Starting phenix.real_space_refine on Sun Jan 19 03:03:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ut7_42532/01_2025/8ut7_42532.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ut7_42532/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ut7_42532/01_2025/8ut7_42532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ut7_42532/01_2025/8ut7_42532.map" model { file = "/net/cci-nas-00/data/ceres_data/8ut7_42532/01_2025/8ut7_42532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ut7_42532/01_2025/8ut7_42532.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 9.32, per 1000 atoms: 0.71 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: 3.25 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.79 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: 4.83 Time building geometry restraints manager: 3.79 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: 4.940 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.050 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.720 ------------------------------------------------------------------------------- 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 : 0.006 0.138 13281 Z= 0.409 Angle : 1.096 12.682 18027 Z= 0.609 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (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 TRP 0.019 0.004 TRP E 127 HIS 0.010 0.002 HIS A 156 PHE 0.019 0.003 PHE A 353 TYR 0.021 0.004 TYR C 195 ARG 0.019 0.002 ARG A 499 *********************** 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 : 1.375 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: 1.4707 time to fit residues: 259.4663 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 : 1.445 ------------------------------------------------------------------------------- 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 140 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 130 optimal weight: 0.0570 chunk 50 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.8104 ------------------------------------------------------------------------------- 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 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.152115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.126673 restraints weight = 13575.902| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.63 r_work: 0.3303 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13281 Z= 0.220 Angle : 0.577 7.698 18027 Z= 0.305 Chirality : 0.043 0.212 2082 Planarity : 0.004 0.040 2357 Dihedral : 4.915 38.862 2314 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.96 % Allowed : 7.28 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.20), residues: 1448 helix: 2.29 (0.24), residues: 353 sheet: 0.41 (0.26), residues: 298 loop : -0.15 (0.19), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 421 HIS 0.004 0.001 HIS C 18 PHE 0.014 0.002 PHE A 353 TYR 0.014 0.001 TYR A 195 ARG 0.009 0.001 ARG E 208 *********************** 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 185 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 1.530 Fit side-chains revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8232 (m-30) cc_final: 0.7904 (m-30) REVERT: A 144 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.6931 (ptmt) REVERT: A 310 LYS cc_start: 0.8754 (mttt) cc_final: 0.8404 (mtmt) REVERT: A 346 MET cc_start: 0.7750 (ttp) cc_final: 0.7429 (ttp) REVERT: A 401 GLU cc_start: 0.7823 (mt-10) cc_final: 0.6793 (mm-30) REVERT: A 460 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8144 (mt-10) REVERT: A 498 ASN cc_start: 0.8018 (m-40) cc_final: 0.7667 (m110) REVERT: C 119 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8230 (mt-10) REVERT: C 201 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7804 (ptt90) REVERT: C 356 GLN cc_start: 0.7747 (tp-100) cc_final: 0.7546 (tp-100) REVERT: C 383 ARG cc_start: 0.7947 (ptm-80) cc_final: 0.7147 (ptt90) REVERT: C 498 ASN cc_start: 0.8107 (m-40) cc_final: 0.7890 (m110) REVERT: E 50 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6765 (pt0) REVERT: E 315 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8175 (mmtt) outliers start: 25 outliers final: 6 residues processed: 170 average time/residue: 1.5047 time to fit residues: 276.5737 Evaluate side-chains 145 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain C residue 124 SER 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 153 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 72 optimal weight: 0.0070 overall best weight: 1.8004 ------------------------------------------------------------------------------- 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 C 122 ASN C 158 ASN C 407 GLN C 435 HIS ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.148603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.123854 restraints weight = 13690.892| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.50 r_work: 0.3201 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13281 Z= 0.360 Angle : 0.620 10.601 