Starting phenix.real_space_refine on Wed Mar 4 13:17:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n7v_49100/03_2026/9n7v_49100.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n7v_49100/03_2026/9n7v_49100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n7v_49100/03_2026/9n7v_49100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n7v_49100/03_2026/9n7v_49100.map" model { file = "/net/cci-nas-00/data/ceres_data/9n7v_49100/03_2026/9n7v_49100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n7v_49100/03_2026/9n7v_49100.cif" } resolution = 3.15 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= 0.018 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 58 5.16 5 C 8502 2.51 5 N 2294 2.21 5 O 2682 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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13536 Number of models: 1 Model: "" Number of chains: 17 Chain: "H" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 838 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain breaks: 2 Chain: "L" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 758 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain breaks: 1 Chain: "A" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2509 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 18, 'TRANS': 301} Chain breaks: 1 Chain: "a" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 1, 'TRANS': 162} Chain: "C" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2517 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 18, 'TRANS': 302} Chain breaks: 1 Chain: "c" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 1, 'TRANS': 162} Chain: "B" Number of atoms: 2551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2551 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 18, 'TRANS': 307} Chain: "b" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 1, 'TRANS': 162} 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: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "a" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" 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: "b" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.06, per 1000 atoms: 0.23 Number of scatterers: 13536 At special positions: 0 Unit cell: (102.95, 84.1, 144.275, 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 58 16.00 O 2682 8.00 N 2294 7.00 C 8502 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS a 137 " distance=2.04 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 146 " distance=2.03 Simple disulfide: pdb=" SG CYS a 144 " - pdb=" SG CYS a 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS c 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 77 " distance=2.02 Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 146 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 313 " distance=2.02 Simple disulfide: pdb=" SG CYS c 144 " - pdb=" SG CYS c 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS b 137 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 77 " distance=2.03 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 146 " distance=2.02 Simple disulfide: pdb=" SG CYS b 144 " - pdb=" SG CYS b 148 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " BETA1-6 " NAG E 1 " - " FUC E 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 401 " - " ASN A 33 " " NAG A 402 " - " ASN A 286 " " NAG A 403 " - " ASN A 172 " " NAG A 404 " - " ASN A 297 " " NAG B 401 " - " ASN B 21 " " NAG B 402 " - " ASN B 33 " " NAG B 403 " - " ASN B 286 " " NAG B 404 " - " ASN B 297 " " NAG B 405 " - " ASN B 172 " " NAG B 406 " - " ASN B 97 " " NAG C 401 " - " ASN C 21 " " NAG C 402 " - " ASN C 33 " " NAG C 403 " - " ASN C 286 " " NAG C 404 " - " ASN C 297 " " NAG C 405 " - " ASN C 172 " " NAG D 1 " - " ASN A 97 " " NAG E 1 " - " ASN A 21 " " NAG F 1 " - " ASN C 97 " " NAG a 301 " - " ASN a 154 " " NAG b 301 " - " ASN b 154 " " NAG c 301 " - " ASN c 154 " Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 582.5 milliseconds 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3092 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 38 sheets defined 23.3% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 107 through 116 Processing helix chain 'A' and resid 194 through 202 Processing helix chain 'a' and resid 37 through 58 removed outlier: 3.691A pdb=" N LYS a 58 " --> pdb=" O SER a 54 " (cutoff:3.500A) Processing helix chain 'a' and resid 71 through 73 No H-bonds generated for 'chain 'a' and resid 71 through 73' Processing helix chain 'a' and resid 74 through 127 Processing helix chain 'a' and resid 145 