Starting phenix.real_space_refine on Wed Jun 11 20:23:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ut6_42531/06_2025/8ut6_42531.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ut6_42531/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ut6_42531/06_2025/8ut6_42531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ut6_42531/06_2025/8ut6_42531.map" model { file = "/net/cci-nas-00/data/ceres_data/8ut6_42531/06_2025/8ut6_42531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ut6_42531/06_2025/8ut6_42531.cif" } resolution = 2.8 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= 0.026 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-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.41, per 1000 atoms: 0.72 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: 3.17 Conformation dependent library (CDL) restraints added in 1.7 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 43 sheets defined 28.4% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 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: 4.82 Time building geometry restraints manager: 3.80 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: 7.580 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: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 34.820 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.080 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:14.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.100 ------------------------------------------------------------------------------- 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 (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: 0.42 (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 TRP 0.014 0.002 TRP A 421 HIS 0.009 0.001 HIS A 156 PHE 0.030 0.002 PHE A 353 TYR 0.020 0.002 TYR E 195 ARG 0.010 0.001 ARG E 109 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 21) link_NAG-ASN : angle 1.80027 ( 63) link_BETA1-4 : bond 0.00230 ( 3) link_BETA1-4 : angle 2.47823 ( 9) hydrogen bonds : bond 0.11585 ( 568) hydrogen bonds : angle 7.06587 ( 1629) SS BOND : bond 0.00369 ( 18) SS BOND : angle 2.05888 ( 36) covalent geometry : bond 0.00583 (13281) covalent geometry : angle 0.94663 (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 133 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7393 (t) cc_final: 0.6975 (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: 1.1851 time to fit residues: 173.7766 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 : 1.616 ------------------------------------------------------------------------------- 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 140 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 150 optimal weight: 0.0020 overall best weight: 1.1792 ------------------------------------------------------------------------------- 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 295 GLN A 355 HIS A 454 GLN C 56 HIS C 363 GLN C 435 HIS E 363 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.166570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.147545 restraints weight = 15198.596| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.56 r_work: 0.3560 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13323 Z= 0.187 Angle : 0.618 9.717 18135 Z= 0.321 Chirality : 0.044 0.239 2082 Planarity : 0.005 0.061 2357 Dihedral : 5.626 59.865 2314 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.96 % Allowed : 12.06 % 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: 0.45 (0.20), residues: 1448 helix: 1.91 (0.24), residues: 353 sheet: 0.17 (0.28), residues: 273 loop : -0.35 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 421 HIS 0.005 0.001 HIS A 184 PHE 0.018 0.002 PHE A 353 TYR 0.013 0.002 TYR C 486 ARG 0.006 0.001 ARG C 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 21) link_NAG-ASN : angle 1.72288 ( 63) link_BETA1-4 : bond 0.00136 ( 3) link_BETA1-4 : angle 2.35931 ( 9) hydrogen bonds : bond 0.04580 ( 568) hydrogen bonds : angle 5.69859 ( 1629) SS BOND : bond 0.00564 ( 18) SS BOND : angle 1.28310 ( 36) covalent geometry : bond 0.00413 (13281) covalent geometry : angle 0.60683 (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 160 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 1.489 Fit side-chains revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7257 (mttt) cc_final: 0.6974 (ttmm) REVERT: A 340 GLU cc_start: 0.6484 (mt-10) cc_final: 0.6124 (tt0) REVERT: A 344 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.5706 (mp0) REVERT: A 396 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7008 (mt-10) REVERT: C 382 ASN cc_start: 0.8008 (t0) cc_final: 0.7707 (t0) REVERT: E 139 CYS cc_start: 0.6854 (m) cc_final: 0.6561 (m) REVERT: