Starting phenix.real_space_refine on Thu May 15 13:29:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ut7_42532/05_2025/8ut7_42532.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ut7_42532/05_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_42532/05_2025/8ut7_42532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ut7_42532/05_2025/8ut7_42532.map" model { file = "/net/cci-nas-00/data/ceres_data/8ut7_42532/05_2025/8ut7_42532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ut7_42532/05_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-5687/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: 9.23, 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: 3.17 Conformation dependent library (CDL) restraints added in 1.6 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: 1.96 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: 4.70 Time building geometry restraints manager: 3.70 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: 8.610 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: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.100 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:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.560 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 21) link_NAG-ASN : angle 2.77633 ( 63) link_BETA1-4 : bond 0.00383 ( 3) link_BETA1-4 : angle 2.34045 ( 9) hydrogen bonds : bond 0.11854 ( 575) hydrogen bonds : angle 7.11971 ( 1638) SS BOND : bond 0.30390 ( 16) SS BOND : angle 11.38436 ( 32) covalent geometry : bond 0.00643 (13281) covalent geometry : angle 1.09617 (18027) *********************** 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 : 1.295 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: 1.3705 time to fit residues: 242.1557 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 : 1.386 ------------------------------------------------------------------------------- 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: 0.9990 chunk 67 optimal weight: 0.9980 chunk 130 optimal weight: 0.0570 chunk 50 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.152164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.126735 restraints weight = 13573.777| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.62 r_work: 0.3298 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1173 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= 0.156 Angle : 0.595 7.743 18131 Z= 0.311 Chirality : 0.043 0.212 2082 Planarity : 0.004 0.040 2357 Dihedral : 4.932 39.442 2314 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.88 % Allowed : 7.36 % 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: 0.80 (0.20), residues: 1448 helix: 2.31 (0.24), residues: 353 sheet: 0.38 (0.27), residues: 284 loop : -0.17 (0.19), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 421 HIS 0.004 0.001 HIS C 18 PHE 0.013 0.002 PHE A 353 TYR 0.014 0.001 TYR A 195 ARG 0.008 0.001 ARG C 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 21) link_NAG-ASN : angle 1.80756 ( 63) link_BETA1-4 : bond 0.00074 ( 3) link_BETA1-4 : angle 1.95117 ( 9) hydrogen bonds : bond 0.04179 ( 575) hydrogen bonds : angle 5.55539 ( 1638) SS BOND : bond 0.00898 ( 16) SS BOND : angle 1.68016 ( 32) covalent geometry : bond 0.00339 (13281) covalent geometry : angle 0.58124 (18027) *********************** 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: 24 poor density : 161 time to evaluate : 1.397 Fit side-chains revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8235 (m-30) cc_final: 0.7904 (m-30) REVERT: A 144 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6941 (ptmt) REVERT: A 310 LYS cc_start: 0.8756 (mttt) cc_final: 0.8402 (mtmt) REVERT: A 346 MET cc_start: 0.7739 (ttp) cc_final: 0.7532 (ttm) REVERT: A 401 GLU cc_start: 0.7858 (mt-10) cc_final: 0.6810 (mm-30) REVERT: A 460 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8156 (mt-10) REVERT: A 498 ASN cc_start: 0.8019 (m-40) cc_final: 0.7664 (m110) REVERT: C 119 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8300 (mt-10) REVERT: C 201 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7784 (ptt90) REVERT: C 383 ARG cc_start: 0.7951 (ptm-80) cc_final: 0.7123 (ptt90) REVERT: C 498 ASN cc_start: 0.8106 (m-40) cc_final: 0.7891 (m110) REVERT: E 50 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6765 (pt0) REVERT: E 315 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8171 (mmtt) outliers start: 24 outliers final: 6 residues processed: 169 average time/residue: 1.4512 time to fit residues: 265.3641 Evaluate side-chains 147 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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: 0.0370 chunk 124 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 357 ASN C 122 ASN C 158 ASN C 407 GLN C 435 HIS C 454 GLN E 435 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.149912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.125202 restraints weight = 13650.168| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.50 r_work: 