18027 Z= 0.322 Chirality : 0.045 0.233 2082 Planarity : 0.005 0.046 2357 Dihedral : 5.160 30.917 2312 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.11 % Allowed : 8.93 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.20), residues: 1448 helix: 2.05 (0.25), residues: 351 sheet: -0.20 (0.27), residues: 298 loop : -0.57 (0.19), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 234 HIS 0.008 0.001 HIS E 18 PHE 0.016 0.002 PHE A 353 TYR 0.014 0.002 TYR C 161 ARG 0.011 0.001 ARG C 321 *********************** 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 172 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.7008 (t0) cc_final: 0.6318 (m-40) REVERT: A 104 ASP cc_start: 0.8200 (m-30) cc_final: 0.7856 (m-30) REVERT: A 310 LYS cc_start: 0.8800 (mttt) cc_final: 0.8502 (mtmt) REVERT: A 346 MET cc_start: 0.8049 (ttp) cc_final: 0.7596 (ttp) REVERT: A 391 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8596 (mmtp) REVERT: A 401 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7073 (mm-30) REVERT: A 460 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8230 (mt-10) REVERT: C 111 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7735 (tp) REVERT: C 344 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6886 (mp0) REVERT: C 383 ARG cc_start: 0.8030 (ptm-80) cc_final: 0.7366 (ptt90) REVERT: E 53 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7237 (m-30) REVERT: E 415 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7777 (m-30) outliers start: 27 outliers final: 10 residues processed: 160 average time/residue: 1.5060 time to fit residues: 260.4898 Evaluate side-chains 148 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 1.409 ------------------------------------------------------------------------------- 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 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 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 131 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 111 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 435 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.149952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.125353 restraints weight = 13537.551| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.49 r_work: 0.3273 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13281 Z= 0.209 Angle : 0.518 8.837 18027 Z= 0.270 Chirality : 0.042 0.214 2082 Planarity : 0.004 0.044 2357 Dihedral : 4.833 26.161 2312 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.57 % Allowed : 9.95 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.20), residues: 1448 helix: 2.24 (0.25), residues: 352 sheet: -0.37 (0.27), residues: 301 loop : -0.60 (0.19), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.002 0.001 HIS E 18 PHE 0.016 0.001 PHE C 338 TYR 0.009 0.001 TYR C 486 ARG 0.006 0.001 ARG C 321 *********************** 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 154 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.393 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6877 (t0) cc_final: 0.6253 (m-40) REVERT: A 50 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7391 (pt0) REVERT: A 104 ASP cc_start: 0.8121 (m-30) cc_final: 0.7814 (m-30) REVERT: A 276 LYS cc_start: 0.8084 (mptt) cc_final: 0.7617 (ttpt) REVERT: A 310 LYS cc_start: 0.8755 (mttt) cc_final: 0.8510 (mtmt) REVERT: A 346 MET cc_start: 0.8047 (ttp) cc_final: 0.7638 (ttp) REVERT: A 401 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7024 (mm-30) REVERT: A 460 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8166 (mt-10) REVERT: A 498 ASN cc_start: 0.8093 (m-40) cc_final: 0.7814 (m110) REVERT: C 111 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7533 (tp) REVERT: C 344 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6903 (mp0) REVERT: C 383 ARG cc_start: 0.7898 (ptm-80) cc_final: 0.7347 (ptt90) REVERT: E 201 ARG cc_start: 0.8044 (ttp80) cc_final: 0.7812 (ttp-170) REVERT: E 208 ARG cc_start: 0.8122 (ttp80) cc_final: 0.7853 (ttp-170) REVERT: E 315 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8453 (mmtt) REVERT: E 415 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7754 (m-30) outliers start: 20 outliers final: 5 residues processed: 144 average time/residue: 1.6343 time to fit residues: 252.8429 Evaluate side-chains 136 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 124 SER 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 442 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 32 optimal weight: 0.1980 chunk 131 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 127 optimal weight: 0.2980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 17 HIS ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 GLN E 435 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.147333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.122652 restraints weight = 13650.789| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.50 r_work: 0.3234 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13281 