Starting phenix.real_space_refine on Thu Jul 31 06:30:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ut7_42532/07_2025/8ut7_42532.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ut7_42532/07_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_42532/07_2025/8ut7_42532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ut7_42532/07_2025/8ut7_42532.map" model { file = "/net/cci-nas-00/data/ceres_data/8ut7_42532/07_2025/8ut7_42532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ut7_42532/07_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-5711/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: 9.80, per 1000 atoms: 0.75 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: 3.20 Conformation dependent library (CDL) restraints added in 1.5 seconds 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3176 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 41 sheets defined 28.6% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 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: 5.22 Time building geometry restraints manager: 3.81 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: 0.010 Normalize map: mean=0, sd=1: 217.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.840 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 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:15.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 269.150 ------------------------------------------------------------------------------- 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 : 1.634 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: 2.0542 time to fit residues: 363.2353 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 : 2.417 ------------------------------------------------------------------------------- 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 = 58)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.126755 restraints weight = 13573.775| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.62 r_work: 0.3298 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 : 1.889 Fit side-chains revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8242 (m-30) cc_final: 0.7913 (m-30) REVERT: A 144 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.6948 (ptmt) REVERT: A 310 LYS cc_start: 0.8755 (mttt) cc_final: 0.8404 (mtmt) REVERT: A 346 MET cc_start: 0.7747 (ttp) cc_final: 0.7540 (ttm) REVERT: A 401 GLU cc_start: 0.7862 (mt-10) cc_final: 0.6810 (mm-30) REVERT: A 460 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8152 (mt-10) REVERT: A 498 ASN cc_start: 0.8022 (m-40) cc_final: 0.7668 (m110) REVERT: C 119 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8299 (mt-10) REVERT: C 201 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7786 (ptt90) REVERT: C 383 ARG cc_start: 0.7947 (ptm-80) cc_final: 0.7119 (ptt90) REVERT: C 498 ASN cc_start: 0.8108 (m-40) cc_final: 0.7892 (m110) REVERT: E 50 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6771 (pt0) REVERT: E 315 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8177 (mmtt) outliers start: 24 outliers final: 6 residues processed: 169 average time/residue: 1.5149 time to fit residues: 277.0751 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 : 1.309 ------------------------------------------------------------------------------- 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: 0.2980 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: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 197 GLN A 357 ASN C 122 ASN C 158 ASN C 407 GLN C 435 HIS ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.149455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.124398 restraints weight = 13689.508| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.55 r_work: 0.3226 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1808 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= 0.207 Angle : 0.604 9.802 18131 Z= 0.311 Chirality : 0.044 0.228 2082 Planarity : 0.004 0.045 2357 Dihedral : 4.983 28.367 2312 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.11 % Allowed : 8.93 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.20), residues: 1448 helix: 2.20 (0.25), residues: 351 sheet: -0.17 (0.27), residues: 298 loop : -0.53 (0.19), residues: 799 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 0.011 0.001 ARG C 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 21) link_NAG-ASN : angle 1.81022 ( 63) link_BETA1-4 : bond 0.00289 ( 3) link_BETA1-4 : angle 2.71031 ( 9) hydrogen bonds : bond 0.04225 ( 575) hydrogen bonds : angle 5.42149 ( 1638) SS BOND : bond 0.00421 ( 16) SS BOND : angle 1.55457 ( 32) covalent geometry : bond 0.00468 (13281) covalent geometry : angle 0.58936 (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 171 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6995 (t0) cc_final: 0.6320 (m-40) REVERT: A 104 ASP cc_start: 0.8163 (m-30) cc_final: 0.7827 (m-30) REVERT: A 310 LYS cc_start: 0.8774 (mttt) cc_final: 0.8521 (mtmt) REVERT: A 346 MET cc_start: 0.8029 (ttp) cc_final: 0.7605 (ttp) REVERT: A 401 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7097 (mm-30) REVERT: A 460 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8178 (mt-10) REVERT: C 111 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7604 (tp) REVERT: C 344 