0.3221 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13321 Z= 0.201 Angle : 0.597 9.639 18131 Z= 0.307 Chirality : 0.044 0.228 2082 Planarity : 0.004 0.045 2357 Dihedral : 4.941 27.766 2312 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.19 % Allowed : 8.69 % Favored : 89.12 % 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: 0.31 (0.20), residues: 1448 helix: 2.16 (0.25), residues: 353 sheet: -0.16 (0.27), residues: 298 loop : -0.53 (0.19), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 421 HIS 0.007 0.001 HIS E 18 PHE 0.017 0.002 PHE C 338 TYR 0.014 0.002 TYR C 161 ARG 0.010 0.001 ARG C 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 21) link_NAG-ASN : angle 1.79196 ( 63) link_BETA1-4 : bond 0.00227 ( 3) link_BETA1-4 : angle 2.64842 ( 9) hydrogen bonds : bond 0.04208 ( 575) hydrogen bonds : angle 5.40548 ( 1638) SS BOND : bond 0.00473 ( 16) SS BOND : angle 1.56718 ( 32) covalent geometry : bond 0.00454 (13281) covalent geometry : angle 0.58283 (18027) *********************** 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: 28 poor density : 144 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6980 (t0) cc_final: 0.6301 (m-40) REVERT: A 104 ASP cc_start: 0.8179 (m-30) cc_final: 0.7841 (m-30) REVERT: A 310 LYS cc_start: 0.8766 (mttt) cc_final: 0.8505 (mtmt) REVERT: A 346 MET cc_start: 0.8020 (ttp) cc_final: 0.7584 (ttp) REVERT: A 401 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7083 (mm-30) REVERT: A 460 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8214 (mt-10) REVERT: C 111 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7554 (tp) REVERT: C 344 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6911 (mp0) REVERT: C 383 ARG cc_start: 0.8008 (ptm-80) cc_final: 0.7372 (ptt90) REVERT: E 53 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7220 (m-30) REVERT: E 415 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7753 (m-30) outliers start: 28 outliers final: 9 residues processed: 159 average time/residue: 1.5212 time to fit residues: 260.3603 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 : 1.348 ------------------------------------------------------------------------------- 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 114 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain E residue 40 THR 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: 3.9990 chunk 156 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.149293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.124352 restraints weight = 13556.575| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.54 r_work: 0.3258 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13321 Z= 0.194 Angle : 0.565 9.876 18131 Z= 0.289 Chirality : 0.043 0.219 2082 Planarity : 0.004 0.045 2357 Dihedral : 5.002 27.201 2312 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.19 % Allowed : 9.55 % Favored : 88.25 % 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: 2.18 (0.26), residues: 352 sheet: -0.24 (0.28), residues: 289 loop : -0.66 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 421 HIS 0.005 0.001 HIS E 18 PHE 0.017 0.002 PHE C 338 TYR 0.010 0.002 TYR A 195 ARG 0.007 0.001 ARG A 261 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 21) link_NAG-ASN : angle 1.84080 ( 63) link_BETA1-4 : bond 0.00248 ( 3) link_BETA1-4 : angle 2.50391 ( 9) hydrogen bonds : bond 0.03969 ( 575) hydrogen bonds : angle 5.30908 ( 1638) SS BOND : bond 0.00451 ( 16) SS BOND : angle 1.15672 ( 32) covalent geometry : bond 0.00440 (13281) covalent geometry : angle 0.55061 (18027) *********************** 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 165 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 1.359 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6905 (t0) cc_final: 0.6308 (m-40) REVERT: A 104 ASP cc_start: 0.8180 (m-30) cc_final: 0.7836 (m-30) REVERT: A 276 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7631 (ttpt) REVERT: A 310 LYS cc_start: 0.8778 (mttt) cc_final: 0.8523 (mtmt) REVERT: A 346 MET cc_start: 0.8051 (ttp) cc_final: 0.7669 (ttp) REVERT: A 401 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7091 (mm-30) REVERT: A 460 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8251 (mt-10) REVERT: C 111 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7624 (tp) REVERT: C 344 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6917 (mp0) REVERT: C 383 ARG cc_start: 0.7901 (ptm-80) cc_final: 0.7355 (ptt90) REVERT: E 32 ASP cc_start: 0.6961 (t0) cc_final: 0.6655 (t70) REVERT: E 315 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8466 (mmtt) REVERT: E 415 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7747 (m-30) outliers start: 28 outliers final: 12 residues processed: 150 average time/residue: 1.4357 time to fit residues: 232.5224 Evaluate side-chains 148 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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 391 LYS Chi-restraints excluded: chain C residue 111 LEU 