Starting phenix.real_space_refine on Sat Aug 23 16:02:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ut6_42531/08_2025/8ut6_42531.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ut6_42531/08_2025/8ut6_42531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ut6_42531/08_2025/8ut6_42531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ut6_42531/08_2025/8ut6_42531.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ut6_42531/08_2025/8ut6_42531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ut6_42531/08_2025/8ut6_42531.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 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 Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13046 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 630 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'TRANS': 125} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 126 Planarities with less than four sites: {'UNK:plan-1': 126} Unresolved non-hydrogen planarities: 126 Chain: "H" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 535 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'TRANS': 106} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 107 Planarities with less than four sites: {'UNK:plan-1': 107} Unresolved non-hydrogen planarities: 107 Chain: "A" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3851 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 467} Chain breaks: 1 Chain: "C" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3851 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 467} Chain breaks: 1 Chain: "E" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3843 Classifications: {'peptide': 486} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 466} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 3.46, per 1000 atoms: 0.27 Number of scatterers: 13046 At special positions: 0 Unit cell: (84.1, 122.525, 145.725, 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=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.04 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " 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=2.04 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 C 473 " - pdb=" SG CYS C 477 " 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=2.04 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 473 " - pdb=" SG CYS E 477 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=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: 1.20 Conformation dependent library (CDL) restraints added in 589.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3176 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 43 sheets defined 28.4% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 87 through 90 Processing helix chain 'G' and resid 108 through 113 removed outlier: 3.700A pdb=" N UNK G 113 " --> pdb=" O UNK G 110 " (cutoff:3.500A) 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: 3.783A 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: 4.086A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLY A 78 " --> pdb=" O GLN A 75 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 196 removed outlier: 3.568A pdb=" N GLN A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 404 through 456 Processing helix chain 'A' and resid 476 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: 4.918A pdb=" N GLY C 78 " --> pdb=" O GLN C 75 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (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: 3.710A pdb=" N ASP E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 4.862A 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 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 Processing sheet with id=AA3, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.545A pdb=" N UNK G 36 " --> pdb=" O UNK G 48 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N UNK G 50 " --> pdb=" O UNK G 34 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N UNK G 34 " --> pdb=" O UNK G 50 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N UNK G 52 " --> pdb=" O UNK G 32 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N UNK G 32 " --> pdb=" O UNK G 52 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N UNK G 33 " --> pdb=" O UNK G 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.712A pdb=" N UNK H 11 " --> pdb=" O UNK H 107 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.712A