Z= 0.337 Angle : 0.574 10.304 18027 Z= 0.295 Chirality : 0.044 0.225 2082 Planarity : 0.004 0.045 2357 Dihedral : 5.084 28.749 2312 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.88 % Allowed : 10.02 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1448 helix: 2.18 (0.26), residues: 352 sheet: -0.35 (0.28), residues: 289 loop : -0.71 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 421 HIS 0.006 0.001 HIS E 18 PHE 0.016 0.002 PHE C 338 TYR 0.011 0.002 TYR A 195 ARG 0.008 0.001 ARG A 261 *********************** 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 162 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 1.429 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6889 (t0) cc_final: 0.6315 (m-40) REVERT: A 50 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7535 (pt0) REVERT: A 104 ASP cc_start: 0.8176 (m-30) cc_final: 0.7844 (m-30) REVERT: A 276 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7704 (ttpt) REVERT: A 310 LYS cc_start: 0.8798 (mttt) cc_final: 0.8539 (mtmt) REVERT: A 346 MET cc_start: 0.8115 (ttp) cc_final: 0.7750 (ttp) REVERT: A 401 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7025 (mm-30) REVERT: A 460 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8239 (mt-10) REVERT: C 344 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6920 (mp0) REVERT: C 383 ARG cc_start: 0.7935 (ptm-80) cc_final: 0.7373 (ptt90) REVERT: E 32 ASP cc_start: 0.7004 (t0) cc_final: 0.6733 (t70) REVERT: E 208 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7990 (ttp-170) REVERT: E 415 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7856 (m-30) outliers start: 24 outliers final: 10 residues processed: 150 average time/residue: 1.5689 time to fit residues: 253.5364 Evaluate side-chains 146 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 A residue 460 GLU 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 E residue 40 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 131 THR 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 160 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 1 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 341 ASN E 435 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.143359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.118240 restraints weight = 13890.415| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.56 r_work: 0.3155 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 13281 Z= 0.580 Angle : 0.721 13.537 18027 Z= 0.365 Chirality : 0.049 0.237 2082 Planarity : 0.005 0.049 2357 Dihedral : 6.017 42.029 2312 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.43 % Allowed : 10.10 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.20), residues: 1448 helix: 1.65 (0.25), residues: 352 sheet: -0.56 (0.28), residues: 295 loop : -0.95 (0.19), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 127 HIS 0.010 0.002 HIS E 18 PHE 0.018 0.002 PHE C 338 TYR 0.016 0.003 TYR A 233 ARG 0.011 0.001 ARG A 150 *********************** 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: 31 poor density : 134 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6882 (t0) cc_final: 0.6313 (m-40) REVERT: A 50 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7635 (pt0) REVERT: A 276 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7777 (ttpt) REVERT: A 310 LYS cc_start: 0.8841 (mttt) cc_final: 0.8525 (mtmt) REVERT: A 401 GLU cc_start: 0.7977 (mt-10) cc_final: 0.6996 (mm-30) REVERT: A 460 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8270 (mt-10) REVERT: C 344 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6861 (mp0) REVERT: C 383 ARG cc_start: 0.7953 (ptm-80) cc_final: 0.7355 (ptt90) REVERT: E 208 ARG cc_start: 0.8345 (ttp80) cc_final: 0.8096 (ttp-170) REVERT: E 211 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8438 (mt0) REVERT: E 315 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8479 (mmtt) REVERT: E 415 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7885 (m-30) outliers start: 31 outliers final: 15 residues processed: 152 average time/residue: 1.6189 time to fit residues: 264.9363 Evaluate side-chains 149 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 A residue 460 GLU 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 E residue 40 THR Chi-restraints excluded: chain E residue 48 THR 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 401 GLU 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 15 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.147122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.122707 restraints weight = 13678.002| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.49 r_work: 0.3247 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13281 Z= 0.223 Angle : 0.531 9.536 18027 Z= 0.275 Chirality : 0.042 0.207 2082 Planarity : 0.004 0.044 2357 Dihedral : 5.295 40.259 2312 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.64 % Allowed : 11.04 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1448 