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 260 ILE Chi-restraints excluded: chain E residue 45 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 339 ILE 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: 1.9990 chunk 131 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 chunk 146 optimal weight: 0.0170 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 overall best weight: 1.1822 ------------------------------------------------------------------------------- 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 363 GLN E 435 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.148462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.123917 restraints weight = 13589.892| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.49 r_work: 0.3255 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13321 Z= 0.174 Angle : 0.548 9.650 18131 Z= 0.279 Chirality : 0.043 0.216 2082 Planarity : 0.004 0.044 2357 Dihedral : 4.909 26.111 2312 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.11 % Allowed : 9.95 % 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 (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: 0.16 (0.20), residues: 1448 helix: 2.26 (0.26), residues: 352 sheet: -0.41 (0.27), residues: 295 loop : -0.67 (0.19), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.004 0.001 HIS E 18 PHE 0.017 0.002 PHE C 338 TYR 0.010 0.002 TYR C 486 ARG 0.008 0.001 ARG A 261 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 21) link_NAG-ASN : angle 1.74358 ( 63) link_BETA1-4 : bond 0.00200 ( 3) link_BETA1-4 : angle 2.42964 ( 9) hydrogen bonds : bond 0.03875 ( 575) hydrogen bonds : angle 5.24730 ( 1638) SS BOND : bond 0.00382 ( 16) SS BOND : angle 1.29998 ( 32) covalent geometry : bond 0.00397 (13281) covalent geometry : angle 0.53454 (18027) *********************** 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 164 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 1.483 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6888 (t0) cc_final: 0.6289 (m-40) REVERT: A 104 ASP cc_start: 0.8171 (m-30) cc_final: 0.7840 (m-30) REVERT: A 276 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7645 (ttpt) REVERT: A 310 LYS cc_start: 0.8801 (mttt) cc_final: 0.8546 (mtmt) REVERT: A 346 MET cc_start: 0.8082 (ttp) cc_final: 0.7740 (ttp) REVERT: A 401 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7116 (mm-30) REVERT: A 460 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8228 (mt-10) REVERT: A 498 ASN cc_start: 0.8083 (m-40) cc_final: 0.7792 (m110) REVERT: C 344 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6906 (mp0) REVERT: C 356 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7495 (tt0) REVERT: C 383 ARG cc_start: 0.7880 (ptm-80) cc_final: 0.7304 (ptt90) REVERT: E 32 ASP cc_start: 0.6984 (t0) cc_final: 0.6729 (t70) REVERT: E 315 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8454 (mmtt) REVERT: E 415 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7763 (m-30) outliers start: 27 outliers final: 12 residues processed: 154 average time/residue: 1.4182 time to fit residues: 236.5046 Evaluate side-chains 146 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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 114 SER 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 356 GLN Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 45 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 339 ILE 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: 4.9990 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 1 optimal weight: 20.0000 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 357 ASN C 17 HIS C 33 GLN C 158 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 HIS ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 341 ASN E 435 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.144623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.119378 restraints weight = 13843.465| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.57 r_work: 0.3164 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 13321 Z= 0.334 Angle : 0.691 12.544 18131 Z= 0.345 Chirality : 0.048 0.229 2082 Planarity : 0.005 0.048 2357 Dihedral : 5.759 38.586 2312 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.51 % Allowed : 9.87 % Favored : 87.63 % 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: -0.20 (0.20), residues: 1448 helix: 1.83 (0.26), residues: 352 sheet: -0.51 (0.28), residues: 293 loop : -0.89 (0.19), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 127 HIS 0.008 0.001 HIS E 18 PHE 0.018 0.002 PHE C 338 TYR 0.014 0.002 TYR A 233 ARG 0.011 0.001 ARG A 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 21) link_NAG-ASN : angle 2.14589 ( 63) link_BETA1-4 : bond 0.00614 ( 3) link_BETA1-4 : angle 3.40007 ( 9) hydrogen bonds : bond 0.04573 ( 575) hydrogen bonds : angle 5.65625 ( 1638) SS BOND : bond 0.00540 ( 16) SS BOND : angle 1.40302 ( 32) covalent geometry : bond 0.00788 (13281) covalent geometry : angle 0.67401 (18027) *********************** 