pdb=" N UNK H 11 " --> pdb=" O UNK H 107 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 366 removed outlier: 4.584A pdb=" N TYR A 351 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA9, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AB1, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AB2, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.103A pdb=" N ILE A 51 " --> pdb=" O GLY A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 58 through 60 Processing sheet with id=AB4, first strand: chain 'A' and resid 100 through 101 removed outlier: 3.574A pdb=" N TYR A 257 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.727A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB7, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.879A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB9, first strand: chain 'A' and resid 303 through 305 Processing sheet with id=AC1, first strand: chain 'C' and resid 360 through 366 removed outlier: 4.412A pdb=" N TYR C 351 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AC3, first strand: chain 'C' and resid 40 through 41 Processing sheet with id=AC4, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC5, first strand: chain 'C' and resid 51 through 52 removed outlier: 6.545A pdb=" N ILE C 51 " --> pdb=" O GLY C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.766A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 100 through 101 removed outlier: 5.237A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 100 through 101 removed outlier: 7.679A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AD1, first strand: chain 'C' and resid 136 through 140 removed outlier: 4.567A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD3, first strand: chain 'C' and resid 281 through 283 removed outlier: 4.237A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 303 through 305 Processing sheet with id=AD5, first strand: chain 'E' and resid 361 through 365 Processing sheet with id=AD6, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AD7, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD8, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD9, first strand: chain 'E' and resid 51 through 54 removed outlier: 6.029A pdb=" N ILE E 51 " --> pdb=" O GLY E 275 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N CYS E 277 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP E 53 " --> pdb=" O CYS E 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, 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=AE2, first strand: chain 'E' and resid 100 through 101 removed outlier: 4.959A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 100 through 101 removed outlier: 7.830A pdb=" N ILE E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 136 through 140 Processing sheet with id=AE5, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AE6, first strand: chain 'E' and resid 281 through 283 removed outlier: 4.265A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 303 through 305 606 hydrogen bonds defined for protein. 1629 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4407 1.34 - 1.47: 3094 1.47 - 1.59: 5707 1.59 - 1.72: 1 1.72 - 1.84: 72 Bond restraints: 13281 Sorted by residual: bond pdb=" CG PRO C 162 " pdb=" CD PRO C 162 " ideal model delta sigma weight residual 1.503 1.379 0.124 3.40e-02 8.65e+02 1.32e+01 bond pdb=" CA UNK G 118 " pdb=" CB UNK G 118 " ideal model delta sigma weight residual 1.530 1.475 0.055 2.00e-02 2.50e+03 7.56e+00 bond pdb=" CB PRO C 162 " pdb=" CG PRO C 162 " ideal model delta sigma weight residual 1.492 1.620 -0.128 5.00e-02 4.00e+02 6.53e+00 bond pdb=" N PRO C 162 " pdb=" CD PRO C 162 " ideal model delta sigma weight residual 1.473 1.507 -0.034 1.40e-02 5.10e+03 5.96e+00 bond pdb=" CA UNK H 65 " pdb=" CB UNK H 65 " ideal model delta sigma weight residual 1.530 1.486 0.044 2.00e-02 2.50e+03 4.75e+00 ... (remaining 13276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 17546 2.59 - 5.17: 442 5.17 - 7.76: 29 7.76 - 10.34: 8 10.34 - 12.93: 2 Bond angle restraints: 18027 Sorted by residual: angle pdb=" CA PRO C 162 " pdb=" N PRO C 162 " pdb=" CD PRO C 162 " ideal model delta sigma weight residual 112.00 99.07 12.93 1.40e+00 5.10e-01 8.52e+01 angle pdb=" N PRO C 162 " pdb=" CD PRO C 162 " pdb=" CG PRO C 162 " ideal model delta sigma weight residual 103.20 95.04 8.16 1.50e+00 4.44e-01 2.96e+01 angle pdb=" C UNK H 99 " pdb=" N UNK H 100 " pdb=" CA UNK H 100 " ideal model delta sigma weight residual 121.70 114.70 7.00 1.80e+00 3.09e-01 1.51e+01 angle pdb=" CB MET A 168 " pdb=" CG MET A 168 " pdb=" SD MET A 168 " ideal model delta sigma weight residual 112.70 102.44 10.26 3.00e+00 1.11e-01 1.17e+01 angle pdb=" N ARG C 354 " pdb=" CA ARG C 354 " pdb=" C ARG C 354 " ideal model delta sigma weight residual 109.24 103.65 5.59 1.67e+00 3.59e-01 1.12e+01 ... (remaining 18022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7655 17.99 - 35.98: 464 35.98 - 53.96: 158 53.96 - 71.95: 44 71.95 - 89.94: 15 Dihedral angle restraints: 8336 sinusoidal: 3427 harmonic: 4909 Sorted by residual: dihedral pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " pdb=" SG CYS C 277 " pdb=" CB CYS C 277 " ideal model delta sinusoidal sigma weight residual 93.00 43.25 49.75 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CA LYS C 276 " pdb=" C LYS C 276 " pdb=" N CYS C 277 " pdb=" CA CYS C 277 " ideal model delta harmonic sigma weight residual -180.00 -153.69 -26.31 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CB CYS A 64 " pdb=" SG CYS A 64 " pdb=" SG CYS A 76 " pdb=" CB CYS A 76 " ideal model delta sinusoidal sigma weight residual -86.00 -126.91 40.91 1 1.00e+01 1.00e-02 2.35e+01 ... (remaining 8333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1554 0.053 - 0.105: 418 0.105 - 0.158: 98 0.158 - 0.210: 7 0.210 - 0.263: 5 Chirality restraints: 2082 Sorted by residual: chirality pdb=" C1 NAG A 606 " pdb=" ND2 ASN A 483 " pdb=" C2 NAG A 606 " pdb=" O5 NAG A 606 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA PRO C 162 " pdb=" N PRO C 162 " pdb=" C PRO C 162 " pdb=" CB PRO C 162 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.45e+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 -2.17 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 2079 not shown) Planarity restraints: 2378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 161 " -0.095 5.00e-02 4.00e+02 1.32e-01 2.80e+01 pdb=" N PRO C 162 " 0.228 5.00e-02 4.00e+02 pdb=" CA PRO C 162 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO C 162 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA UNK H 99 " -0.020 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C UNK H 99 " 0.067 2.00e-02 2.50e+03 pdb=" O UNK H 99 " -0.025 2.00e-02 2.50e+03 pdb=" N UNK H 100 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK G 116 " 0.020 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C UNK G 116 " -0.067 2.00e-02 2.50e+03 pdb=" O UNK G 116 " 0.025 2.00e-02 2.50e+03 pdb=" N UNK G 117 " 0.022 2.00e-02 2.50e+03 ... (remaining 2375 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 222 2.65 - 3.21: 11261 3.21 - 3.77: 20438 3.77 - 4.34: 29146 4.34 - 4.90: 47705 Nonbonded interactions: 108772 Sorted by model distance: nonbonded pdb=" O ASP E 438 " pdb=" OG SER E 442 " model vdw 2.085 3.040 nonbonded pdb=" NE2 GLN C 210 " pdb=" OD2 ASP E 101 " model vdw 2.144 3.120 nonbonded pdb=" OD2 ASP A 408 " pdb=" OG SER E 110 " model vdw 2.171 3.040 nonbonded pdb=" NZ LYS A 380 " pdb=" OE1 GLU A 432 " model vdw 2.179 3.120 nonbonded pdb=" OD1 ASN C 121 " pdb=" NZ LYS C 259 " model vdw 2.208 3.120 ... (remaining 108767 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 501 or resid 601 through 606)) selection = (chain 'C' and (resid 8 through 501 or resid 601 through 606)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.930 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.850 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 13323 Z= 0.264 Angle : 0.956 12.926 18135 Z= 0.495 Chirality : 0.052 0.263 2082 Planarity : 0.006 0.132 2357 Dihedral : 13.948 89.941 5106 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 13.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.19), residues: 1448 helix: 1.40 (0.23), residues: 351 sheet: 0.56 (0.28), residues: 294 loop : -0.29 (0.19), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 109 TYR 0.020 0.002 TYR E 195 PHE 0.030 0.002 PHE A 353 TRP 0.014 0.002 TRP A 421 HIS 0.009 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00583 (13281) covalent geometry : angle 0.94663 (18027) SS BOND : bond 0.00369 ( 18) SS BOND : angle 2.05888 ( 36) hydrogen bonds : bond 0.11585 ( 568) hydrogen bonds : angle 7.06587 ( 1629) link_BETA1-4 : bond 0.00230 ( 3) link_BETA1-4 : angle 2.47823 ( 9) link_NAG-ASN : bond 0.00360 ( 21) link_NAG-ASN : angle 1.80027 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7393 (t) cc_final: 0.6976 (p) REVERT: A 415 ASP cc_start: 0.7405 (t0) cc_final: 0.6859 (m-30) REVERT: C 382 ASN cc_start: 0.7884 (t0) cc_final: 0.7603 (t0) outliers start: 0 outliers final: 1 residues processed: 133 average time/residue: 0.5996 time to fit residues: 87.4415 Evaluate side-chains 121 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.0000 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 57 GLN A 75 GLN A 211 GLN A 355 HIS A 454 GLN C 435 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.170376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.151525 restraints weight = 15278.763| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.55 r_work: 0.3595 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13323 Z= 0.141 Angle : 0.568 8.532 18135 Z= 0.297 Chirality : 0.043 0.229 2082 Planarity : 0.004 0.058 2357 Dihedral : 5.409 59.404 2314 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.80 % Allowed : 12.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.20), residues: 1448 helix: 2.08 (0.24), residues: 353 sheet: 0.27 (0.29), residues: 273 loop : -0.30 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 321 TYR 0.011 0.001 TYR C 486 PHE 0.018 0.001 PHE A 353 TRP 0.011 0.001 TRP A 421 HIS 0.004 0.001 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00302 (13281) covalent geometry : angle 0.55753 (18027) SS BOND : bond 0.00343 ( 18) SS BOND : angle 1.18886 ( 36) hydrogen bonds : bond 0.04333 ( 568) hydrogen bonds : angle 5.58907 ( 1629) link_BETA1-4 : bond 0.00319 ( 3) link_BETA1-4 : angle 1.98519 ( 9) link_NAG-ASN : bond 0.00287 ( 21) link_NAG-ASN : angle 1.58362 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 46 SER cc_start: 0.7462 (t) cc_final: 0.7092 (p) REVERT: A 82 LYS cc_start: 0.7097 (mttt) cc_final: 0.6849 (ttmm) REVERT: A 344 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.5719 (mp0) REVERT: C 344 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6625 (mp0) REVERT: C 382 ASN cc_start: 0.7927 (t0) cc_final: 0.7665 (t0) REVERT: E 261 ARG cc_start: 0.6945 (mmt90) cc_final: 0.6031 (ptt180) outliers start: 23 outliers final: 5 residues processed: 154 average time/residue: 0.6246 time to fit residues: 104.7905 Evaluate side-chains 127 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 45 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 10 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 HIS A 75 GLN A 454 GLN A 488 HIS C 56 HIS C 341 ASN C 363 GLN C 435 HIS E 96 ASN E 211 GLN E 296 ASN E 312 ASN E 363 GLN E 407 GLN E 497 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.159898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.142634 restraints weight = 15636.572| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.48 r_work: 0.3475 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 13323 Z= 0.321 Angle : 0.742 15.296 18135 Z= 0.376 Chirality : 0.048 0.250 2082 Planarity : 0.005 0.053 2357 Dihedral : 6.091 55.757 2312 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.43 % Allowed : 12.14 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.20), residues: 1448 helix: 1.47 (0.25), residues: 353 sheet: -0.45 (0.28), residues: 269 loop : -0.62 (0.19), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 150 TYR 0.016 0.003 TYR C 161 PHE 0.019 0.002 PHE C 87 TRP 0.018 0.002 TRP A 234 HIS 0.009 0.002 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00725 (13281) covalent geometry : angle 0.72884 (18027) SS BOND : bond 0.00595 ( 18) SS BOND : angle 1.28611 ( 36) hydrogen bonds : bond 0.04933 ( 568) hydrogen bonds : angle 5.95778 ( 1629) link_BETA1-4 : bond 0.00220 ( 3) link_BETA1-4 : angle 2.99943 ( 9) link_NAG-ASN : bond 0.00385 ( 21) link_NAG-ASN : angle 2.03181 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 LYS cc_start: 0.7471 (mttt) cc_final: 0.6867 (mtpm) REVERT: A 340 GLU cc_start: 0.6715 (mt-10) cc_final: 0.6361 (tt0) REVERT: A 344 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.5773 (mp0) REVERT: A 396 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7569 (pm20) REVERT: C 33 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7639 (mt0) REVERT: C 382 ASN cc_start: 0.8059 (t0) cc_final: 0.7764 (t0) REVERT: E 139 CYS cc_start: 0.6988 (m) cc_final: 0.6695 (m) REVERT: E 242 ILE cc_start: 0.8067 (mt) cc_final: 0.7800 (mp) REVERT: E 261 ARG