helix: 2.05 (0.26), residues: 352 sheet: -0.61 (0.27), residues: 295 loop : -0.86 (0.19), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.003 0.001 HIS E 18 PHE 0.017 0.001 PHE C 338 TYR 0.011 0.001 TYR C 486 ARG 0.008 0.001 ARG C 321 *********************** 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 157 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.307 Fit side-chains REVERT: A 31 ASN cc_start: 0.6916 (t0) cc_final: 0.6395 (m110) REVERT: A 50 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7530 (pt0) REVERT: A 276 LYS cc_start: 0.8161 (mptt) cc_final: 0.7701 (ttpt) REVERT: A 310 LYS cc_start: 0.8829 (mttt) cc_final: 0.8559 (mtmt) REVERT: A 346 MET cc_start: 0.8086 (ttp) cc_final: 0.7848 (ttp) REVERT: A 401 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7047 (tm-30) REVERT: A 498 ASN cc_start: 0.8104 (m-40) cc_final: 0.7895 (m110) REVERT: C 280 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8063 (mt-10) REVERT: C 344 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6865 (mp0) REVERT: E 208 ARG cc_start: 0.8245 (ttp80) cc_final: 0.8031 (ttp-170) REVERT: E 211 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8347 (mt0) REVERT: E 315 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8452 (mmtt) outliers start: 21 outliers final: 11 residues processed: 149 average time/residue: 1.6157 time to fit residues: 259.5004 Evaluate side-chains 143 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 335 ILE 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 280 GLU 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 211 GLN 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 19 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 157 optimal weight: 0.1980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 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 = 0.3649 r_free = 0.3649 target = 0.147814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.123187 restraints weight = 13682.712| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.50 r_work: 0.3244 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 : 0.004 0.041 13281 Z= 0.254 Angle : 0.538 9.533 18027 Z= 0.277 Chirality : 0.043 0.221 2082 Planarity : 0.004 0.045 2357 Dihedral : 5.100 33.571 2312 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.41 % Allowed : 11.90 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1448 helix: 2.11 (0.26), residues: 354 sheet: -0.55 (0.27), residues: 293 loop : -0.85 (0.19), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.003 0.001 HIS E 18 PHE 0.016 0.001 PHE C 338 TYR 0.010 0.002 TYR C 486 ARG 0.008 0.001 ARG C 321 *********************** 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 158 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 1.223 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6910 (t0) cc_final: 0.6443 (m110) REVERT: A 50 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7546 (pt0) REVERT: A 104 ASP cc_start: 0.8141 (m-30) cc_final: 0.7690 (m-30) REVERT: A 235 THR cc_start: 0.9116 (t) cc_final: 0.8875 (m) REVERT: A 276 LYS cc_start: 0.8159 (mptt) cc_final: 0.7729 (ttpt) REVERT: A 310 LYS cc_start: 0.8824 (mttt) cc_final: 0.8554 (mtmt) REVERT: A 389 ASN cc_start: 0.7630 (m-40) cc_final: 0.6316 (p0) REVERT: A 401 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7051 (tm-30) REVERT: A 498 ASN cc_start: 0.8116 (m-40) cc_final: 0.7882 (m110) REVERT: C 280 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8083 (mt-10) REVERT: E 208 ARG cc_start: 0.8245 (ttp80) cc_final: 0.8036 (ttp-170) REVERT: E 315 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8446 (mmtt) outliers start: 18 outliers final: 10 residues processed: 150 average time/residue: 1.5578 time to fit residues: 251.7829 Evaluate side-chains 141 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE 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 280 GLU 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 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 132 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 156 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.144816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.119796 restraints weight = 13628.175| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.54 r_work: 0.3185 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 13281 Z= 0.443 Angle : 0.641 11.979 18027 Z= 0.326 Chirality : 0.046 0.227 2082 Planarity : 0.005 0.047 2357 Dihedral : 5.630 38.980 2312 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.33 % Allowed : 12.53 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.20), residues: 1448 helix: 1.89 (0.26), residues: 352 sheet: -0.63 (0.28), residues: 293 loop : -0.96 (0.19), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 127 HIS 0.006 0.001 HIS E 18 PHE 0.018 0.002 PHE C 338 TYR 0.013 0.002 TYR A 233 ARG 0.011 0.001 ARG C 321 *********************** 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 143 