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 168 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6907 (t0) cc_final: 0.6328 (m-40) REVERT: A 50 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7627 (pt0) REVERT: A 276 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7748 (ttpt) REVERT: A 280 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8379 (mm-30) REVERT: A 310 LYS cc_start: 0.8821 (mttt) cc_final: 0.8511 (mtmt) REVERT: A 335 ILE cc_start: 0.7425 (OUTLIER) cc_final: 0.7009 (pt) REVERT: A 346 MET cc_start: 0.8068 (ttp) cc_final: 0.7864 (ttp) REVERT: A 401 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7020 (mm-30) REVERT: A 460 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8241 (mt-10) REVERT: C 201 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.8045 (ptt90) REVERT: C 344 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6939 (mp0) REVERT: C 356 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7598 (tt0) REVERT: C 383 ARG cc_start: 0.7939 (ptm-80) cc_final: 0.7339 (ptt90) REVERT: E 208 ARG cc_start: 0.8301 (ttp80) cc_final: 0.8052 (ttp-170) REVERT: E 211 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8414 (mt0) REVERT: E 415 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7860 (m-30) outliers start: 32 outliers final: 15 residues processed: 155 average time/residue: 1.5393 time to fit residues: 256.8073 Evaluate side-chains 154 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 1.351 ------------------------------------------------------------------------------- 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 276 LYS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain C residue 97 CYS 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 356 GLN Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 92 LYS Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 211 GLN Chi-restraints excluded: chain E residue 339 ILE 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: 0.8980 chunk 2 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.148444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.123964 restraints weight = 13592.501| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.49 r_work: 0.3250 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13321 Z= 0.146 Angle : 0.527 9.307 18131 Z= 0.269 Chirality : 0.042 0.209 2082 Planarity : 0.004 0.044 2357 Dihedral : 5.070 35.283 2312 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.88 % Allowed : 11.04 % Favored : 87.08 % 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: -0.11 (0.20), residues: 1448 helix: 2.10 (0.26), residues: 354 sheet: -0.58 (0.26), residues: 315 loop : -0.89 (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 0.017 0.001 PHE C 338 TYR 0.010 0.001 TYR C 486 ARG 0.007 0.001 ARG A 261 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 21) link_NAG-ASN : angle 1.79489 ( 63) link_BETA1-4 : bond 0.00121 ( 3) link_BETA1-4 : angle 2.18316 ( 9) hydrogen bonds : bond 0.03768 ( 575) hydrogen bonds : angle 5.23028 ( 1638) SS BOND : bond 0.00325 ( 16) SS BOND : angle 1.18676 ( 32) covalent geometry : bond 0.00324 (13281) covalent geometry : angle 0.51316 (18027) *********************** 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 166 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 1.276 Fit side-chains REVERT: A 31 ASN cc_start: 0.6953 (t0) cc_final: 0.6454 (m-40) REVERT: A 50 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7532 (pt0) REVERT: A 104 ASP cc_start: 0.8134 (m-30) cc_final: 0.7710 (m-30) REVERT: A 276 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7680 (ttpt) REVERT: A 310 LYS cc_start: 0.8833 (mttt) cc_final: 0.8589 (mtmt) REVERT: A 401 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7106 (tm-30) REVERT: C 201 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7993 (ptt90) REVERT: C 280 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: E 315 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8486 (mmtt) outliers start: 24 outliers final: 8 residues processed: 156 average time/residue: 1.4746 time to fit residues: 247.6696 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 : 1.341 ------------------------------------------------------------------------------- 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 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=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: 3.9990 chunk 135 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 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 = 0.3633 r_free = 0.3633 target = 0.146315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.121623 restraints weight = 13711.268| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.50 r_work: 0.3207 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2505 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= 0.237 Angle : 0.607 10.776 18131 Z= 0.305 Chirality : 0.044 0.223 2082 Planarity : 0.004 0.046 2357 Dihedral : 5.322 35.001 2312 