through 155 Processing helix chain 'a' and resid 158 through 170 removed outlier: 3.676A pdb=" N TYR a 162 " --> pdb=" O ASP a 158 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU a 164 " --> pdb=" O PRO a 160 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU a 165 " --> pdb=" O LYS a 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 107 through 116 removed outlier: 3.551A pdb=" N SER C 116 " --> pdb=" O ARG C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 203 Processing helix chain 'c' and resid 37 through 58 Processing helix chain 'c' and resid 74 through 127 Processing helix chain 'c' and resid 145 through 155 Processing helix chain 'c' and resid 158 through 173 removed outlier: 4.065A pdb=" N GLU c 164 " --> pdb=" O PRO c 160 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU c 165 " --> pdb=" O LYS c 161 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASN c 169 " --> pdb=" O GLU c 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 74 through 78 removed outlier: 3.852A pdb=" N GLU B 78 " --> pdb=" O PRO B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 removed outlier: 3.523A pdb=" N LEU B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 202 Processing helix chain 'b' and resid 37 through 58 Processing helix chain 'b' and resid 74 through 127 Processing helix chain 'b' and resid 145 through 155 Processing helix chain 'b' and resid 158 through 171 removed outlier: 4.156A pdb=" N TYR b 162 " --> pdb=" O ASP b 158 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU b 164 " --> pdb=" O PRO b 160 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLU b 165 " --> pdb=" O LYS b 161 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU b 171 " --> pdb=" O LYS b 167 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 45 through 50 removed outlier: 6.471A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 45 through 50 removed outlier: 6.471A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS H 35 " --> pdb=" O ALA H 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 12 through 13 removed outlier: 4.329A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 20 through 24 Processing sheet with id=AA6, first strand: chain 'a' and resid 33 through 36 removed outlier: 3.624A pdb=" N GLY a 33 " --> pdb=" O HIS a 26 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY A 16 " --> pdb=" O GLY a 23 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS a 137 " --> pdb=" O ILE a 133 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.170A pdb=" N ASP A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA9, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AB1, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.363A pdb=" N LEU A 51 " --> pdb=" O HIS A 283 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N CYS A 285 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 60 through 63 removed outlier: 6.608A pdb=" N LEU A 60 " --> pdb=" O VAL A 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 118 through 124 removed outlier: 5.229A pdb=" N SER A 120 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLU A 268 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE A 265 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 182 " --> pdb=" O MET A 267 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 158 through 160 Processing sheet with id=AB5, first strand: chain 'A' and resid 186 through 191 Processing sheet with id=AB6, first strand: chain 'A' and resid 217 through 220 removed outlier: 4.091A pdb=" N LYS A 218 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 211 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 294 through 296 removed outlier: 3.519A pdb=" N THR A 291 " --> pdb=" O GLY A 294 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 311 " --> pdb=" O THR a 64 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR a 64 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 16 through 17 Processing sheet with id=AB9, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AC1, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC2, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.979A pdb=" N LEU C 51 " --> pdb=" O HIS C 283 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N CYS C 285 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.629A pdb=" N LEU C 60 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AC5, first strand: chain 'C' and resid 158 through 159 Processing sheet with id=AC6, first strand: chain 'C' and resid 173 through 176 Processing sheet with id=AC7, first strand: chain 'C' and