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6939 (mp0) REVERT: C 383 ARG cc_start: 0.7983 (ptm-80) cc_final: 0.7338 (ptt90) REVERT: E 53 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7231 (m-30) REVERT: E 415 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7773 (m-30) outliers start: 27 outliers final: 9 residues processed: 159 average time/residue: 1.5546 time to fit residues: 266.4776 Evaluate side-chains 145 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 1.372 ------------------------------------------------------------------------------- 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: 4.9990 chunk 76 optimal weight: 0.7980 chunk 86 optimal weight: 0.0980 chunk 156 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.147468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.121463 restraints weight = 13584.277| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.68 r_work: 0.3242 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13321 Z= 0.150 Angle : 0.529 8.759 18131 Z= 0.272 Chirality : 0.042 0.216 2082 Planarity : 0.004 0.044 2357 Dihedral : 4.776 24.725 2312 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.96 % Allowed : 9.71 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.26 (0.20), residues: 1448 helix: 2.31 (0.25), residues: 352 sheet: -0.33 (0.27), residues: 301 loop : -0.59 (0.19), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.003 0.001 HIS E 18 PHE 0.016 0.001 PHE C 338 TYR 0.009 0.001 TYR C 486 ARG 0.008 0.001 ARG A 261 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 21) link_NAG-ASN : angle 1.70404 ( 63) link_BETA1-4 : bond 0.00090 ( 3) link_BETA1-4 : angle 2.23655 ( 9) hydrogen bonds : bond 0.03786 ( 575) hydrogen bonds : angle 5.21476 ( 1638) SS BOND : bond 0.00350 ( 16) SS BOND : angle 1.23808 ( 32) covalent geometry : bond 0.00333 (13281) covalent geometry : angle 0.51549 (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 161 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 1.314 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6748 (t0) cc_final: 0.6054 (m-40) REVERT: A 104 ASP cc_start: 0.8309 (m-30) cc_final: 0.7947 (m-30) REVERT: A 276 LYS cc_start: 0.8083 (mptt) cc_final: 0.7436 (ttpt) REVERT: A 310 LYS cc_start: 0.8783 (mttt) cc_final: 0.8435 (mtmt) REVERT: A 346 MET cc_start: 0.7999 (ttp) cc_final: 0.7499 (ttp) REVERT: A 401 GLU cc_start: 0.7850 (mt-10) cc_final: 0.6898 (mm-30) REVERT: A 460 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8261 (mt-10) REVERT: C 111 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7370 (tp) REVERT: C 344 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6840 (mp0) REVERT: C 383 ARG cc_start: 0.7843 (ptm-80) cc_final: 0.7216 (ptt90) REVERT: E 201 ARG cc_start: 0.8007 (ttp80) cc_final: 0.7782 (ttp-170) REVERT: E 344 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7492 (mp0) REVERT: E 415 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7648 (m-30) outliers start: 25 outliers final: 9 residues processed: 149 average time/residue: 1.5288 time to fit residues: 245.1662 Evaluate side-chains 140 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 231 SER 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 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: 0.6980 chunk 131 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 127 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.148284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.123545 restraints weight = 13644.918| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.50 r_work: 0.3212 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13321 Z= 0.180 Angle : 0.550 9.580 18131 Z= 0.280 Chirality : 0.043 0.221 2082 Planarity : 0.004 0.045 2357 Dihedral : 4.827 24.859 2312 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.96 % Allowed : 9.95 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.20), residues: 1448 helix: 2.30 (0.26), residues: 352 sheet: -0.37 (0.27), residues: 295 loop : -0.63 (0.19), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.005 0.001 HIS E 18 PHE 0.016 0.002 PHE C 338 TYR 0.010 0.002 TYR C 486 ARG 0.007 0.001 ARG A 261 Details of bonding type rmsd link_NAG-ASN : bond 0.00199 ( 21) link_NAG-ASN : angle 1.73479 ( 63) link_BETA1-4 : bond 0.00209 ( 3) link_BETA1-4 : angle 2.46716 ( 9) hydrogen bonds : bond 0.03886 ( 575) hydrogen bonds : angle 5.22021 ( 1638) SS BOND : bond 0.00426 ( 16) SS BOND : angle 1.32639 ( 32) covalent geometry : bond 0.00410 (13281) covalent geometry : angle 0.53642 (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 160 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6882 (t0) cc_final: 0.6285 (m-40) REVERT: A 50 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7467 (pt0) REVERT: A 104 ASP cc_start: 0.8203 (m-30) cc_final: 0.7871 (m-30) REVERT: A 276 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7656 (ttpt) REVERT: A 310 LYS cc_start: 0.8754 (mttt) cc_final: 0.8504 (mtmt) REVERT: A 346 MET cc_start: 0.8051 (ttp) cc_final: 0.7676 (ttp) REVERT: A 401 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7052 (mm-30) REVERT: A 460 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8219 (mt-10) REVERT: A 498 ASN cc_start: 0.8090 (m-40) cc_final: 0.7797 (m110) REVERT: C 344 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6908 (mp0) REVERT: C 383 