722 5.07 - 7.61: 37 7.61 - 10.15: 7 10.15 - 12.68: 3 Bond angle restraints: 18027 Sorted by residual: angle pdb=" C PRO C 324 " pdb=" N GLU C 325 " pdb=" CA GLU C 325 " ideal model delta sigma weight residual 121.70 129.64 -7.94 1.80e+00 3.09e-01 1.94e+01 angle pdb=" CA ALA E 476 " pdb=" C ALA E 476 " pdb=" O ALA E 476 " ideal model delta sigma weight residual 120.55 116.05 4.50 1.06e+00 8.90e-01 1.80e+01 angle pdb=" CG ARG C 321 " pdb=" CD ARG C 321 " pdb=" NE ARG C 321 " ideal model delta sigma weight residual 112.00 120.90 -8.90 2.20e+00 2.07e-01 1.64e+01 angle pdb=" C ARG A 456 " pdb=" CA ARG A 456 " pdb=" CB ARG A 456 " ideal model delta sigma weight residual 117.23 111.73 5.50 1.36e+00 5.41e-01 1.64e+01 angle pdb=" C CYS C 52 " pdb=" CA CYS C 52 " pdb=" CB CYS C 52 " ideal model delta sigma weight residual 109.53 116.11 -6.58 1.65e+00 3.67e-01 1.59e+01 ... (remaining 18022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 7808 16.99 - 33.99: 326 33.99 - 50.98: 131 50.98 - 67.98: 51 67.98 - 84.97: 14 Dihedral angle restraints: 8330 sinusoidal: 3421 harmonic: 4909 Sorted by residual: dihedral pdb=" CB CYS E 64 " pdb=" SG CYS E 64 " pdb=" SG CYS E 76 " pdb=" CB CYS E 76 " ideal model delta sinusoidal sigma weight residual -86.00 -125.47 39.47 1 1.00e+01 1.00e-02 2.19e+01 dihedral pdb=" CA CYS A 97 " pdb=" CB CYS A 97 " pdb=" SG CYS A 97 " pdb=" SG CYS A 139 " ideal model delta sinusoidal sigma weight residual 79.00 3.13 75.87 1 2.00e+01 2.50e-03 1.81e+01 dihedral pdb=" CA CYS C 97 " pdb=" CB CYS C 97 " pdb=" SG CYS C 97 " pdb=" SG CYS C 139 " ideal model delta sinusoidal sigma weight residual -73.00 -1.24 -71.76 1 2.00e+01 2.50e-03 1.65e+01 ... (remaining 8327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1280 0.044 - 0.088: 523 0.088 - 0.132: 206 0.132 - 0.176: 63 0.176 - 0.220: 10 Chirality restraints: 2082 Sorted by residual: chirality pdb=" C1 NAG E 604 " pdb=" ND2 ASN E 246 " pdb=" C2 NAG E 604 " pdb=" O5 NAG E 604 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C1 NAG A 604 " pdb=" ND2 ASN A 246 " pdb=" C2 NAG A 604 " pdb=" O5 NAG A 604 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA UNK G 99 " pdb=" N UNK G 99 " pdb=" C UNK G 99 " pdb=" CB UNK G 99 " both_signs ideal model delta sigma weight residual False 2.52 2.32 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 2079 not shown) Planarity restraints: 2378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS E 477 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C CYS E 477 " 0.059 2.00e-02 2.50e+03 pdb=" O CYS E 477 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE E 478 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 74 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C PRO A 74 " 0.057 2.00e-02 2.50e+03 pdb=" O PRO A 74 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN A 75 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK H 69 " -0.014 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C UNK H 69 " 0.052 2.00e-02 2.50e+03 pdb=" O UNK H 69 " -0.020 2.00e-02 2.50e+03 pdb=" N UNK H 70 " -0.018 2.00e-02 2.50e+03 ... (remaining 2375 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 774 2.72 - 3.26: 12217 3.26 - 3.81: 21787 3.81 - 4.35: 27954 4.35 - 4.90: 46493 Nonbonded interactions: 109225 Sorted by model distance: nonbonded pdb=" O GLY E 218 " pdb=" NH1 ARG E 220 " model vdw 2.173 3.120 nonbonded pdb=" OE2 GLU A 401 " pdb=" CD ARG E 208 " model vdw 2.181 3.440 nonbonded pdb=" OD2 ASP A 408 " pdb=" OG SER E 110 " model vdw 2.266 3.040 nonbonded pdb=" OE1 GLU A 457 " pdb=" NH2 ARG A 499 " model vdw 2.297 3.120 nonbonded pdb=" OG SER A 110 " pdb=" OD2 ASP C 408 " model vdw 2.306 3.040 ... (remaining 109220 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 8 through 501 or resid 601 through 606)) selection = (chain 'C' and (resid 8 through 501 or resid 601 through 606)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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: 7.220 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.510 Find NCS groups from input model: 0.160 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:8.