resid 236 through 244 removed outlier: 3.603A pdb=" N GLU C 182 " --> pdb=" O MET C 267 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 289 through 290 removed outlier: 3.899A pdb=" N CYS C 289 " --> pdb=" O ILE C 296 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 302 through 303 Processing sheet with id=AD1, first strand: chain 'c' and resid 130 through 132 removed outlier: 3.520A pdb=" N LYS c 131 " --> pdb=" O GLU c 139 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'b' and resid 32 through 35 removed outlier: 4.033A pdb=" N GLY b 23 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY B 16 " --> pdb=" O GLY b 23 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 13 " --> pdb=" O PHE b 138 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 25 through 27 Processing sheet with id=AD4, first strand: chain 'B' and resid 40 through 41 Processing sheet with id=AD5, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AD6, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.013A pdb=" N LEU B 51 " --> pdb=" O HIS B 283 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N CYS B 285 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 60 through 63 Processing sheet with id=AD8, first strand: chain 'B' and resid 118 through 124 removed outlier: 5.326A pdb=" N SER B 120 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLU B 268 " --> pdb=" O SER B 120 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 158 through 160 Processing sheet with id=AE1, first strand: chain 'B' and resid 171 through 176 removed outlier: 3.512A pdb=" N VAL B 211 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS B 218 " --> pdb=" O VAL B 211 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 309 through 310 removed outlier: 3.692A pdb=" N THR B 309 " --> pdb=" O VAL b 66 " (cutoff:3.500A) 461 hydrogen bonds defined for protein. 1293 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: 2.35 Time building geometry restraints manager: 1.45 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: 4284 1.34 - 1.46: 3248 1.46 - 1.58: 6228 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 13836 Sorted by residual: bond pdb=" CG1 ILE B 189 " pdb=" CD1 ILE B 189 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.25e+00 bond pdb=" CG LEU B 328 " pdb=" CD1 LEU B 328 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.18e+00 bond pdb=" N GLN L 1 " pdb=" CA GLN L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" CB ILE A 176 " pdb=" CG2 ILE A 176 " ideal model delta sigma weight residual 1.521 1.575 -0.054 3.30e-02 9.18e+02 2.64e+00 bond pdb=" N SER B 336 " pdb=" CA SER B 336 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.51e+00 ... (remaining 13831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 18467 3.29 - 6.58: 274 6.58 - 9.87: 11 9.87 - 13.16: 0 13.16 - 16.45: 1 Bond angle restraints: 18753 Sorted by residual: angle pdb=" C5 NAG E 1 " pdb=" C6 NAG E 1 " pdb=" O6 NAG E 1 " ideal model delta sigma weight residual 109.77 126.22 -16.45 3.00e+00 1.11e-01 3.00e+01 angle pdb=" C GLN B 335 " pdb=" N SER B 336 " pdb=" CA SER B 336 " ideal model delta sigma weight residual 121.70 127.99 -6.29 1.80e+00 3.09e-01 1.22e+01 angle pdb=" N SER B 336 " pdb=" CA SER B 336 " pdb=" C SER B 336 " ideal model delta sigma weight residual 111.00 120.06 -9.06 2.80e+00 1.28e-01 1.05e+01 angle pdb=" N PHE A 265 " pdb=" CA PHE A 265 " pdb=" C PHE A 265 " ideal model delta sigma weight residual 107.49 114.17 -6.68 2.16e+00 2.14e-01 9.57e+00 angle pdb=" N GLY L 93 " pdb=" CA GLY L 93 " pdb=" C GLY L 93 " ideal model delta sigma weight residual 111.50 106.21 5.29 1.74e+00 3.30e-01 9.25e+00 ... (remaining 18748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 7891 17.69 - 35.37: 566 35.37 - 53.06: 93 53.06 - 70.74: 14 70.74 - 88.43: 9 Dihedral angle restraints: 8573 sinusoidal: 3744 harmonic: 4829 Sorted by residual: dihedral pdb=" CB CYS a 144 " pdb=" SG CYS a 144 " pdb=" SG CYS a 148 " pdb=" CB CYS a 148 " ideal model delta sinusoidal sigma weight residual 93.00 163.11 -70.11 1 1.00e+01 1.00e-02 6.33e+01 dihedral pdb=" CB CYS b 144 " pdb=" SG CYS b 144 " pdb=" SG CYS b 148 " pdb=" CB CYS b 148 " ideal model delta sinusoidal sigma weight residual 93.00 143.00 -50.00 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CB CYS B 65 " pdb=" SG CYS B 65 " pdb=" SG CYS B 77 " pdb=" CB CYS B 77 " ideal model delta sinusoidal sigma weight residual -86.00 -120.84 34.84 1 1.00e+01 1.00e-02 1.72e+01 ... (remaining 8570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1576 0.053 - 0.106: 