ARG cc_start: 0.7863 (ptm-80) cc_final: 0.7267 (ptt90) REVERT: E 208 ARG cc_start: 0.8174 (ttp80) cc_final: 0.7920 (ttp-170) REVERT: E 315 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8476 (mmtt) REVERT: E 415 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7762 (m-30) outliers start: 25 outliers final: 13 residues processed: 150 average time/residue: 1.5056 time to fit residues: 244.0915 Evaluate side-chains 144 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 114 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 339 ILE Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 160 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 1 optimal weight: 20.0000 chunk 28 optimal weight: 0.6980 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: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN C 17 HIS C 33 GLN C 158 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 HIS ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.144000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.118899 restraints weight = 13863.363| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.56 r_work: 0.3164 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 13321 Z= 0.350 Angle : 0.718 13.388 18131 Z= 0.359 Chirality : 0.049 0.236 2082 Planarity : 0.005 0.049 2357 Dihedral : 5.937 40.463 2312 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.43 % Allowed : 10.26 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.20), residues: 1448 helix: 1.75 (0.25), residues: 352 sheet: -0.54 (0.28), residues: 295 loop : -0.90 (0.19), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 421 HIS 0.009 0.002 HIS E 18 PHE 0.018 0.002 PHE C 338 TYR 0.015 0.002 TYR A 233 ARG 0.010 0.001 ARG A 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 21) link_NAG-ASN : angle 2.23620 ( 63) link_BETA1-4 : bond 0.00580 ( 3) link_BETA1-4 : angle 3.52961 ( 9) hydrogen bonds : bond 0.04698 ( 575) hydrogen bonds : angle 5.73763 ( 1638) SS BOND : bond 0.00548 ( 16) SS BOND : angle 1.49807 ( 32) covalent geometry : bond 0.00820 (13281) covalent geometry : angle 0.70034 (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: 31 poor density : 137 time to evaluate : 1.312 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6919 (t0) cc_final: 0.6333 (m-40) REVERT: A 50 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7607 (pt0) REVERT: A 276 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7787 (ttpt) REVERT: A 280 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8378 (mm-30) REVERT: A 310 LYS cc_start: 0.8827 (mttt) cc_final: 0.8515 (mtmt) REVERT: A 346 MET cc_start: 0.8070 (ttp) cc_final: 0.7859 (ttp) REVERT: A 401 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7003 (mm-30) REVERT: A 460 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8256 (mt-10) REVERT: C 344 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6912 (mp0) REVERT: C 356 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7592 (tt0) REVERT: C 383 ARG cc_start: 0.7949 (ptm-80) cc_final: 0.7348 (ptt90) REVERT: E 208 ARG cc_start: 0.8330 (ttp80) cc_final: 0.8070 (ttp-170) REVERT: E 211 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8429 (mt0) REVERT: E 315 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8478 (mmtt) REVERT: E 344 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7724 (mp0) REVERT: E 415 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7847 (m-30) outliers start: 31 outliers final: 15 residues processed: 155 average time/residue: 1.5167 time to fit residues: 252.6558 Evaluate side-chains 153 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 1.299 ------------------------------------------------------------------------------- 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 460 GLU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain 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 315 LYS Chi-restraints excluded: chain E residue 339 ILE Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 15 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 341 ASN E 435 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.146737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.122321 restraints weight = 13635.286| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.49 r_work: 0.3235 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13321 Z= 0.191 Angle : 0.571 10.266 18131 Z= 0.289 Chirality : 0.043 0.216 2082 Planarity : 0.004 0.045 2357 Dihedral : 5.425 40.339 2312 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.96 % Allowed : 10.73 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1448 helix: 2.02 (0.26), residues: 352 sheet: -0.53 (0.28), residues: 289 loop : -0.89 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.008 0.001 ARG C 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 21) link_NAG-ASN : angle 1.90766 ( 63) link_BETA1-4 : bond 0.00188 ( 3) link_BETA1-4 : angle 2.52943 ( 9) hydrogen bonds : bond 0.03988 ( 575) hydrogen bonds : angle 5.38705 ( 1638) SS BOND : bond 0.00468 ( 16) SS BOND : angle 1.45807 ( 32) covalent geometry : bond 0.00436 (13281) covalent geometry : angle 0.55541 (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 162 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 1.307 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6926 (t0) cc_final: 