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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 : 0.012 0.861 13321 Z= 0.607 Angle : 1.205 55.494 18131 Z= 0.651 Chirality : 0.057 0.220 2082 Planarity : 0.006 0.046 2357 Dihedral : 12.342 84.973 5106 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: 0.80 (0.19), residues: 1448 helix: 1.57 (0.23), residues: 354 sheet: 0.56 (0.27), residues: 302 loop : 0.13 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG A 499 TYR 0.021 0.004 TYR C 195 PHE 0.019 0.003 PHE A 353 TRP 0.019 0.004 TRP E 127 HIS 0.010 0.002 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00643 (13281) covalent geometry : angle 1.09617 (18027) SS BOND : bond 0.30390 ( 16) SS BOND : angle 11.38436 ( 32) hydrogen bonds : bond 0.11854 ( 575) hydrogen bonds : angle 7.11971 ( 1638) link_BETA1-4 : bond 0.00383 ( 3) link_BETA1-4 : angle 2.34045 ( 9) link_NAG-ASN : bond 0.00370 ( 21) link_NAG-ASN : angle 2.77633 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 45 SER cc_start: 0.8410 (p) cc_final: 0.8035 (m) REVERT: A 380 LYS cc_start: 0.7506 (mtmm) cc_final: 0.6866 (mtmm) REVERT: A 401 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6714 (mm-30) REVERT: A 432 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8134 (mm-30) REVERT: C 104 ASP cc_start: 0.8019 (t0) cc_final: 0.7731 (t0) REVERT: C 356 GLN cc_start: 0.7594 (tp-100) cc_final: 0.7296 (tp40) REVERT: C 367 LEU cc_start: 0.8686 (mt) cc_final: 0.8193 (mt) REVERT: C 383 ARG cc_start: 0.7552 (ptm-80) cc_final: 0.6644 (ptt90) REVERT: C 498 ASN cc_start: 0.8090 (m-40) cc_final: 0.7887 (m110) REVERT: E 75 GLN cc_start: 0.7712 (mt0) cc_final: 0.7484 (mt0) REVERT: E 344 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7385 (mp0) REVERT: E 359 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6971 (mt-10) REVERT: E 475 ASN cc_start: 0.7367 (m-40) cc_final: 0.6820 (m110) outliers start: 0 outliers final: 1 residues processed: 163 average time/residue: 0.5963 time to fit residues: 105.0719 Evaluate side-chains 136 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.0370 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 197 GLN A 355 HIS ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN C 407 GLN C 435 HIS C 454 GLN E 435 HIS E 488 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.154240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.128938 restraints weight = 13664.307| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.63 r_work: 0.3330 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13321 Z= 0.133 Angle : 0.575 7.583 18131 Z= 0.301 Chirality : 0.042 0.207 2082 Planarity : 0.004 0.038 2357 Dihedral : 4.833 38.838 2314 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.80 % Allowed : 7.36 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: 0.90 (0.20), residues: 1448 helix: 2.37 (0.24), residues: 355 sheet: 0.44 (0.27), residues: 284 loop : -0.10 (0.19), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 208 TYR 0.013 0.001 TYR A 195 PHE 0.013 0.001 PHE A 353 TRP 0.011 0.001 TRP A 421 HIS 0.003 0.001 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00280 (13281) covalent geometry : angle 0.56206 (18027) SS BOND : bond 0.00369 ( 16) SS BOND : angle 1.68186 ( 32) hydrogen bonds : bond 0.04139 ( 575) hydrogen bonds : angle 5.50603 ( 1638) link_BETA1-4 : bond 0.00203 ( 3) link_BETA1-4 : angle 1.74052 ( 9) link_NAG-ASN : bond 0.00279 ( 21) link_NAG-ASN : angle 1.74293 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8219 (m-30) cc_final: 0.7906 (m-30) REVERT: A 144 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.6962 (ptmt) REVERT: A 310 LYS cc_start: 0.8737 (mttt) cc_final: 0.8419 (mtmt) REVERT: A 401 GLU cc_start: 0.7869 (mt-10) cc_final: 0.6856 (mm-30) REVERT: A 460 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8121 (mt-10) REVERT: A 498 ASN cc_start: 0.8035 (m-40) cc_final: 0.7667 (m110) REVERT: C 119 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8195 (mt-10) REVERT: C 201 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7771 (ptt90) REVERT: C 383 ARG cc_start: 0.7969 (ptm-80) cc_final: 0.7181 (ptt90) REVERT: E 50 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6781 (pt0) REVERT: E 315 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8176 (mmtt) REVERT: E 344 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7410 (mp0) outliers start: 23 outliers final: 4 residues processed: 172 average time/residue: 0.6254 time to fit residues: 115.9695 Evaluate side-chains 146 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain C residue 201 ARG Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 339 ILE Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 10 optimal weight: 10.0000 chunk 136 