419 0.106 - 0.158: 98 0.158 - 0.211: 12 0.211 - 0.264: 6 Chirality restraints: 2111 Sorted by residual: chirality pdb=" C1 NAG C 405 " pdb=" ND2 ASN C 172 " pdb=" C2 NAG C 405 " pdb=" O5 NAG C 405 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C1 NAG a 301 " pdb=" ND2 ASN a 154 " pdb=" C2 NAG a 301 " pdb=" O5 NAG a 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C1 NAG A 403 " pdb=" ND2 ASN A 172 " pdb=" C2 NAG A 403 " pdb=" O5 NAG A 403 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2108 not shown) Planarity restraints: 2403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 406 " 0.045 2.00e-02 2.50e+03 4.43e-02 2.45e+01 pdb=" C7 NAG B 406 " 0.034 2.00e-02 2.50e+03 pdb=" C8 NAG B 406 " 0.020 2.00e-02 2.50e+03 pdb=" N2 NAG B 406 " -0.075 2.00e-02 2.50e+03 pdb=" O7 NAG B 406 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 146 " 0.054 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO A 147 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 147 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 147 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 404 " -0.026 2.00e-02 2.50e+03 2.56e-02 8.22e+00 pdb=" C7 NAG A 404 " -0.020 2.00e-02 2.50e+03 pdb=" C8 NAG A 404 " -0.012 2.00e-02 2.50e+03 pdb=" N2 NAG A 404 " 0.043 2.00e-02 2.50e+03 pdb=" O7 NAG A 404 " 0.014 2.00e-02 2.50e+03 ... (remaining 2400 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 313 2.68 - 3.23: 13184 3.23 - 3.79: 20991 3.79 - 4.34: 29283 4.34 - 4.90: 48975 Nonbonded interactions: 112746 Sorted by model distance: nonbonded pdb=" O GLY A 63 " pdb=" OG1 THR A 92 " model vdw 2.120 3.040 nonbonded pdb=" O SER L 2 " pdb=" OG1 THR L 26 " model vdw 2.125 3.040 nonbonded pdb=" O THR A 92 " pdb=" OG SER A 95 " model vdw 2.132 3.040 nonbonded pdb=" OG SER C 85 " pdb=" O SER C 119 " model vdw 2.132 3.040 nonbonded pdb=" OG1 THR B 287 " pdb=" O ILE B 296 " model vdw 2.153 3.040 ... (remaining 112741 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' selection = (chain 'B' and (resid 11 through 147 or resid 151 through 333 or resid 403 throu \ gh 406)) selection = (chain 'C' and (resid 11 through 333 or resid 402 through 405)) } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } 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: 13.390 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: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.140 Find NCS groups from input model: 0.300 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 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 0.075 13876 Z= 0.243 Angle : 0.953 16.445 18858 Z= 0.495 Chirality : 0.052 0.264 2111 Planarity : 0.006 0.082 2382 Dihedral : 12.280 88.430 5436 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.07 % Allowed : 0.27 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.20 (0.19), residues: 1641 helix: 0.47 (0.25), residues: 346 sheet: -2.78 (0.29), residues: 267 loop : -1.85 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 262 TYR 0.029 0.002 TYR B 108 PHE 0.042 0.004 PHE C 154 TRP 0.034 0.003 TRP C 160 HIS 0.015 0.002 HIS a 111 Details of bonding type rmsd covalent geometry : bond 0.00585 (13836) covalent geometry : angle 0.93846 (18753) SS BOND : bond 0.00561 ( 15) SS BOND : angle 2.07292 ( 30) hydrogen bonds : bond 0.13999 ( 458) hydrogen bonds : angle 7.69324 ( 1293) link_BETA1-4 : bond 0.00592 ( 3) link_BETA1-4 : angle 1.21074 ( 9) link_BETA1-6 : bond 0.00086 ( 1) link_BETA1-6 : angle 8.41771 ( 3) link_NAG-ASN : bond 0.00545 ( 21) link_NAG-ASN : angle 2.07042 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 432 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 53 ASN cc_start: 0.6494 (m-40) cc_final: 0.6091 (m-40) REVERT: A 78 GLU cc_start: 0.6768 (pm20) cc_final: 0.6451 (pm20) REVERT: A 284 ASP cc_start: 0.7549 (t0) cc_final: 0.7165 (t0) REVERT: A 293 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7099 (mm-30) REVERT: a 24 TYR cc_start: 0.7689 (m-80) cc_final: 0.7297 (m-80) REVERT: a 75 LYS cc_start: 0.8383 (tptt) cc_final: 0.8137 (tppt) REVERT: a 82 LYS cc_start: 0.8538 (tttp) cc_final: 0.7884 (ttmt) REVERT: a 86 ASP cc_start: 0.8164 (m-30) cc_final: 0.7715 (m-30) REVERT: a 127 LYS cc_start: 0.8041 (mmtt) cc_final: 0.7444 (mttp) REVERT: C 84 SER cc_start: 0.7880 (m) cc_final: 0.7565 (t) REVERT: C 147 PRO cc_start: 0.5992 (Cg_endo) cc_final: 0.5761 (Cg_exo) REVERT: c 37 ASP cc_start: 0.6260 (t0) cc_final: 0.5910 (m-30) REVERT: c 94 TYR cc_start: 0.9230 (t80) cc_final: 0.9006 (t80) REVERT: c 139 GLU cc_start: 0.6092 (mm-30) cc_final: 0.5867 (mm-30) REVERT: B 204 ASN