0.6407 (m-40) REVERT: A 50 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7513 (pt0) REVERT: A 276 LYS cc_start: 0.8191 (mptt) cc_final: 0.7750 (ttpt) REVERT: A 310 LYS cc_start: 0.8820 (mttt) cc_final: 0.8548 (mtmt) REVERT: A 335 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.7051 (pt) REVERT: A 401 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7024 (tm-30) REVERT: A 498 ASN cc_start: 0.8120 (m-40) cc_final: 0.7912 (m110) REVERT: C 356 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: E 208 ARG cc_start: 0.8256 (ttp80) cc_final: 0.8040 (ttp-170) REVERT: E 315 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8448 (mmtt) outliers start: 25 outliers final: 13 residues processed: 153 average time/residue: 1.5996 time to fit residues: 262.6957 Evaluate side-chains 144 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 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 401 GLU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 19 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.146593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.121939 restraints weight = 13717.107| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.50 r_work: 0.3210 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13321 Z= 0.211 Angle : 0.590 10.431 18131 Z= 0.297 Chirality : 0.044 0.222 2082 Planarity : 0.004 0.046 2357 Dihedral : 5.347 38.124 2312 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.64 % Allowed : 12.06 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1448 helix: 2.06 (0.26), residues: 352 sheet: -0.60 (0.27), residues: 293 loop : -0.88 (0.19), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 421 HIS 0.005 0.001 HIS E 18 PHE 0.017 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 0.00251 ( 21) link_NAG-ASN : angle 1.93079 ( 63) link_BETA1-4 : bond 0.00145 ( 3) link_BETA1-4 : angle 2.71881 ( 9) hydrogen bonds : bond 0.04053 ( 575) hydrogen bonds : angle 5.36758 ( 1638) SS BOND : bond 0.00396 ( 16) SS BOND : angle 1.89499 ( 32) covalent geometry : bond 0.00487 (13281) covalent geometry : angle 0.57200 (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 155 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 1.524 Fit side-chains REVERT: A 31 ASN cc_start: 0.6954 (t0) cc_final: 0.6448 (m-40) REVERT: A 50 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7544 (pt0) REVERT: A 276 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7756 (ttpt) REVERT: A 310 LYS cc_start: 0.8812 (mttt) cc_final: 0.8545 (mtmt) REVERT: A 335 ILE cc_start: 0.7285 (OUTLIER) cc_final: 0.7023 (pt) REVERT: A 401 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7044 (tm-30) REVERT: A 498 ASN cc_start: 0.8131 (m-40) cc_final: 0.7899 (m110) REVERT: C 280 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8136 (mt-10) REVERT: E 208 ARG cc_start: 0.8264 (ttp80) cc_final: 0.8050 (ttp-170) REVERT: E 315 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8456 (mmtt) outliers start: 21 outliers final: 14 residues processed: 146 average time/residue: 1.5064 time to fit residues: 237.3212 Evaluate side-chains 141 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 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 124 SER Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain E residue 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 339 ILE Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 132 optimal weight: 2.9990 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: 4.9990 chunk 156 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.145519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.121065 restraints weight = 13601.126| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.48 r_work: 0.3175 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 13321 Z= 0.257 Angle : 0.628 11.234 18131 Z= 0.316 Chirality : 0.045 0.224 2082 Planarity : 0.005 0.046 2357 Dihedral : 5.518 39.504 2312 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.80 % Allowed : 12.22 % 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: -0.25 (0.20), residues: 1448 helix: 1.94 (0.26), residues: 352 sheet: -0.63 (0.27), residues: 293 loop : -0.95 (0.19), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 234 HIS 0.006 0.001 HIS E 18 PHE 0.017 0.002 PHE C 338 TYR 0.012 0.002 TYR A 233 ARG 0.009 0.001 ARG C 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 21) link_NAG-ASN : angle 2.09652 ( 63) link_BETA1-4 : bond 0.00282 ( 3) link_BETA1-4 : angle 2.95582 ( 9) hydrogen bonds : bond 0.04244 ( 575) hydrogen bonds : angle 5.46676 ( 1638) SS BOND : bond 0.00437 ( 16) SS BOND : angle 1.85303 ( 32) covalent geometry : bond 0.00598 (13281) covalent geometry : angle 0.60932 (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 150 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.321 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6937 (t0) cc_final: 0.6457 (m-40) REVERT: A 50 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7569 (pt0) REVERT: A 276 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7782 (ttpt) REVERT: A 310 LYS cc_start: 0.8828 (mttt) cc_final: 0.8535 (mtmt) REVERT: A 389 ASN cc_start: 0.7682 (m-40) cc_final: 0.6279 (p0) REVERT: A 401 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7034 (tm-30) REVERT: C 280 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: C 356 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: E 208 ARG cc_start: 0.8276 (ttp80) cc_final: 0.8052 (ttp-170) REVERT: E 211 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8359 (mt0) REVERT: E 315 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8455 (mmtt) REVERT: E 415 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7782 (m-30) REVERT: E 501 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.6485 (mt0) outliers start: 23 outliers final: 16 residues processed: 139 average time/residue: 1.6868 time to fit residues: 254.1071 Evaluate side-chains 148 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 1.461 ------------------------------------------------------------------------------- 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 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 92 LYS 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 339 ILE Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 415 ASP Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 442 SER Chi-restraints excluded: chain E residue 501 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 135 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 30 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 E 435 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.149102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.124703 restraints weight = 13623.854| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.48 r_work: 0.3255 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13321 Z= 0.134 Angle : 0.524 8.666 18131 Z= 0.268 Chirality : 0.042 0.242 2082 Planarity : 0.004 0.043 2357 Dihedral : 4.977 33.697 2312 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.49 % Allowed : 12.37 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1448 helix: 2.15 (0.26), residues: 354 sheet: -0.63 (0.26), residues: 315 loop : -0.92 (0.19), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.003 0.001 HIS E 18 PHE 0.016 0.001 PHE C 338 TYR 0.010 0.001 TYR C 486 ARG 0.009 0.001 ARG C 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 21) link_NAG-ASN : angle 1.83390 ( 63) link_BETA1-4 : bond 0.00048 ( 3) link_BETA1-4 : angle 2.06715 ( 9) hydrogen bonds : bond 0.03707 ( 575) hydrogen bonds : angle 5.16248 ( 1638) SS BOND : bond 0.00309 ( 16) SS BOND : angle 1.53807 ( 32) covalent geometry : bond 0.00299 (13281) covalent geometry : angle 0.50805 (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 156 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 1.813 Fit side-chains revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6898 (t0) cc_final: 0.6471 (m110) REVERT: A 50 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7530 (pt0) REVERT: A 104 ASP cc_start: 0.8125 (m-30) cc_final: 0.7673 (m-30) REVERT: A 235 THR cc_start: 0.9111 (t) cc_final: 0.8864 (m) REVERT: A 276 LYS cc_start: 0.8134 (mptt) cc_final: 0.7712 (ttpt) REVERT: A 310 LYS cc_start: 0.8812 (mttt) cc_final: 0.8562 (mtmt) REVERT: A 389 ASN cc_start: 0.7616 (m-40) cc_final: 0.6309 (p0) REVERT: A 401 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7066 (tm-30) REVERT: C 280 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: C 356 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7439 (tt0) REVERT: E 315 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8442 (mmtt) REVERT: E 356 GLN cc_start: 0.7735 (tt0) cc_final: 0.7503 (tt0) outliers start: 19 outliers final: 9 residues processed: 149 average time/residue: 2.1473 time to fit residues: 342.6937 Evaluate side-chains 144 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE 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 339 ILE Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 146 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 0.0470 chunk 107 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 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: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN C 158 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 435 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.146458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.121867 restraints weight = 13642.009| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.49 r_work: 0.3199 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13321 Z= 0.236 Angle : 0.607 10.690 18131 Z= 0.307 Chirality : 0.045 0.228 2082 Planarity : 0.004 0.046 2357 Dihedral : 5.302 35.837 2312 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.41 % Allowed : 12.76 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1448 helix: 2.05 (0.26), residues: 352 sheet: -0.55 (0.28), residues: 293 loop : -0.91 (0.19), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 421 HIS 0.005 0.001 HIS E 18 PHE 0.015 0.002 PHE C 338 TYR 0.012 0.002 TYR C 486 ARG 0.012 0.001 ARG C 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 21) link_NAG-ASN : angle 1.99643 ( 63) link_BETA1-4 : bond 0.00231 ( 3) link_BETA1-4 : angle 2.80367 ( 9) hydrogen bonds : bond 0.04133 ( 575) hydrogen bonds : angle 5.35209 ( 1638) SS BOND : bond 0.00456 ( 16) SS BOND : angle 1.64483 ( 32) covalent geometry : bond 0.00547 (13281) covalent geometry : angle 0.58964 (18027) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10305.42 seconds wall clock time: 183 minutes 53.82 seconds (11033.82 seconds total)