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.72 % Allowed : 11.82 % Favored : 86.45 % 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: -0.09 (0.20), residues: 1448 helix: 2.09 (0.26), residues: 352 sheet: -0.54 (0.28), residues: 293 loop : -0.86 (0.19), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 234 HIS 0.005 0.001 HIS E 18 PHE 0.017 0.002 PHE C 338 TYR 0.011 0.002 TYR A 233 ARG 0.010 0.001 ARG C 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 21) link_NAG-ASN : angle 1.91613 ( 63) link_BETA1-4 : bond 0.00255 ( 3) link_BETA1-4 : angle 2.90298 ( 9) hydrogen bonds : bond 0.04135 ( 575) hydrogen bonds : angle 5.37320 ( 1638) SS BOND : bond 0.00441 ( 16) SS BOND : angle 1.90261 ( 32) covalent geometry : bond 0.00550 (13281) covalent geometry : angle 0.58900 (18027) *********************** 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: 22 poor density : 136 time to evaluate : 1.328 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6936 (t0) cc_final: 0.6450 (m-40) REVERT: A 50 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7577 (pt0) REVERT: A 276 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7715 (ttpt) REVERT: A 310 LYS cc_start: 0.8847 (mttt) cc_final: 0.8566 (mtmt) REVERT: A 335 ILE cc_start: 0.7275 (OUTLIER) cc_final: 0.7053 (pt) REVERT: A 401 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7020 (tm-30) REVERT: A 498 ASN cc_start: 0.7985 (m-40) cc_final: 0.7685 (m110) REVERT: C 201 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7973 (ptt90) REVERT: C 280 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8106 (mt-10) REVERT: C 356 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7537 (tt0) REVERT: E 315 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8473 (mmtt) REVERT: E 415 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7848 (m-30) outliers start: 22 outliers final: 12 residues processed: 148 average time/residue: 1.4722 time to fit residues: 234.9696 Evaluate side-chains 147 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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 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 280 GLU Chi-restraints excluded: chain C residue 356 GLN Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 92 LYS 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 415 ASP 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: 3.9990 chunk 90 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 108 optimal weight: 0.1980 chunk 158 optimal weight: 0.8980 overall best weight: 1.3982 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.147126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.122616 restraints weight = 13555.104| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.48 r_work: 0.3234 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 13321 Z= 0.196 Angle : 0.573 10.079 18131 Z= 0.291 Chirality : 0.043 0.217 2082 Planarity : 0.004 0.045 2357 Dihedral : 5.210 34.128 2312 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.72 % Allowed : 12.29 % Favored : 85.98 % 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: -0.10 (0.20), residues: 1448 helix: 2.11 (0.26), residues: 352 sheet: -0.51 (0.28), residues: 289 loop : -0.89 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.004 0.001 HIS E 18 PHE 0.018 0.002 PHE C 338 TYR 0.011 0.002 TYR C 486 ARG 0.009 0.001 ARG C 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 21) link_NAG-ASN : angle 1.88677 ( 63) link_BETA1-4 : bond 0.00178 ( 3) link_BETA1-4 : angle 2.54189 ( 9) hydrogen bonds : bond 0.03967 ( 575) hydrogen bonds : angle 5.30172 ( 1638) SS BOND : bond 0.00390 ( 16) SS BOND : angle 1.71506 ( 32) covalent geometry : bond 0.00451 (13281) covalent geometry : angle 0.55625 (18027) *********************** 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 153 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 1.492 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6977 (t0) cc_final: 0.6552 (m-40) REVERT: A 50 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7629 (pt0) REVERT: A 104 ASP cc_start: 0.8145 (m-30) cc_final: 0.7695 (m-30) REVERT: A 276 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7754 (ttpt) REVERT: A 310 LYS cc_start: 0.8831 (mttt) cc_final: 0.8583 (mtmt) REVERT: A 401 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7188 (mm-30) REVERT: A 498 ASN cc_start: 0.7954 (m-40) cc_final: 0.7635 (m110) REVERT: C 201 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7986 (ptt90) REVERT: C 280 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8122 (mt-10) REVERT: C 356 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7545 (tt0) REVERT: E 211 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8377 (mt0) REVERT: E 315 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8482 (mmtt) outliers start: 22 outliers final: 15 residues processed: 144 average time/residue: 1.5492 time to fit residues: 240.5759 Evaluate side-chains 150 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 335 ILE