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 31 ASN A 197 GLN A 357 ASN A 454 GLN C 122 ASN C 158 ASN C 407 GLN C 435 HIS ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 HIS ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.147786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.123018 restraints weight = 13849.286| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.51 r_work: 0.3208 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 13321 Z= 0.282 Angle : 0.679 11.292 18131 Z= 0.347 Chirality : 0.047 0.293 2082 Planarity : 0.005 0.046 2357 Dihedral : 5.319 32.421 2312 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.66 % Allowed : 8.54 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: 0.17 (0.20), residues: 1448 helix: 1.96 (0.25), residues: 351 sheet: -0.21 (0.27), residues: 302 loop : -0.58 (0.19), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 321 TYR 0.015 0.002 TYR C 161 PHE 0.017 0.002 PHE A 353 TRP 0.011 0.002 TRP E 234 HIS 0.008 0.002 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00652 (13281) covalent geometry : angle 0.66281 (18027) SS BOND : bond 0.00689 ( 16) SS BOND : angle 1.69911 ( 32) hydrogen bonds : bond 0.04567 ( 575) hydrogen bonds : angle 5.61006 ( 1638) link_BETA1-4 : bond 0.00510 ( 3) link_BETA1-4 : angle 3.09871 ( 9) link_NAG-ASN : bond 0.00284 ( 21) link_NAG-ASN : angle 2.01489 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8204 (m-30) cc_final: 0.7849 (m-30) REVERT: A 310 LYS cc_start: 0.8808 (mttt) cc_final: 0.8504 (mtmt) REVERT: A 391 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8636 (mmtp) REVERT: A 401 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7064 (mm-30) REVERT: C 111 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7739 (tp) REVERT: C 344 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6987 (mp0) REVERT: C 356 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7726 (tp40) REVERT: C 383 ARG cc_start: 0.8068 (ptm-80) cc_final: 0.7405 (ptt90) REVERT: E 53 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7236 (m-30) REVERT: E 189 LYS cc_start: 0.8122 (mtpp) cc_final: 0.7896 (mtpp) REVERT: E 501 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.6470 (mt0) outliers start: 34 outliers final: 13 residues processed: 164 average time/residue: 0.6435 time to fit residues: 113.7702 Evaluate side-chains 153 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 356 GLN Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 92 LYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 442 SER Chi-restraints excluded: chain E residue 501 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 101 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 127 optimal weight: 0.0040 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN C 33 GLN C 158 ASN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.149689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.125037 restraints weight = 13541.189| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.50 r_work: 0.3265 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13321 Z= 0.153 Angle : 0.544 9.114 18131 Z= 0.280 Chirality : 0.043 0.216 2082 Planarity : 0.004 0.044 2357 Dihedral : 4.943 27.394 2312 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.88 % Allowed : 9.79 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: 0.17 (0.20), residues: 1448 helix: 2.18 (0.26), residues: 352 sheet: -0.37 (0.27), residues: 301 loop : -0.63 (0.19), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 201 TYR 0.009 0.001 TYR A 195 PHE 0.017 0.001 PHE C 338 TRP 0.009 0.001 TRP A 421 HIS 0.003 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00339 (13281) covalent geometry : angle 0.53000 (18027) SS BOND : bond 0.00371 ( 16) SS BOND : angle 1.48592 ( 32) hydrogen bonds : bond 0.03841 ( 575) hydrogen bonds : angle 5.28670 ( 1638) link_BETA1-4 : bond 0.00151 ( 3) link_BETA1-4 : angle 2.24088 ( 9) link_NAG-ASN : bond 0.00192 ( 21) link_NAG-ASN : angle 1.72444 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6926 (t0) cc_final: 0.6310 (m-40) REVERT: A 104 ASP cc_start: 0.8127 (m-30) cc_final: 0.7824 (m-30) REVERT: A 276 LYS cc_start: 0.8097 (mptt) cc_final: 0.7676 (ttpt) REVERT: A 310 LYS cc_start: 0.8802 (mttt) cc_final: 0.8576 (mtmt) REVERT: A 361 ARG cc_start: 0.8175 (ttm170) cc_final: 0.7962 (mtt-85) REVERT: A 401 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7077 (mm-30) REVERT: A 498 ASN cc_start: 0.8113 (m-40) cc_final: 0.7900 (m110) REVERT: C 111 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7572 (tp) REVERT: C 344 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6926 (mp0) REVERT: C 383 ARG cc_start: 0.7924 (ptm-80) cc_final: 0.7387 (ptt90) REVERT: E 201 ARG cc_start: 0.8035 (ttp80) cc_final: 0.7796 (ttp-170) REVERT: E 208 ARG cc_start: 0.8194 (ttp80) cc_final: 0.7937 (ttp-170) REVERT: E 501 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.6554 (mt0) outliers start: 24 outliers final: 7 residues processed: 146 average time/residue: 0.7327 time to fit residues: 114.5187 Evaluate side-chains 138 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 442 SER Chi-restraints excluded: chain E residue 501 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 109 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN C 158 ASN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.149257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.124493 restraints weight = 13693.619| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.51 r_work: 0.3262 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13321 Z= 0.161 Angle : 0.538 9.163 18131 Z= 0.275 Chirality : 0.042 0.220 2082 Planarity : 0.004 0.044 2357 Dihedral : 4.827 24.955 2312 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.04 % Allowed : 10.02 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: 0.19 (0.20), residues: 1448 helix: 2.27 (0.26), residues: 352 sheet: -0.40 (0.27), residues: 295 loop : -0.64 (0.19), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 261 TYR 0.010 0.001 TYR C 486 PHE 0.016 0.001 PHE C 338 TRP 0.009 0.001 TRP A 421 HIS 0.004 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00363 (13281) covalent geometry : angle 0.52423 (18027) SS BOND : bond 0.00367 ( 16) SS BOND : angle 1.29249 ( 32) hydrogen bonds : bond 0.03815 ( 575) hydrogen bonds : angle 5.20048 ( 1638) link_BETA1-4 : bond 0.00169 ( 3) link_BETA1-4 : angle 2.38143 ( 9) link_NAG-ASN : bond 0.00194 ( 21) link_NAG-ASN : angle 1.71220 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6862 (t0) cc_final: 0.6270 (m-40) REVERT: A 104 ASP cc_start: 0.8156 (m-30) cc_final: 0.7839 (m-30) REVERT: A 276 LYS cc_start: 0.8126 (mptt) cc_final: 0.7677 (ttpt) REVERT: A 310 LYS cc_start: 0.8766 (mttt) cc_final: 0.8507 (mtmt) REVERT: A 361 ARG cc_start: 0.8149 (ttm170) cc_final: 0.7933 (mtt-85) REVERT: A 401 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7020 (mm-30) REVERT: A 498 ASN cc_start: 0.8085 (m-40) cc_final: 0.7790 (m110) REVERT: C 344 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6928 (mp0) REVERT: C 383 ARG cc_start: 0.7869 (ptm-80) cc_final: 0.7300 (ptt90) REVERT: E 208 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7947 (ttp-170) REVERT: E 315 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8465 (mmtt) REVERT: E 415 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7795 (m-30) outliers start: 26 outliers final: 10 residues processed: 153 average time/residue: 0.6848 time to fit residues: 112.6768 Evaluate side-chains 143 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 12 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 147 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN A 407 GLN C 17 HIS C 33 GLN C 158 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.144198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.119113 restraints weight = 13635.766| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.55 r_work: 0.3156 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 13321 Z= 0.362 Angle : 0.724 13.341 18131 Z= 0.363 Chirality : 0.049 0.236 2082 Planarity : 0.005 0.049 2357 Dihedral : 5.938 39.724 2312 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.35 % Allowed : 10.49 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: -0.28 (0.20), residues: 1448 helix: 1.73 (0.25), residues: 352 sheet: -0.52 (0.28), residues: 295 loop : -0.93 (0.19), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 150 TYR 0.015 0.002 TYR A 233 PHE 0.018 0.002 PHE C 338 TRP 0.011 0.002 TRP A 127 HIS 0.009 0.002 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00846 (13281) covalent geometry : angle 0.70646 (18027) SS BOND : bond 0.00588 ( 16) SS BOND : angle 1.47879 ( 32) hydrogen bonds : bond 0.04731 ( 575) hydrogen bonds : angle 5.74788 ( 1638) link_BETA1-4 : bond 0.00683 ( 3) link_BETA1-4 : angle 3.58227 ( 9) link_NAG-ASN : bond 0.00413 ( 21) link_NAG-ASN : angle 2.23718 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6915 (t0) cc_final: 0.6331 (m-40) REVERT: A 50 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7638 (pt0) REVERT: A 276 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7800 (ttpt) REVERT: A 280 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8375 (mm-30) REVERT: A 310 LYS cc_start: 0.8829 (mttt) cc_final: 0.8522 (mtmt) REVERT: A 335 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.6998 (pt) REVERT: A 346 MET cc_start: 0.8101 (ttp) cc_final: 0.7791 (ttp) REVERT: A 401 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7012 (mm-30) REVERT: C 201 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.8039 (ptt90) REVERT: C 280 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8165 (mt-10) REVERT: C 344 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6872 (mp0) REVERT: C 383 ARG cc_start: 0.7948 (ptm-80) cc_final: 0.7352 (ptt90) REVERT: E 208 ARG cc_start: 0.8326 (ttp80) cc_final: 0.8071 (ttp-170) REVERT: E 211 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8435 (mt0) REVERT: E 315 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8487 (mmtt) REVERT: E 415 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7880 (m-30) outliers start: 30 outliers final: 15 residues processed: 155 average time/residue: 0.6386 time to fit residues: 106.4582 Evaluate side-chains 152 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 201 ARG Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 211 GLN Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 68 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 159 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 25 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN C 33 GLN C 158 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 341 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.148917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.124409 restraints weight = 13602.013| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.50 r_work: 0.3259 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13321 Z= 0.135 Angle : 0.527 9.060 18131 Z= 0.271 Chirality : 0.042 0.209 2082 Planarity : 0.004 0.044 2357 Dihedral : 5.142 36.176 2312 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.96 % Allowed : 11.28 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: -0.15 (0.20), residues: 1448 helix: 2.08 (0.26), residues: 354 sheet: -0.58 (0.26), residues: 315 loop : -0.93 (0.19), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 261 TYR 0.010 0.001 TYR C 486 PHE 0.018 0.001 PHE C 338 TRP 0.009 0.001 TRP A 421 HIS 0.003 0.001 HIS E 355 Details of bonding type rmsd covalent geometry : bond 0.00297 (13281) covalent geometry : angle 0.51356 (18027) SS BOND : bond 0.00373 ( 16) SS BOND : angle 1.21417 ( 32) hydrogen bonds : bond 0.03762 ( 575) hydrogen bonds : angle 5.25546 ( 1638) link_BETA1-4 : bond 0.00105 ( 3) link_BETA1-4 : angle 2.09398 ( 9) link_NAG-ASN : bond 0.00213 ( 21) link_NAG-ASN : angle 1.76273 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6882 (t0) cc_final: 0.6381 (m-40) REVERT: A 50 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7503 (pt0) REVERT: A 104 ASP cc_start: 0.8103 (m-30) cc_final: 0.7725 (m-30) REVERT: A 235 THR cc_start: 0.9099 (t) cc_final: 0.8872 (m) REVERT: A 276 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7724 (ttpt) REVERT: A 310 LYS cc_start: 0.8811 (mttt) cc_final: 0.8552 (mtmt) REVERT: A 346 MET cc_start: 0.7919 (ttp) cc_final: 0.7675 (ttp) REVERT: A 401 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7042 (tm-30) REVERT: A 498 ASN cc_start: 0.8044 (m-40) cc_final: 0.7710 (m110) REVERT: C 201 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7924 (ptt90) REVERT: C 344 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6851 (mp0) REVERT: E 208 ARG cc_start: 0.8275 (ttp80) cc_final: 0.8065 (ttp-170) REVERT: E 315 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8463 (mmtt) outliers start: 25 outliers final: 9 residues processed: 153 average time/residue: 0.6442 time to fit residues: 106.0999 Evaluate side-chains 139 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 201 ARG Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 156 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 0.0870 chunk 52 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 124 optimal weight: 0.9980 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN C 