cc_start: 0.7188 (mmt90) cc_final: 0.6249 (ptt180) outliers start: 31 outliers final: 14 residues processed: 160 average time/residue: 0.6045 time to fit residues: 105.1502 Evaluate side-chains 135 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 33 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 439 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 101 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 75 GLN A 454 GLN C 341 ASN C 435 HIS E 363 GLN E 407 GLN E 454 GLN E 497 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.162549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.143732 restraints weight = 15342.543| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.55 r_work: 0.3490 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13323 Z= 0.167 Angle : 0.571 12.892 18135 Z= 0.293 Chirality : 0.043 0.234 2082 Planarity : 0.004 0.048 2357 Dihedral : 5.327 46.009 2312 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.58 % Allowed : 13.47 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.20), residues: 1448 helix: 1.80 (0.26), residues: 351 sheet: -0.52 (0.27), residues: 273 loop : -0.68 (0.19), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 150 TYR 0.010 0.002 TYR A 233 PHE 0.014 0.002 PHE A 353 TRP 0.009 0.001 TRP A 421 HIS 0.004 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00368 (13281) covalent geometry : angle 0.55850 (18027) SS BOND : bond 0.00376 ( 18) SS BOND : angle 0.96346 ( 36) hydrogen bonds : bond 0.04152 ( 568) hydrogen bonds : angle 5.57389 ( 1629) link_BETA1-4 : bond 0.00220 ( 3) link_BETA1-4 : angle 2.23343 ( 9) link_NAG-ASN : bond 0.00250 ( 21) link_NAG-ASN : angle 1.81089 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7472 (t) cc_final: 0.7100 (p) REVERT: A 82 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.6988 (ttmm) REVERT: A 340 GLU cc_start: 0.6601 (mt-10) cc_final: 0.6164 (tt0) REVERT: A 344 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.5789 (mp0) REVERT: A 396 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7479 (pm20) REVERT: C 382 ASN cc_start: 0.8024 (t0) cc_final: 0.7729 (t0) REVERT: E 139 CYS cc_start: 0.6894 (m) cc_final: 0.6581 (m) REVERT: E 242 ILE cc_start: 0.8058 (mt) cc_final: 0.7752 (mp) REVERT: E 261 ARG cc_start: 0.7157 (mmt90) cc_final: 0.6159 (ptt180) outliers start: 33 outliers final: 12 residues processed: 156 average time/residue: 0.6077 time to fit residues: 102.9793 Evaluate side-chains 133 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 335 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 109 optimal weight: 3.9990 chunk 69 optimal weight: 0.0270 chunk 34 optimal weight: 0.8980 chunk 157 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN C 18 HIS C 341 ASN C 363 GLN C 435 HIS E 296 ASN E 363 GLN E 497 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.165439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.147091 restraints weight = 15293.063| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.52 r_work: 0.3542 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13323 Z= 0.132 Angle : 0.533 11.964 18135 Z= 0.273 Chirality : 0.042 0.229 2082 Planarity : 0.004 0.042 2357 Dihedral : 4.995 43.798 2312 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.43 % Allowed : 13.78 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.20), residues: 1448 helix: 1.93 (0.26), residues: 351 sheet: -0.51 (0.28), residues: 273 loop : -0.66 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 321 TYR 0.010 0.001 TYR A 233 PHE 0.014 0.001 PHE C 392 TRP 0.010 0.001 TRP A 421 HIS 0.005 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00288 (13281) covalent geometry : angle 0.52013 (18027) SS BOND : bond 0.00325 ( 18) SS BOND : angle 1.09976 ( 36) hydrogen bonds : bond 0.03922 ( 568) hydrogen bonds : angle 5.36232 ( 1629) link_BETA1-4 : bond 0.00223 ( 3) link_BETA1-4 : angle 1.99717 ( 9) link_NAG-ASN : bond 0.00246 ( 21) link_NAG-ASN : angle 1.72681 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7442 (t) cc_final: 0.7107 (p) REVERT: A 82 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6905 (ttmm) REVERT: A 340 GLU cc_start: 0.6519 (mt-10) cc_final: 0.6160 (tt0) REVERT: A 344 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.5836 (mp0) REVERT: C 382 ASN cc_start: 0.8018 (t0) cc_final: 0.7703 (t0) REVERT: E 139 CYS cc_start: 0.6797 (m) cc_final: 0.6480 (m) REVERT: E 261 