cc_start: 0.7650 (m-40) cc_final: 0.6611 (p0) REVERT: B 237 MET cc_start: 0.8432 (ttm) cc_final: 0.8032 (ttm) REVERT: B 313 CYS cc_start: 0.8004 (p) cc_final: 0.7772 (p) REVERT: b 86 ASP cc_start: 0.7192 (m-30) cc_final: 0.6911 (m-30) REVERT: b 109 ASP cc_start: 0.8032 (t0) cc_final: 0.7651 (t0) outliers start: 1 outliers final: 1 residues processed: 433 average time/residue: 0.1224 time to fit residues: 76.2473 Evaluate side-chains 276 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 275 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN L 38 HIS A 173 GLN ** a 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 HIS ** C 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 ASN c 129 ASN c 142 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.175838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.156999 restraints weight = 19128.877| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.11 r_work: 0.3808 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13876 Z= 0.201 Angle : 0.691 8.217 18858 Z= 0.363 Chirality : 0.045 0.240 2111 Planarity : 0.005 0.039 2382 Dihedral : 6.234 59.554 2316 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.36 % Allowed : 9.59 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.92 (0.19), residues: 1641 helix: 0.54 (0.25), residues: 360 sheet: -2.13 (0.30), residues: 274 loop : -1.77 (0.17), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 112 TYR 0.021 0.002 TYR c 159 PHE 0.028 0.002 PHE A 105 TRP 0.019 0.002 TRP C 160 HIS 0.012 0.001 HIS c 142 Details of bonding type rmsd covalent geometry : bond 0.00455 (13836) covalent geometry : angle 0.68128 (18753) SS BOND : bond 0.00592 ( 15) SS BOND : angle 1.40008 ( 30) hydrogen bonds : bond 0.05793 ( 458) hydrogen bonds : angle 6.20259 ( 1293) link_BETA1-4 : bond 0.00513 ( 3) link_BETA1-4 : angle 1.32064 ( 9) link_BETA1-6 : bond 0.00054 ( 1) link_BETA1-6 : angle 2.36882 ( 3) link_NAG-ASN : bond 0.00498 ( 21) link_NAG-ASN : angle 1.77388 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 299 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.7061 (pm20) cc_final: 0.6629 (pm20) REVERT: A 284 ASP cc_start: 0.7666 (t0) cc_final: 0.7338 (t0) REVERT: A 293 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7251 (mm-30) REVERT: a 24 TYR cc_start: 0.7907 (m-80) cc_final: 0.7524 (m-80) REVERT: a 62 GLN cc_start: 0.7868 (mp10) cc_final: 0.7628 (mp10) REVERT: a 82 LYS cc_start: 0.8549 (tttp) cc_final: 0.8274 (ttmt) REVERT: a 105 GLU cc_start: 0.7910 (tt0) cc_final: 0.7521 (tt0) REVERT: a 127 LYS cc_start: 0.7949 (mmtt) cc_final: 0.7351 (mttp) REVERT: a 157 TYR cc_start: 0.6998 (t80) cc_final: 0.6754 (t80) REVERT: C 46 LYS cc_start: 0.7735 (mmmt) cc_final: 0.7473 (tptp) REVERT: C 84 SER cc_start: 0.7966 (m) cc_final: 0.7733 (t) REVERT: C 147 PRO cc_start: 0.6058 (Cg_endo) cc_final: 0.5815 (Cg_exo) REVERT: c 116 LYS cc_start: 0.5401 (mmtt) cc_final: 0.4908 (mmmt) REVERT: B 204 ASN cc_start: 0.7947 (m-40) cc_final: 0.6651 (p0) REVERT: B 237 MET cc_start: 0.8463 (ttm) cc_final: 0.8085 (ttm) REVERT: B 313 CYS cc_start: 0.8137 (p) cc_final: 0.7931 (p) REVERT: b 98 LEU cc_start: 0.9135 (mm) cc_final: 0.8926 (mm) REVERT: b 109 ASP cc_start: 0.8408 (t0) cc_final: 0.7894 (t0) REVERT: b 159 TYR cc_start: 0.6767 (t80) cc_final: 0.6553 (t80) outliers start: 49 outliers final: 37 residues processed: 329 average time/residue: 0.1194 time to fit residues: 57.3253 Evaluate side-chains 286 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 249 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain a residue 15 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain c residue 18 VAL Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 112 ASP Chi-restraints excluded: chain c residue 148 CYS Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 97 ASN Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain b residue 18 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 2 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 129 optimal weight: 0.3980 chunk 23 optimal weight: 0.0470 chunk 152 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN L 53 ASN A 41 ASN A 238 ASN ** a 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 28 ASN a 95 ASN ** C 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 142 HIS b 50 ASN ** b 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.177803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.158785 restraints weight = 19407.151| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.16 r_work: 0.3827 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13876 