E 168 MET cc_start: 0.6614 (tpp) cc_final: 0.6395 (mmm) REVERT: E 235 THR cc_start: 0.8094 (OUTLIER) cc_final: 0.7886 (m) REVERT: E 242 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7700 (mp) REVERT: E 261 ARG cc_start: 0.7019 (mmt90) cc_final: 0.6095 (ptt180) outliers start: 25 outliers final: 8 residues processed: 149 average time/residue: 1.6571 time to fit residues: 271.8506 Evaluate side-chains 129 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 2.178 ------------------------------------------------------------------------------- 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 192 ILE 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 E residue 235 THR Chi-restraints excluded: chain E residue 242 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 72 optimal weight: 0.0070 overall best weight: 1.2802 ------------------------------------------------------------------------------- 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 211 GLN A 488 HIS C 363 GLN C 435 HIS E 96 ASN E 211 GLN E 312 ASN E 363 GLN E 454 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.163312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.144412 restraints weight = 15371.428| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.56 r_work: 0.3514 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13323 Z= 0.191 Angle : 0.603 13.629 18135 Z= 0.309 Chirality : 0.044 0.228 2082 Planarity : 0.004 0.048 2357 Dihedral : 5.303 47.879 2312 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.35 % Allowed : 12.92 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.20), residues: 1448 helix: 1.87 (0.26), residues: 353 sheet: -0.31 (0.28), residues: 269 loop : -0.51 (0.19), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 421 HIS 0.006 0.001 HIS A 184 PHE 0.014 0.002 PHE A 353 TYR 0.011 0.002 TYR E 94 ARG 0.007 0.001 ARG C 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 21) link_NAG-ASN : angle 1.79178 ( 63) link_BETA1-4 : bond 0.00178 ( 3) link_BETA1-4 : angle 2.34758 ( 9) hydrogen bonds : bond 0.04369 ( 568) hydrogen bonds : angle 5.56902 ( 1629) SS BOND : bond 0.00409 ( 18) SS BOND : angle 1.05825 ( 36) covalent geometry : bond 0.00421 (13281) covalent geometry : angle 0.59087 (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 173 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7526 (t) cc_final: 0.7135 (p) REVERT: A 340 GLU cc_start: 0.6663 (mt-10) cc_final: 0.6274 (tt0) REVERT: A 344 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.5754 (mp0) REVERT: A 396 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: C 33 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7541 (mt0) REVERT: C 382 ASN cc_start: 0.8059 (t0) cc_final: 0.7759 (t0) REVERT: E 139 CYS cc_start: 0.6977 (m) cc_final: 0.6679 (m) REVERT: E 242 ILE cc_start: 0.8027 (mt) cc_final: 0.7781 (mp) REVERT: E 261 ARG cc_start: 0.7112 (mmt90) cc_final: 0.6147 (ptt180) outliers start: 30 outliers final: 9 residues processed: 160 average time/residue: 1.3357 time to fit residues: 233.4804 Evaluate side-chains 134 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 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 33 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 187 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 111 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 C 341 ASN C 363 GLN C 435 HIS E 296 ASN E 312 ASN E 363 GLN E 407 GLN E 497 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.162216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.143309 restraints weight = 15291.640| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.56 r_work: 0.3506 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13323 Z= 0.210 Angle : 0.608 12.758 18135 Z= 0.310 Chirality : 0.044 0.241 2082 Planarity : 0.005 0.047 2357 Dihedral : 5.418 48.706 2312 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.74 % Allowed : 12.69 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.20), residues: 1448 helix: 1.72 (0.26), residues: 353 sheet: -0.66 (0.27), residues: 281 loop : -0.64 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.005 0.001 HIS A 18 PHE 0.013 0.002 PHE A 353 TYR 0.011 0.002 TYR E 491 ARG 0.004 0.000 ARG C 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 21) link_NAG-ASN : angle 1.82453 ( 63) link_BETA1-4 : bond 0.00162 ( 3) link_BETA1-4 : angle 2.58284 ( 9) hydrogen bonds : bond 0.04250 ( 568) hydrogen bonds : angle 5.61837 ( 1629) SS BOND : bond 0.00487 ( 18) SS BOND : angle 1.11267 ( 36) covalent geometry : bond 0.00471 (13281) covalent geometry : angle 0.59514 (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 169 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.7020 (ttmm) REVERT: A 340 GLU cc_start: 0.6623 (mt-10) cc_final: 0.6214 (tt0) REVERT: A 344 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.5808 (mp0) REVERT: A 396 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7504 (pm20) REVERT: C 382 ASN cc_start: 0.8063 (t0) cc_final: 0.7751 (t0) REVERT: E 139 CYS cc_start: 0.6986 (m) cc_final: 0.6705 (m) REVERT: E 242 ILE cc_start: 0.8066 (mt) cc_final: 0.7817 (mp) REVERT: E 261 ARG cc_start: 0.7165 (mmt90) cc_final: 0.6189 (ptt180) outliers start: 35 outliers final: 14 residues processed: 159 average time/residue: 1.2838 time to fit residues: 222.1367 Evaluate side-chains 137 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 1.349 ------------------------------------------------------------------------------- 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 192 ILE 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 312 ASN 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 374 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 32 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 127 optimal weight: 0.0970 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 363 GLN ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 ASN E 296 ASN E 312 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 = 0.3765 r_free = 0.3765 target = 0.160467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.143307 restraints weight = 15389.825| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.47 r_work: 0.3469 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13323 Z= 0.242 Angle : 0.640 13.612 18135 Z= 0.324 Chirality : 0.045 0.241 2082 Planarity : 0.005 0.051 2357 Dihedral : 5.661 50.365 2312 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.66 % Allowed : 13.70 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.20), residues: 1448 helix: 1.60 (0.26), residues: 355 sheet: -0.80 (0.27), residues: 273 loop : -0.81 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.010 0.002 HIS A 17 PHE 0.013 0.002 PHE C 392 TYR 0.012 0.002 TYR C 161 ARG 0.005 0.001 ARG C 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 21) link_NAG-ASN : angle 1.92534 ( 63) link_BETA1-4 : bond 0.00230 ( 3) link_BETA1-4 : angle 2.56330 ( 9) hydrogen bonds : bond 0.04373 ( 568) hydrogen bonds : angle 5.73275 ( 1629) SS BOND : bond 0.00478 ( 18) SS BOND : angle 1.13160 ( 36) covalent geometry : bond 0.00549 (13281) covalent geometry : angle 0.62680 (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 150 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.7118 (ttmm) REVERT: A 189 LYS cc_start: 0.7448 (mttt) cc_final: 0.6813 (mtpm) REVERT: A 340 GLU cc_start: 0.6600 (mt-10) cc_final: 0.6245 (tt0) REVERT: A 344 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.5821 (mp0) REVERT: A 396 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7540 (pm20) REVERT: C 382 ASN cc_start: 0.8042 (t0) cc_final: 0.7755 (t0) REVERT: E 139 CYS cc_start: 0.6977 (m) cc_final: 0.6727 (m) REVERT: E 242 ILE cc_start: 0.8082 (mt) cc_final: 0.7829 (mp) REVERT: E 261 ARG cc_start: 0.7211 (mmt90) cc_final: 0.6236 (ptt180) REVERT: E 401 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.6643 (pm20) outliers start: 34 outliers final: 13 residues processed: 138 average time/residue: 1.3820 time to fit residues: 208.0016 Evaluate side-chains 128 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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 192 ILE 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 312 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 160 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 E 296 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 = 0.3757 r_free = 0.3757 target = 0.159702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.142660 restraints weight = 15569.652| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.47 r_work: 0.3481 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13323 Z= 0.256 Angle : 0.652 14.026 18135 Z= 0.330 Chirality : 0.045 0.241 2082 Planarity : 0.005 0.053 2357 Dihedral : 5.921 50.993 2312 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.90 % Allowed : 13.70 % Favored : 83.40 % 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: -0.51 (0.20), residues: 1448 helix: 1.54 (0.26), residues: 355 sheet: -1.03 (0.27), residues: 273 loop : -0.93 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.008 0.002 HIS A 17 PHE 0.013 0.002 PHE C 87 TYR 0.012 0.002 TYR C 161 ARG 0.005 0.001 ARG C 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 21) link_NAG-ASN : angle 2.04334 ( 63) link_BETA1-4 : bond 0.00132 ( 3) link_BETA1-4 : angle 2.58569 ( 9) hydrogen bonds : bond 0.04391 ( 568) hydrogen bonds : angle 5.82101 ( 1629) SS BOND : bond 0.00479 ( 18) SS BOND : angle 1.05134 ( 36) covalent geometry : bond 0.00581 (13281) covalent geometry : angle 0.63840 (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 159 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.7118 (ttmm) REVERT: A 172 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: A 189 LYS cc_start: 0.7470 (mttt) cc_final: 0.6829 (mtpm) REVERT: A 261 ARG cc_start: 0.6973 (mtm110) cc_final: 0.6495 (mtt90) REVERT: A 340 GLU cc_start: 0.6556 (mt-10) cc_final: 0.6331 (tt0) REVERT: A 396 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7526 (pm20) REVERT: C 33 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7613 (mt0) REVERT: C 382 ASN cc_start: 0.8069 (t0) cc_final: 0.7772 (t0) REVERT: E 139 CYS cc_start: 0.6974 (m) cc_final: 0.6738 (m) REVERT: E 208 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7217 (ptt180) REVERT: E 242 ILE cc_start: 0.8058 (mt) cc_final: 0.7820 (mp) REVERT: E 261 ARG cc_start: 0.7208 (mmt90) cc_final: 0.6237 (ptt180) REVERT: E 401 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6686 (pm20) outliers start: 37 outliers final: 17 residues processed: 148 average time/residue: 1.3213 time to fit residues: 212.8126 Evaluate side-chains 135 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 1.468 ------------------------------------------------------------------------------- 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 172 GLU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 335 ILE 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 18 HIS 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 E residue 34 ILE Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 208 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 15 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 ASN E 296 ASN E 363 GLN E 407 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 = 0.3771 r_free = 0.3771 target = 0.161099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.144156 restraints weight = 15365.490| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.46 r_work: 0.3500 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13323 Z= 0.186 Angle : 0.593 12.990 18135 Z= 0.300 Chirality : 0.043 0.236 2082 Planarity : 0.004 0.050 2357 Dihedral : 5.686 49.550 2312 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.51 % Allowed : 14.64 % Favored : 82.85 % 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: -0.44 (0.20), residues: 1448 helix: 1.69 (0.26), residues: 355 sheet: -1.01 (0.27), residues: 274 loop : -0.92 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 421 HIS 0.016 0.002 HIS C 18 PHE 0.011 0.002 PHE A 120 TYR 0.010 0.002 TYR A 233 ARG 0.003 0.000 ARG E 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 21) link_NAG-ASN : angle 1.92588 ( 63) link_BETA1-4 : bond 0.00192 ( 3) link_BETA1-4 : angle 2.28951 ( 9) hydrogen bonds : bond 0.04145 ( 568) hydrogen bonds : angle 5.66795 ( 1629) SS BOND : bond 0.00401 ( 18) SS BOND : angle 0.95692 ( 36) covalent geometry : bond 0.00417 (13281) covalent geometry : angle 0.57956 (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 157 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.7099 (ttmm) REVERT: A 261 ARG cc_start: 0.6947 (mtm110) cc_final: 0.6471 (mtt90) REVERT: A 312 ASN cc_start: 0.7830 (t0) cc_final: 0.7526 (p0) REVERT: A 396 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7451 (pm20) REVERT: C 33 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7606 (mt0) REVERT: C 382 ASN cc_start: 0.8014 (t0) cc_final: 0.7739 (t0) REVERT: E 50 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7928 (mt-10) REVERT: E 139 CYS cc_start: 0.6952 (m) cc_final: 0.6695 (m) REVERT: E 242 ILE cc_start: 0.8055 (mt) cc_final: 0.7804 (mp) REVERT: E 261 ARG cc_start: 0.7169 (mmt90) cc_final: 0.6173 (ptt180) REVERT: E 401 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6541 (pm20) outliers start: 32 outliers final: 15 residues processed: 146 average time/residue: 1.2615 time to fit residues: 201.6329 Evaluate side-chains 134 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 18 HIS 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 192 ILE 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 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 335 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 19 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 chunk 97 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 E 296 ASN E 363 GLN E 407 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 = 0.161236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.141888 restraints weight = 15577.448| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.65 r_work: 0.3502 