ARG cc_start: 0.7097 (mmt90) cc_final: 0.6127 (ptt180) outliers start: 31 outliers final: 14 residues processed: 151 average time/residue: 0.6889 time to fit residues: 112.8334 Evaluate side-chains 137 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 335 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 12 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 454 GLN ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 ASN C 363 GLN E 296 ASN E 312 ASN E 363 GLN ** E 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.157913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.140764 restraints weight = 15396.911| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.47 r_work: 0.3451 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 13323 Z= 0.351 Angle : 0.749 15.089 18135 Z= 0.378 Chirality : 0.049 0.246 2082 Planarity : 0.006 0.055 2357 Dihedral : 6.186 56.255 2312 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.35 % Allowed : 13.94 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.20), residues: 1448 helix: 1.29 (0.26), residues: 356 sheet: -0.96 (0.27), residues: 273 loop : -0.90 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 150 TYR 0.016 0.003 TYR C 161 PHE 0.019 0.002 PHE C 87 TRP 0.020 0.003 TRP A 234 HIS 0.038 0.003 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00810 (13281) covalent geometry : angle 0.73507 (18027) SS BOND : bond 0.00618 ( 18) SS BOND : angle 1.28816 ( 36) hydrogen bonds : bond 0.04783 ( 568) hydrogen bonds : angle 5.98208 ( 1629) link_BETA1-4 : bond 0.00341 ( 3) link_BETA1-4 : angle 3.02360 ( 9) link_NAG-ASN : bond 0.00377 ( 21) link_NAG-ASN : angle 2.16743 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.7145 (ttmm) REVERT: A 189 LYS cc_start: 0.7471 (mttt) cc_final: 0.6822 (mtpm) REVERT: A 340 GLU cc_start: 0.6590 (mt-10) cc_final: 0.6360 (tt0) REVERT: A 385 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7833 (mp) REVERT: C 33 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7646 (mt0) REVERT: C 382 ASN cc_start: 0.8104 (t0) cc_final: 0.7824 (t0) REVERT: E 139 CYS cc_start: 0.7009 (m) cc_final: 0.6763 (m) REVERT: E 261 ARG cc_start: 0.7255 (mmt90) cc_final: 0.6255 (ptt180) REVERT: E 299 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7931 (mtp85) REVERT: E 401 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6705 (pm20) outliers start: 30 outliers final: 12 residues processed: 140 average time/residue: 0.6791 time to fit residues: 103.2800 Evaluate side-chains 130 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 33 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 299 ARG Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 401 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 68 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 159 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 8 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 371 GLN A 454 GLN C 18 HIS C 341 ASN E 363 GLN E 497 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.162576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.145666 restraints weight = 15380.510| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.47 r_work: 0.3507 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13323 Z= 0.150 Angle : 0.567 12.586 18135 Z= 0.288 Chirality : 0.042 0.230 2082 Planarity : 0.004 0.046 2357 Dihedral : 5.423 44.684 2312 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.96 % Allowed : 15.27 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.20), residues: 1448 helix: 1.76 (0.26), residues: 353 sheet: -0.89 (0.27), residues: 274 loop : -0.84 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 321 TYR 0.011 0.002 TYR A 233 PHE 0.011 0.001 PHE E 125 TRP 0.009 0.001 TRP A 421 HIS 0.010 0.001 HIS A 17 Details of bonding type rmsd covalent geometry : bond 0.00329 (13281) covalent geometry : angle 0.55423 (18027) SS BOND : bond 0.00371 ( 18) SS BOND : angle 0.95157 ( 36) hydrogen bonds : bond 0.04014 ( 568) hydrogen bonds : angle 5.54921 ( 1629) link_BETA1-4 : bond 0.00191 ( 3) link_BETA1-4 : angle 2.03001 ( 9) link_NAG-ASN : bond 0.00269 ( 21) link_NAG-ASN : angle 1.87723 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7489 (t) cc_final: 0.7128 (p) REVERT: A 82 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.7046 (ttmm) REVERT: A 92 LYS cc_start: 0.7321 (pptt) cc_final: 0.5509 (ttpp) REVERT: A 312 ASN cc_start: 0.7825 (t0) cc_final: 0.7530 (p0) REVERT: A 340 GLU cc_start: 0.6507 (mt-10) cc_final: 0.6302 (tt0) REVERT: A 344 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.5816 (mp0) REVERT: A 385 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7803 (mp) REVERT: A 438 ASP cc_start: 0.7697 (m-30) cc_final: 0.7366 (m-30) REVERT: C 382 ASN cc_start: 0.8013 (t0) cc_final: 0.7719 (t0) REVERT: E 139 CYS cc_start: 0.6891 (m) cc_final: 0.6608 (m) REVERT: E 261 ARG cc_start: 0.7125 (mmt90) cc_final: 0.6143 (ptt180) REVERT: E 401 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6552 (pm20) outliers start: 25 outliers final: 11 residues processed: 145 average time/residue: 0.6575 time to fit residues: 103.9256 Evaluate side-chains 135 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 401 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 156 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN C 18 HIS C 341 ASN C 363 GLN C 435 HIS E 17 HIS E 363 GLN E 497 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.162320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.143688 restraints weight = 15267.243| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.53 r_work: 0.3509 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13323 Z= 0.172 Angle : 0.577 12.682 18135 Z= 0.291 Chirality : 0.043 0.233 2082 Planarity : 0.004 0.047 2357 Dihedral : 5.421 45.241 2312 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.19 % Allowed : 15.11 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.20), residues: 1448 helix: 1.78 (0.26), residues: 355 sheet: -0.89 (0.27), residues: 280 loop : -0.81 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 321 TYR 0.010 0.002 TYR E 491 PHE 0.012 0.001 PHE E 125 TRP 0.010 0.001 TRP A 421 HIS 0.010 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00387 (13281) covalent geometry : angle 0.56432 (18027) SS BOND : bond 0.00372 ( 18) SS BOND : angle 0.92858 ( 36) hydrogen bonds : bond 0.04031 ( 568) hydrogen bonds : angle 5.51567 ( 1629) link_BETA1-4 : bond 0.00164 ( 3) link_BETA1-4 : angle 2.18655 ( 9) link_NAG-ASN : bond 0.00273 ( 21) link_NAG-ASN : angle 1.86759 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7499 (t) cc_final: 0.7136 (p) REVERT: A 82 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.7045 (ttmm) REVERT: A 92 LYS cc_start: 0.7339 (pptt) cc_final: 0.5517 (ttpp) REVERT: A 312 ASN cc_start: 0.7818 (t0) cc_final: 0.7517 (p0) REVERT: A 385 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7808 (mp) REVERT: C 382 ASN cc_start: 0.8008 (t0) cc_final: 0.7724 (t0) REVERT: E 139 CYS cc_start: 0.6923 (m) cc_final: 0.6650 (m) REVERT: E 261 ARG cc_start: 0.7134 (mmt90) cc_final: 0.6114 (ptt180) REVERT: E 401 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6556 (pm20) outliers start: 28 outliers final: 14 residues processed: 143 average time/residue: 0.5939 time to fit residues: 93.1692 Evaluate side-chains 131 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 401 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 124 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 84 optimal weight: 0.2980 chunk 57 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN C 18 HIS C 341 ASN C 435 HIS E 363 GLN E 497 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.160770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.143725 restraints weight = 15433.958| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.47 r_work: 0.3498 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13323 Z= 0.227 Angle : 0.634 13.434 18135 Z= 0.318 Chirality : 0.045 0.280 2082 Planarity : 0.005 0.049 2357 Dihedral : 5.751 52.415 2312 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.11 % Allowed : 15.58 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.20), residues: 1448 helix: 1.65 (0.26), residues: 355 sheet: -1.00 (0.27), residues: 274 loop : -0.89 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 150 TYR 0.011 0.002 TYR C 161 PHE 0.013 0.002 PHE E 125 TRP 0.012 0.002 TRP A 234 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00516 (13281) covalent geometry : angle 0.61973 (18027) SS BOND : bond 0.00443 ( 18) SS BOND : angle 0.97840 ( 36) hydrogen bonds : bond 0.04242 ( 568) hydrogen bonds : angle 5.66887 ( 1629) link_BETA1-4 : bond 0.00108 ( 3) link_BETA1-4 : angle 2.39935 ( 9) link_NAG-ASN : bond 0.00297 ( 21) link_NAG-ASN : angle 2.06567 