Z= 0.141 Angle : 0.616 8.295 18858 Z= 0.322 Chirality : 0.042 0.237 2111 Planarity : 0.004 0.037 2382 Dihedral : 5.954 61.491 2316 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.49 % Allowed : 12.33 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.73 (0.19), residues: 1641 helix: 0.73 (0.26), residues: 359 sheet: -2.09 (0.28), residues: 311 loop : -1.57 (0.18), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 323 TYR 0.018 0.001 TYR C 108 PHE 0.014 0.002 PHE A 105 TRP 0.015 0.001 TRP C 160 HIS 0.013 0.001 HIS c 142 Details of bonding type rmsd covalent geometry : bond 0.00309 (13836) covalent geometry : angle 0.60640 (18753) SS BOND : bond 0.00371 ( 15) SS BOND : angle 1.31405 ( 30) hydrogen bonds : bond 0.05307 ( 458) hydrogen bonds : angle 5.96972 ( 1293) link_BETA1-4 : bond 0.00553 ( 3) link_BETA1-4 : angle 0.95405 ( 9) link_BETA1-6 : bond 0.00647 ( 1) link_BETA1-6 : angle 2.36078 ( 3) link_NAG-ASN : bond 0.00343 ( 21) link_NAG-ASN : angle 1.67726 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 277 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 81 GLN cc_start: 0.6542 (OUTLIER) cc_final: 0.6339 (mm-40) REVERT: A 78 GLU cc_start: 0.7019 (pm20) cc_final: 0.6559 (pm20) REVERT: A 284 ASP cc_start: 0.7552 (t0) cc_final: 0.7148 (t0) REVERT: A 293 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7238 (mm-30) REVERT: a 24 TYR cc_start: 0.7830 (m-80) cc_final: 0.7361 (m-80) REVERT: a 82 LYS cc_start: 0.8553 (tttp) cc_final: 0.8277 (ttmt) REVERT: a 127 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7314 (mttp) REVERT: C 84 SER cc_start: 0.7951 (m) cc_final: 0.7714 (t) REVERT: C 147 PRO cc_start: 0.5908 (Cg_endo) cc_final: 0.5643 (Cg_exo) REVERT: c 116 LYS cc_start: 0.5321 (mmtt) cc_final: 0.4825 (mmmt) REVERT: B 198 GLN cc_start: 0.7460 (tt0) cc_final: 0.6965 (tp40) REVERT: B 204 ASN cc_start: 0.7863 (m-40) cc_final: 0.7604 (m-40) REVERT: B 237 MET cc_start: 0.8452 (ttm) cc_final: 0.8114 (ttm) REVERT: B 313 CYS cc_start: 0.8203 (p) cc_final: 0.7981 (p) REVERT: b 98 LEU cc_start: 0.9164 (mm) cc_final: 0.8932 (mm) REVERT: b 109 ASP cc_start: 0.8425 (t0) cc_final: 0.7891 (t0) outliers start: 51 outliers final: 40 residues processed: 312 average time/residue: 0.1172 time to fit residues: 54.1116 Evaluate side-chains 288 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 247 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain a residue 28 ASN Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain c residue 18 VAL Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 112 ASP Chi-restraints excluded: chain c residue 148 CYS Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 260 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 126 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 119 optimal weight: 0.0770 chunk 108 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 95 ASN C 18 HIS ** C 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN c 114 ASN c 142 HIS ** b 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.174846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.155568 restraints weight = 19196.132| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.14 r_work: 0.3787 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13876 Z= 0.167 Angle : 0.630 14.704 18858 Z= 0.326 Chirality : 0.043 0.235 2111 Planarity : 0.004 0.038 2382 Dihedral : 5.713 54.897 2314 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.63 % Allowed : 12.53 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.68 (0.19), residues: 1641 helix: 0.60 (0.26), residues: 359 sheet: -1.95 (0.29), residues: 307 loop : -1.52 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 112 TYR 0.019 0.002 TYR C 108 PHE 0.014 0.002 PHE H 67 TRP 0.014 0.001 TRP B 160 HIS 0.012 0.001 HIS c 142 Details of bonding type rmsd covalent geometry : bond 0.00374 (13836) covalent geometry : angle 0.61861 (18753) SS BOND : bond 0.00391 ( 15) SS BOND : angle 1.63392 ( 30) hydrogen bonds : bond 0.05267 ( 458) hydrogen bonds : angle 5.95019 ( 1293) link_BETA1-4 : bond 0.00542 ( 3) link_BETA1-4 : angle 0.99088 ( 9) link_BETA1-6 : bond 0.00415 ( 1) link_BETA1-6 : angle 2.05396 ( 3) link_NAG-ASN : bond 0.00368 ( 21) link_NAG-ASN : angle 1.84842 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 254 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 53 ASN cc_start: 0.7210 (m-40) cc_final: 0.6881 (m110) REVERT: L 69 LYS cc_start: 0.7559 (tttp) cc_final: 0.7272 (ttmt) REVERT: A 78 GLU cc_start: 0.7092 (pm20) cc_final: 0.6621 (pm20) REVERT: A 140 LYS cc_start: 0.8082 (pttt) cc_final: 0.7842 (pttm) REVERT: A 284 ASP cc_start: 0.7613 (t0) cc_final: 0.7259 (t0) REVERT: A 293 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7301 (mm-30) REVERT: a 24 TYR cc_start: 0.7805 (m-80) cc_final: 0.7413 (m-80) REVERT: a 62 GLN cc_start: 0.7898 (mp10) cc_final: 0.7679 (mp10) REVERT: a 82 LYS cc_start: 0.8534 (tttp) cc_final: 0.8279 (ttmt) REVERT: C 84 SER cc_start: 0.7931 (m) cc_final: 0.7700 (t) REVERT: C 147 PRO cc_start: 0.5899 (Cg_endo) cc_final: 0.5643 (Cg_exo) REVERT: c 116 LYS cc_start: 0.5218 (mmtt) cc_final: 0.4780 (mmmt) REVERT: B 204 ASN cc_start: 0.7882 (m-40) cc_final: 0.6658 (p0) REVERT: B 237 MET cc_start: 0.8457 (ttm) cc_final: 0.8121 (ttm) REVERT: b 98 LEU cc_start: 0.9188 (mm) cc_final: 0.8942 (mm) REVERT: b 109 ASP cc_start: 0.8357 (t0) cc_final: 0.7868 (t0) outliers start: 53 outliers final: 44 residues processed: 292 average time/residue: 0.1182 time to fit residues: 51.1128 Evaluate side-chains 277 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 233 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain a residue 15 THR Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain c residue 18 VAL Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 112 ASP Chi-restraints excluded: chain c residue 148 CYS Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain b residue 85 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 132 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 HIS A 61 HIS ** a 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 50 ASN a 95 ASN ** C 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN c 142 HIS B 166 ASN ** b 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.172004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.152745 restraints weight = 19186.055| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.12 r_work: 0.3753 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13876 Z= 0.186 Angle : 0.653 16.458 18858 Z= 0.333 Chirality : 0.043 0.234 2111 Planarity : 0.004 0.041 2382 Dihedral : 5.970 55.233 2314 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.59 % Allowed : 13.42 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.69 (0.19), residues: 1641 helix: 0.51 (0.26), residues: 359 sheet: -1.83 (0.30), residues: 289 loop : -1.56 (0.18), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 112 TYR 0.022 0.002 TYR B 88 PHE 0.015 0.002 PHE A 210 TRP 0.019 0.001 TRP B 160 HIS 0.009 0.001 HIS c 142 Details of bonding type rmsd covalent geometry : bond 0.00420 (13836) covalent geometry : angle 0.64072 (18753) SS BOND : bond 0.00410 ( 15) SS BOND : angle 1.52293 ( 30) hydrogen bonds : bond 0.05283 ( 458) hydrogen bonds : angle 5.96971 ( 1293) link_BETA1-4 : bond 0.00335 ( 3) link_BETA1-4 : angle 1.10423 ( 9) link_BETA1-6 : bond 0.00582 ( 1) link_BETA1-6 : angle 1.78076 ( 3) link_NAG-ASN : bond 0.00416 ( 21) link_NAG-ASN : angle 1.99076 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 260 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 53 ASN cc_start: 0.7395 (m-40) cc_final: 0.7006 (m110) REVERT: A 78 GLU cc_start: 0.7119 (pm20) cc_final: 0.6836 (pt0) REVERT: A 284 ASP cc_start: 0.7674 (t0) cc_final: 0.7322 (t0) REVERT: A 293 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7340 (mm-30) REVERT: a 24 TYR cc_start: 0.7830 (m-80) cc_final: 0.7469 (m-80) REVERT: a 82 LYS cc_start: 0.8562 (tttp) cc_final: 0.8291 (ttmt) REVERT: C 11 ASP cc_start: 0.7968 (m-30) cc_final: 0.7651 (m-30) REVERT: C 46 LYS cc_start: 0.7906 (mmmt) cc_final: 0.7703 (tptp) REVERT: C 84 SER cc_start: 0.7930 (m) cc_final: 0.7644 (t) REVERT: C 147 PRO cc_start: 0.5917 (Cg_endo) cc_final: 0.5635 (Cg_exo) REVERT: c 29 GLU cc_start: 0.7786 (pp20) cc_final: 0.7487 (pp20) REVERT: c 116 LYS cc_start: 0.5324 (mmtt) cc_final: 0.4895 (mmmt) REVERT: B 204 ASN cc_start: 0.7916 (m-40) cc_final: 0.6703 (p0) REVERT: B 237 MET cc_start: 0.8405 (ttm) cc_final: 0.8139 (ttm) REVERT: B 279 ASP cc_start: 0.7498 (m-30) cc_final: 0.7216 (m-30) REVERT: b 98 LEU cc_start: 0.9215 (mm) cc_final: 0.8949 (mm) REVERT: b 109 ASP cc_start: 0.8448 (t0) cc_final: 0.7925 (t0) outliers start: 67 outliers final: 52 residues processed: 305 average time/residue: 0.1121 time to fit residues: 50.7972 Evaluate side-chains 281 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 229 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain a residue 15 THR Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 43 ASN Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 313 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain c residue 