33 GLN C 158 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.148732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.124201 restraints weight = 13487.012| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.49 r_work: 0.3237 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13321 Z= 0.151 Angle : 0.533 9.184 18131 Z= 0.273 Chirality : 0.042 0.216 2082 Planarity : 0.004 0.043 2357 Dihedral : 4.982 30.548 2312 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.10 % Allowed : 12.69 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: -0.07 (0.20), residues: 1448 helix: 2.22 (0.26), residues: 354 sheet: -0.56 (0.27), residues: 315 loop : -0.91 (0.19), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 261 TYR 0.010 0.001 TYR C 486 PHE 0.016 0.001 PHE C 338 TRP 0.009 0.001 TRP A 421 HIS 0.003 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00339 (13281) covalent geometry : angle 0.51957 (18027) SS BOND : bond 0.00351 ( 16) SS BOND : angle 1.25311 ( 32) hydrogen bonds : bond 0.03785 ( 575) hydrogen bonds : angle 5.16837 ( 1638) link_BETA1-4 : bond 0.00057 ( 3) link_BETA1-4 : angle 2.30351 ( 9) link_NAG-ASN : bond 0.00207 ( 21) link_NAG-ASN : angle 1.75743 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.400 Fit side-chains REVERT: A 31 ASN cc_start: 0.6901 (t0) cc_final: 0.6420 (m-40) REVERT: A 50 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7508 (pt0) REVERT: A 104 ASP cc_start: 0.8133 (m-30) cc_final: 0.7764 (m-30) REVERT: A 235 THR cc_start: 0.9098 (t) cc_final: 0.8878 (m) REVERT: A 276 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7729 (ttpt) REVERT: A 310 LYS cc_start: 0.8810 (mttt) cc_final: 0.8554 (mtmt) REVERT: A 389 ASN cc_start: 0.7546 (m-40) cc_final: 0.6283 (p0) REVERT: A 401 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7050 (tm-30) REVERT: A 498 ASN cc_start: 0.7989 (m-40) cc_final: 0.7648 (m110) REVERT: C 280 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8060 (mt-10) REVERT: E 208 ARG cc_start: 0.8234 (ttp80) cc_final: 0.8025 (ttp-170) REVERT: E 315 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8446 (mmtt) outliers start: 14 outliers final: 8 residues processed: 146 average time/residue: 0.6269 time to fit residues: 98.5371 Evaluate side-chains 141 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 124 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN C 158 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.146609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.121964 restraints weight = 13661.833| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.49 r_work: 0.3224 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13321 Z= 0.235 Angle : 0.600 10.693 18131 Z= 0.304 Chirality : 0.045 0.223 2082 Planarity : 0.004 0.045 2357 Dihedral : 5.300 33.625 2312 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.64 % Allowed : 12.61 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: -0.10 (0.20), residues: 1448 helix: 2.08 (0.26), residues: 354 sheet: -0.52 (0.28), residues: 293 loop : -0.88 (0.19), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 321 TYR 0.011 0.002 TYR A 233 PHE 0.017 0.002 PHE C 338 TRP 0.009 0.002 TRP E 234 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00545 (13281) covalent geometry : angle 0.58413 (18027) SS BOND : bond 0.00416 ( 16) SS BOND : angle 1.28687 ( 32) hydrogen bonds : bond 0.04118 ( 575) hydrogen bonds : angle 5.35423 ( 1638) link_BETA1-4 : bond 0.00214 ( 3) link_BETA1-4 : angle 2.79812 ( 9) link_NAG-ASN : bond 0.00276 ( 21) link_NAG-ASN : angle 1.99978 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6983 (t0) cc_final: 0.6513 (m-40) REVERT: A 50 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7663 (pt0) REVERT: A 276 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7795 (ttpt) REVERT: A 310 LYS cc_start: 0.8831 (mttt) cc_final: 0.8571 (mtmt) REVERT: A 389 ASN cc_start: 0.7667 (m-40) cc_final: 0.6381 (p0) REVERT: A 401 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7090 (tm-30) REVERT: A 498 ASN cc_start: 0.8029 (m-40) cc_final: 0.7622 (m110) REVERT: C 201 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7930 (ptt90) REVERT: C 280 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8121 (mt-10) REVERT: C 356 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: E 208 ARG cc_start: 0.8283 (ttp80) cc_final: 0.8082 (ttp-170) REVERT: E 315 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8487 (mmtt) REVERT: E 415 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7862 (m-30) outliers start: 21 outliers final: 12 residues processed: 143 average time/residue: 0.6669 time to fit residues: 102.8050 Evaluate side-chains 149 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 201 ARG Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 356 GLN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 146 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 chunk 121 optimal weight: 0.4980 chunk 142 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN C 158 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.150124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.125734 restraints weight = 13572.555| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.49 r_work: 0.3277 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13321 Z= 0.121 Angle : 0.507 7.992 18131 Z= 0.261 Chirality : 0.042 0.224 2082 Planarity : 0.004 0.044 2357 Dihedral : 4.797 27.237 2312 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.10 % Allowed : 13.55 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: -0.05 (0.20), residues: 1448 helix: 2.24 (0.26), residues: 354 sheet: -0.53 (0.27), residues: 315 loop : -0.89 (0.19), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 321 TYR 0.009 0.001 TYR C 486 PHE 0.016 0.001 PHE C 338 TRP 0.009 0.001 TRP A 421 HIS 0.002 0.001 HIS E 355 Details of bonding type rmsd covalent geometry : bond 0.00268 (13281) covalent geometry : angle 0.49315 (18027) SS BOND : bond 0.00293 ( 16) SS BOND : angle 1.15611 ( 32) hydrogen bonds : bond 0.03611 ( 575) hydrogen bonds : angle 5.07693 ( 1638) link_BETA1-4 : bond 0.00096 ( 3) link_BETA1-4 : angle 1.93917 ( 9) link_NAG-ASN : bond 0.00355 ( 21) link_NAG-ASN : angle 1.76758 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6925 (t0) cc_final: 0.6510 (m110) REVERT: A 50 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7481 (pt0) REVERT: A 104 ASP cc_start: 0.8108 (m-30) cc_final: 0.7733 (m-30) REVERT: A 235 THR cc_start: 0.9096 (t) cc_final: 0.8869 (m) REVERT: A 276 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7711 (ttpt) REVERT: A 310 LYS cc_start: 0.8795 (mttt) cc_final: 0.8543 (mtmt) REVERT: A 389 ASN cc_start: 0.7536 (m-40) cc_final: 0.6312 (p0) REVERT: A 401 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7083 (tm-30) REVERT: A 498 ASN cc_start: 0.7897 (m-40) cc_final: 0.7435 (m110) REVERT: C 280 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8066 (mt-10) REVERT: C 356 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: E 315 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8440 (mmtt) REVERT: E 356 GLN cc_start: 0.7744 (tt0) cc_final: 0.7520 (tt0) outliers start: 14 outliers final: 10 residues processed: 147 average time/residue: 0.6640 time to fit residues: 105.0783 Evaluate side-chains 147 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 356 GLN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 64 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN C 158 ASN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 435 HIS E 464 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.147047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.122379 restraints weight = 13605.510| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.49 r_work: 0.3214 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13321 Z= 0.230 Angle : 0.594 10.412 18131 Z= 0.302 Chirality : 0.044 0.227 2082 Planarity : 0.004 0.046 2357 Dihedral : 5.177 32.172 2312 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.57 % Allowed : 13.00 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 aren not related in a simple way. whole: -0.14 (0.20), residues: 1448 helix: 2.13 (0.26), residues: 354 sheet: -0.53 (0.27), residues: 313 loop : -0.96 (0.19), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 321 TYR 0.012 0.002 TYR C 161 PHE 0.015 0.002 PHE C 338 TRP 0.009 0.002 TRP C 234 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00532 (13281) covalent geometry : angle 0.57946 (18027) SS BOND : bond 0.00411 ( 16) SS BOND : angle 1.23990 ( 32) hydrogen bonds : bond 0.04093 ( 575) hydrogen bonds : angle 5.30146 ( 1638) link_BETA1-4 : bond 0.00207 ( 3) link_BETA1-4 : angle 2.75036 ( 9) link_NAG-ASN : bond 0.00277 ( 21) link_NAG-ASN : angle 1.93263 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4233.96 seconds wall clock time: 72 minutes 59.32 seconds (4379.32 seconds total)