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 1.416 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6913 (t0) cc_final: 0.6421 (m110) REVERT: A 50 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7600 (pt0) REVERT: A 276 LYS cc_start: 0.8243 (mptt) cc_final: 0.7782 (ttpt) REVERT: A 310 LYS cc_start: 0.8797 (mttt) cc_final: 0.8508 (mtmt) REVERT: A 389 ASN cc_start: 0.7698 (m-40) cc_final: 0.6279 (p0) REVERT: A 401 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7010 (tm-30) REVERT: C 280 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8145 (mt-10) REVERT: E 208 ARG cc_start: 0.8293 (ttp80) cc_final: 0.8070 (ttp-170) REVERT: E 211 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8381 (mt0) REVERT: E 315 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8476 (mmtt) REVERT: E 356 GLN cc_start: 0.7817 (tt0) cc_final: 0.7599 (tt0) REVERT: E 415 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7886 (m-30) outliers start: 17 outliers final: 11 residues processed: 134 average time/residue: 1.6013 time to fit residues: 231.0660 Evaluate side-chains 138 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.457 ------------------------------------------------------------------------------- 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 124 SER Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 260 ILE 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 131 THR Chi-restraints excluded: chain E residue 211 GLN 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 135 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 30 optimal weight: 0.0670 overall best weight: 0.9322 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.148203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.123730 restraints weight = 13637.726| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.48 r_work: 0.3243 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13281 Z= 0.223 Angle : 0.525 9.242 18027 Z= 0.271 Chirality : 0.042 0.258 2082 Planarity : 0.004 0.044 2357 Dihedral : 5.094 34.076 2312 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.25 % Allowed : 12.69 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.20), residues: 1448 helix: 2.07 (0.26), residues: 354 sheet: -0.68 (0.26), residues: 315 loop : -0.96 (0.19), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.003 0.001 HIS E 18 PHE 0.016 0.001 PHE C 338 TYR 0.011 0.001 TYR C 486 ARG 0.010 0.001 ARG C 321 ********************** 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 149 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6907 (t0) cc_final: 0.6436 (m110) REVERT: A 50 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7525 (pt0) REVERT: A 104 ASP cc_start: 0.8150 (m-30) cc_final: 0.7690 (m-30) REVERT: A 235 THR cc_start: 0.9110 (t) cc_final: 0.8856 (m) REVERT: A 276 LYS cc_start: 0.8166 (mptt) cc_final: 0.7704 (ttpt) REVERT: A 310 LYS cc_start: 0.8808 (mttt) cc_final: 0.8546 (mtmt) REVERT: A 389 ASN cc_start: 0.7651 (m-40) cc_final: 0.6312 (p0) REVERT: A 401 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7053 (tm-30) REVERT: C 280 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8109 (mt-10) REVERT: E 32 ASP cc_start: 0.7183 (t70) cc_final: 0.6642 (p0) REVERT: E 208 ARG cc_start: 0.8244 (ttp80) cc_final: 0.8039 (ttp-170) REVERT: E 315 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8447 (mmtt) REVERT: E 356 GLN cc_start: 0.7756 (tt0) cc_final: 0.7521 (tt0) REVERT: E 501 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.6494 (mt0) outliers start: 16 outliers final: 11 residues processed: 143 average time/residue: 1.6399 time to fit residues: 252.0747 Evaluate side-chains 144 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE 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 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 439 LEU Chi-restraints excluded: chain E residue 442 SER Chi-restraints excluded: chain E residue 501 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 146 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 296 ASN E 435 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.147416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.122851 restraints weight = 13623.997| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.49 r_work: 0.3236 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13281 Z= 0.278 Angle : 0.548 9.721 18027 Z= 0.283 Chirality : 0.043 0.228 2082 Planarity : 0.004 0.044 2357 Dihedral : 5.129 33.986 2312 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.25 % Allowed : 12.92 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.20), residues: 1448 helix: 2.05 (0.26), residues: 354 sheet: -0.60 (0.27), residues: 313 loop : -0.95 (0.19), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.003 0.001 HIS E 18 PHE 0.016 0.001 PHE C 338 TYR 0.012 0.002 TYR C 486 ARG 0.011 0.001 ARG C 321 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9158.09 seconds wall clock time: 165 minutes 15.49 seconds (9915.49 seconds total)