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.7083 (ttmm) REVERT: A 312 ASN cc_start: 0.7810 (t0) cc_final: 0.7543 (p0) REVERT: A 385 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7782 (mp) REVERT: C 382 ASN cc_start: 0.8040 (t0) cc_final: 0.7741 (t0) REVERT: E 139 CYS cc_start: 0.6927 (m) cc_final: 0.6671 (m) REVERT: E 261 ARG cc_start: 0.7142 (mmt90) cc_final: 0.6121 (ptt180) REVERT: E 401 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6519 (pm20) outliers start: 27 outliers final: 16 residues processed: 135 average time/residue: 0.6090 time to fit residues: 89.9329 Evaluate side-chains 135 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 401 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 146 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 75 GLN C 18 HIS C 341 ASN C 363 GLN C 435 HIS E 363 GLN E 497 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.163109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.144541 restraints weight = 15397.033| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.53 r_work: 0.3510 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13323 Z= 0.160 Angle : 0.570 12.368 18135 Z= 0.288 Chirality : 0.043 0.240 2082 Planarity : 0.004 0.046 2357 Dihedral : 5.472 56.208 2312 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.96 % Allowed : 15.82 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.20), residues: 1448 helix: 1.83 (0.26), residues: 355 sheet: -0.93 (0.27), residues: 278 loop : -0.82 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 321 TYR 0.010 0.002 TYR A 233 PHE 0.011 0.001 PHE E 125 TRP 0.009 0.001 TRP A 421 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00357 (13281) covalent geometry : angle 0.55776 (18027) SS BOND : bond 0.00363 ( 18) SS BOND : angle 0.90289 ( 36) hydrogen bonds : bond 0.03968 ( 568) hydrogen bonds : angle 5.48094 ( 1629) link_BETA1-4 : bond 0.00209 ( 3) link_BETA1-4 : angle 2.02984 ( 9) link_NAG-ASN : bond 0.00349 ( 21) link_NAG-ASN : angle 1.89869 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7502 (t) cc_final: 0.7157 (p) REVERT: A 82 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.7029 (ttmm) REVERT: A 92 LYS cc_start: 0.7300 (pptt) cc_final: 0.5467 (ttpp) REVERT: A 312 ASN cc_start: 0.7768 (t0) cc_final: 0.7508 (p0) REVERT: A 438 ASP cc_start: 0.7642 (m-30) cc_final: 0.7335 (m-30) REVERT: C 382 ASN cc_start: 0.8068 (t0) cc_final: 0.7757 (t0) REVERT: E 139 CYS cc_start: 0.6893 (m) cc_final: 0.6603 (m) REVERT: E 261 ARG cc_start: 0.7133 (mmt90) cc_final: 0.6114 (ptt180) REVERT: E 401 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6500 (pm20) outliers start: 25 outliers final: 14 residues processed: 135 average time/residue: 0.5892 time to fit residues: 86.8747 Evaluate side-chains 129 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 401 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 64 optimal weight: 5.9990 chunk 71 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 106 optimal weight: 0.0980 chunk 87 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 75 GLN C 18 HIS C 341 ASN C 435 HIS E 363 GLN E 497 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.164580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.146394 restraints weight = 15141.841| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.50 r_work: 0.3526 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13323 Z= 0.144 Angle : 0.553 11.956 18135 Z= 0.280 Chirality : 0.042 0.235 2082 Planarity : 0.004 0.046 2357 Dihedral : 5.359 59.876 2312 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.49 % Allowed : 16.52 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.21), residues: 1448 helix: 1.83 (0.26), residues: 358 sheet: -0.84 (0.27), residues: 272 loop : -0.81 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 261 TYR 0.010 0.001 TYR A 233 PHE 0.013 0.001 PHE E 125 TRP 0.010 0.001 TRP A 421 HIS 0.008 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00319 (13281) covalent geometry : angle 0.54064 (18027) SS BOND : bond 0.00343 ( 18) SS BOND : angle 0.86918 ( 36) hydrogen bonds : bond 0.03898 ( 568) hydrogen bonds : angle 5.36992 ( 1629) link_BETA1-4 : bond 0.00238 ( 3) link_BETA1-4 : angle 1.97372 ( 9) link_NAG-ASN : bond 0.00320 ( 21) link_NAG-ASN : angle 1.83051 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3966.46 seconds wall clock time: 68 minutes 51.68 seconds (4131.68 seconds total)