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13323 Z= 0.203 Angle : 0.608 13.115 18135 Z= 0.306 Chirality : 0.044 0.296 2082 Planarity : 0.004 0.050 2357 Dihedral : 5.726 53.087 2312 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.66 % Allowed : 14.96 % Favored : 82.38 % 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: -0.45 (0.20), residues: 1448 helix: 1.72 (0.26), residues: 355 sheet: -1.03 (0.27), residues: 274 loop : -0.94 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 421 HIS 0.009 0.001 HIS A 17 PHE 0.014 0.002 PHE A 353 TYR 0.010 0.002 TYR A 233 ARG 0.004 0.000 ARG C 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 21) link_NAG-ASN : angle 1.99817 ( 63) link_BETA1-4 : bond 0.00100 ( 3) link_BETA1-4 : angle 2.33512 ( 9) hydrogen bonds : bond 0.04185 ( 568) hydrogen bonds : angle 5.66033 ( 1629) SS BOND : bond 0.00405 ( 18) SS BOND : angle 0.93870 ( 36) covalent geometry : bond 0.00459 (13281) covalent geometry : angle 0.59429 (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 156 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: A 46 SER cc_start: 0.7531 (t) cc_final: 0.7129 (p) REVERT: A 82 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.7022 (ttmm) REVERT: A 189 LYS cc_start: 0.7305 (mttt) cc_final: 0.6625 (mtpm) REVERT: A 261 ARG cc_start: 0.6932 (mtm110) cc_final: 0.6368 (mtt90) REVERT: A 312 ASN cc_start: 0.7797 (t0) cc_final: 0.7453 (p0) REVERT: A 396 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7372 (pm20) REVERT: C 33 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7607 (mt0) REVERT: C 320 MET cc_start: 0.8250 (ptt) cc_final: 0.7892 (ptt) REVERT: C 382 ASN cc_start: 0.7993 (t0) cc_final: 0.7716 (t0) REVERT: E 50 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7895 (mt-10) REVERT: E 139 CYS cc_start: 0.7005 (m) cc_final: 0.6724 (m) REVERT: E 242 ILE cc_start: 0.8063 (mt) cc_final: 0.7792 (mp) REVERT: E 261 ARG cc_start: 0.7234 (mmt90) cc_final: 0.6028 (ptt180) REVERT: E 401 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6496 (pm20) outliers start: 34 outliers final: 16 residues processed: 147 average time/residue: 1.2220 time to fit residues: 196.6953 Evaluate side-chains 134 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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 192 ILE Chi-restraints excluded: chain A residue 335 ILE 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 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 335 ILE 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 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 132 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 128 optimal weight: 0.0040 chunk 159 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 152 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.161633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.142312 restraints weight = 15425.589| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.65 r_work: 0.3510 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13323 Z= 0.194 Angle : 0.596 12.899 18135 Z= 0.301 Chirality : 0.044 0.247 2082 Planarity : 0.004 0.050 2357 Dihedral : 5.701 58.599 2312 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.58 % Allowed : 15.27 % Favored : 82.15 % 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: -0.45 (0.20), residues: 1448 helix: 1.72 (0.26), residues: 355 sheet: -1.03 (0.27), residues: 274 loop : -0.94 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 127 HIS 0.004 0.001 HIS A 17 PHE 0.012 0.002 PHE E 125 TYR 0.010 0.002 TYR A 233 ARG 0.004 0.000 ARG C 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 21) link_NAG-ASN : angle 1.93638 ( 63) link_BETA1-4 : bond 0.00150 ( 3) link_BETA1-4 : angle 2.26933 ( 9) hydrogen bonds : bond 0.04120 ( 568) hydrogen bonds : angle 5.61226 ( 1629) SS BOND : bond 0.00408 ( 18) SS BOND : angle 0.90942 ( 36) covalent geometry : bond 0.00437 (13281) covalent geometry : angle 0.58354 (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 152 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7559 (t) cc_final: 0.7170 (p) REVERT: A 82 LYS cc_start: 0.7327 (OUTLIER) cc_final: 0.7035 (ttmm) REVERT: A 172 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: A 189 LYS cc_start: 0.7296 (mttt) cc_final: 0.6608 (mtpm) REVERT: A 261 ARG cc_start: 0.6871 (mtm110) cc_final: 0.6352 (mtt90) REVERT: A 312 ASN cc_start: 0.7744 (t0) cc_final: 0.7435 (p0) REVERT: A 396 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7364 (pm20) REVERT: C 33 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7536 (mt0) REVERT: C 382 ASN cc_start: 0.7981 (t0) cc_final: 0.7716 (t0) REVERT: E 139 CYS cc_start: 0.7007 (m) cc_final: 0.6725 (m) REVERT: E 242 ILE cc_start: 0.8072 (mt) cc_final: 0.7799 (mp) REVERT: E 261 ARG cc_start: 0.7208 (mmt90) cc_final: 0.6026 (ptt180) REVERT: E 401 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6474 (pm20) outliers start: 33 outliers final: 18 residues processed: 141 average time/residue: 1.3925 time to fit residues: 218.2136 Evaluate side-chains 132 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 172 GLU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 335 ILE 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 18 HIS 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 335 ILE 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 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 135 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 40 optimal weight: 0.1980 chunk 5 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 497 ASN 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 = 0.3813 r_free = 0.3813 target = 0.164023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.144751 restraints weight = 15369.894| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.67 r_work: 0.3534 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2584 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= 0.137 Angle : 0.549 11.933 18135 Z= 0.279 Chirality : 0.042 0.241 2082 Planarity : 0.004 0.047 2357 Dihedral : 5.429 59.432 2312 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.49 % Allowed : 16.76 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.20), residues: 1448 helix: 1.90 (0.26), residues: 354 sheet: -0.87 (0.27), residues: 280 loop : -0.87 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 421 HIS 0.013 0.001 HIS C 18 PHE 0.016 0.001 PHE A 338 TYR 0.013 0.001 TYR C 94 ARG 0.005 0.000 ARG E 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 21) link_NAG-ASN : angle 1.83541 ( 63) link_BETA1-4 : bond 0.00260 ( 3) link_BETA1-4 : angle 2.01276 ( 9) hydrogen bonds : bond 0.03914 ( 568) hydrogen bonds : angle 5.44757 ( 1629) SS BOND : bond 0.00334 ( 18) SS BOND : angle 0.86755 ( 36) covalent geometry : bond 0.00301 (13281) covalent geometry : angle 0.53648 (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 139 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.7502 (t) cc_final: 0.7143 (p) REVERT: A 82 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6993 (ttmm) REVERT: A 261 ARG cc_start: 0.6843 (mtm110) cc_final: 0.6308 (mtt180) REVERT: A 312 ASN cc_start: 0.7756 (t0) cc_final: 0.7399 (p0) REVERT: A 396 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7375 (pm20) REVERT: C 344 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6872 (mt-10) REVERT: C 382 ASN cc_start: 0.7999 (t0) cc_final: 0.7696 (t0) REVERT: E 139 CYS cc_start: 0.6928 (m) cc_final: 0.6622 (m) REVERT: E 242 ILE cc_start: 0.8031 (mt) cc_final: 0.7758 (mp) REVERT: E 261 ARG cc_start: 0.7193 (mmt90) cc_final: 0.5967 (ptt180) outliers start: 19 outliers final: 13 residues processed: 133 average time/residue: 1.3679 time to fit residues: 198.1373 Evaluate side-chains 134 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 75 GLN Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 396 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 Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 335 ILE 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: 7.9990 chunk 56 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 363 GLN ** E 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.158698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.139526 restraints weight = 15598.928| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.62 r_work: 0.3476 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 13323 Z= 0.315 Angle : 0.714 14.303 18135 Z= 0.359 Chirality : 0.048 0.239 2082 Planarity : 0.005 0.052 2357 Dihedral : 6.115 53.854 2312 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.04 % Allowed : 16.05 % Favored : 81.91 % 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: -0.67 (0.20), residues: 1448 helix: 1.46 (0.26), residues: 356 sheet: -1.14 (0.27), residues: 273 loop : -1.06 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.007 0.002 HIS E 18 PHE 0.016 0.002 PHE E 125 TYR 0.015 0.002 TYR C 161 ARG 0.007 0.001 ARG C 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 21) link_NAG-ASN : angle 2.07513 ( 63) link_BETA1-4 : bond 0.00217 ( 3) link_BETA1-4 : angle 2.78888 ( 9) hydrogen bonds : bond 0.04584 ( 568) hydrogen bonds : angle 5.88395 ( 1629) SS BOND : bond 0.00543 ( 18) SS BOND : angle 1.12046 ( 36) covalent geometry : bond 0.00725 (13281) covalent geometry : angle 0.70097 (18027) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9240.20 seconds wall clock time: 161 minutes 13.44 seconds (9673.44 seconds total)