Chi-restraints excluded: chain C residue 97 CYS 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 280 GLU Chi-restraints excluded: chain C residue 356 GLN 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 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 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: 0.9980 chunk 44 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 5 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.149746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.125320 restraints weight = 13590.041| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.49 r_work: 0.3272 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2540 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= 0.125 Angle : 0.511 8.240 18131 Z= 0.261 Chirality : 0.042 0.217 2082 Planarity : 0.004 0.043 2357 Dihedral : 4.786 27.756 2312 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.49 % Allowed : 12.61 % Favored : 85.90 % 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: -0.03 (0.20), residues: 1448 helix: 2.26 (0.26), residues: 354 sheet: -0.58 (0.27), residues: 315 loop : -0.86 (0.20), 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 355 PHE 0.017 0.001 PHE C 338 TYR 0.010 0.001 TYR C 486 ARG 0.010 0.001 ARG C 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 21) link_NAG-ASN : angle 1.77143 ( 63) link_BETA1-4 : bond 0.00061 ( 3) link_BETA1-4 : angle 2.01459 ( 9) hydrogen bonds : bond 0.03619 ( 575) hydrogen bonds : angle 5.07558 ( 1638) SS BOND : bond 0.00298 ( 16) SS BOND : angle 1.46736 ( 32) covalent geometry : bond 0.00279 (13281) covalent geometry : angle 0.49625 (18027) ********************** 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 159 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 1.499 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6913 (t0) cc_final: 0.6520 (m110) REVERT: A 50 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7504 (pt0) REVERT: A 104 ASP cc_start: 0.8110 (m-30) cc_final: 0.7740 (m-30) REVERT: A 235 THR cc_start: 0.9091 (t) cc_final: 0.8858 (m) REVERT: A 276 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7656 (ttpt) REVERT: A 310 LYS cc_start: 0.8815 (mttt) cc_final: 0.8561 (mtmt) REVERT: A 401 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7068 (tm-30) REVERT: A 435 HIS cc_start: 0.8147 (m90) cc_final: 0.6894 (t-90) REVERT: A 498 ASN cc_start: 0.7911 (m-40) cc_final: 0.7583 (m110) REVERT: C 201 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7914 (ptt90) REVERT: C 280 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: C 356 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7502 (tt0) REVERT: E 32 ASP cc_start: 0.7159 (t70) cc_final: 0.6646 (p0) REVERT: E 315 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8445 (mmtt) REVERT: E 356 GLN cc_start: 0.7740 (tt0) cc_final: 0.7511 (tt0) outliers start: 19 outliers final: 10 residues processed: 151 average time/residue: 1.5307 time to fit residues: 248.8300 Evaluate side-chains 148 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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 97 CYS 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 280 GLU Chi-restraints excluded: chain C residue 356 GLN Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 75 GLN 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 442 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 146 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 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: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN 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 E 464 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.144942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.119834 restraints weight = 13677.794| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.56 r_work: 0.3189 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 13321 Z= 0.316 Angle : 0.669 11.954 18131 Z= 0.336 Chirality : 0.047 0.226 2082 Planarity : 0.005 0.046 2357 Dihedral : 5.562 37.894 2312 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.72 % Allowed : 12.53 % 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 (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: -0.23 (0.20), residues: 1448 helix: 1.94 (0.26), residues: 352 sheet: -0.64 (0.27), residues: 299 loop : -0.92 (0.19), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 127 HIS 0.007 0.001 HIS E 18 PHE 0.015 0.002 PHE A 120 TYR 0.013 0.002 TYR A 233 ARG 0.011 0.001 ARG C 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 21) link_NAG-ASN : angle 2.12656 ( 63) link_BETA1-4 : bond 0.00342 ( 3) link_BETA1-4 : angle 3.19841 ( 9) hydrogen bonds : bond 0.04433 ( 575) hydrogen bonds : angle 5.49853 ( 1638) SS BOND : bond 0.00496 ( 16) SS BOND : angle 1.87593 ( 32) covalent geometry : bond 0.00741 (13281) covalent geometry : angle 0.65004 (18027) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9085.00 seconds wall clock time: 157 minutes 45.62 seconds (9465.62 seconds total)