18 VAL Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 102 LEU Chi-restraints excluded: chain c residue 148 CYS Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain b residue 18 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 163 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 145 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 95 ASN ** C 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 142 HIS B 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.172000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.152046 restraints weight = 19085.008| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.22 r_work: 0.3769 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13876 Z= 0.147 Angle : 0.618 16.240 18858 Z= 0.318 Chirality : 0.042 0.221 2111 Planarity : 0.004 0.038 2382 Dihedral : 5.759 54.902 2314 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.04 % Allowed : 14.59 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.53 (0.20), residues: 1641 helix: 0.67 (0.26), residues: 359 sheet: -1.77 (0.29), residues: 299 loop : -1.44 (0.18), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 112 TYR 0.018 0.001 TYR B 263 PHE 0.015 0.002 PHE A 127 TRP 0.018 0.001 TRP B 160 HIS 0.012 0.001 HIS c 142 Details of bonding type rmsd covalent geometry : bond 0.00326 (13836) covalent geometry : angle 0.60297 (18753) SS BOND : bond 0.00465 ( 15) SS BOND : angle 1.44761 ( 30) hydrogen bonds : bond 0.05082 ( 458) hydrogen bonds : angle 5.86029 ( 1293) link_BETA1-4 : bond 0.00479 ( 3) link_BETA1-4 : angle 0.98244 ( 9) link_BETA1-6 : bond 0.00501 ( 1) link_BETA1-6 : angle 1.65531 ( 3) link_NAG-ASN : bond 0.00419 ( 21) link_NAG-ASN : angle 2.17109 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 253 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 57 LYS cc_start: 0.7508 (mtmm) cc_final: 0.6997 (mttt) REVERT: A 78 GLU cc_start: 0.7052 (pm20) cc_final: 0.6724 (pt0) REVERT: A 284 ASP cc_start: 0.7680 (t0) cc_final: 0.7330 (t0) REVERT: A 293 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7291 (mm-30) REVERT: a 24 TYR cc_start: 0.7833 (m-80) cc_final: 0.7437 (m-80) REVERT: a 82 LYS cc_start: 0.8580 (tttp) cc_final: 0.7789 (ttmt) REVERT: a 86 ASP cc_start: 0.8281 (m-30) cc_final: 0.7864 (m-30) REVERT: a 159 TYR cc_start: 0.7022 (t80) cc_final: 0.6535 (t80) REVERT: C 84 SER cc_start: 0.7927 (m) cc_final: 0.7651 (t) REVERT: C 147 PRO cc_start: 0.5828 (Cg_endo) cc_final: 0.5543 (Cg_exo) REVERT: c 50 ASN cc_start: 0.8039 (t0) cc_final: 0.7441 (t0) REVERT: c 116 LYS cc_start: 0.5216 (mmtt) cc_final: 0.4852 (mmmt) REVERT: B 198 GLN cc_start: 0.7453 (tt0) cc_final: 0.7160 (tp40) REVERT: B 204 ASN cc_start: 0.7829 (m-40) cc_final: 0.6663 (p0) REVERT: B 237 MET cc_start: 0.8449 (ttm) cc_final: 0.8097 (ttm) REVERT: b 98 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8916 (mm) REVERT: b 109 ASP cc_start: 0.8458 (t0) cc_final: 0.7964 (t0) outliers start: 59 outliers final: 47 residues processed: 296 average time/residue: 0.1125 time to fit residues: 49.4076 Evaluate side-chains 282 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 234 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 313 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain c residue 22 TYR Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 148 CYS Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain b residue 98 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 127 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 137 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 95 ASN ** C 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 30 GLN c 142 HIS B 166 ASN b 146 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.171722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.152209 restraints weight = 19027.820| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.13 r_work: 0.3757 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13876 Z= 0.167 Angle : 0.644 17.068 18858 Z= 0.327 Chirality : 0.043 0.221 2111 Planarity : 0.004 0.037 2382 Dihedral : 5.889 55.103 2314 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.18 % Allowed : 15.41 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.48 (0.20), residues: 1641 helix: 0.62 (0.26), residues: 360 sheet: -1.65 (0.30), residues: 297 loop : -1.40 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 112 TYR 0.019 0.002 TYR C 108 PHE 0.017 0.002 PHE H 100 TRP 0.021 0.001 TRP A 70 HIS 0.012 0.001 HIS c 142 Details of bonding type rmsd covalent geometry : bond 0.00376 (13836) covalent geometry : angle 0.61710 (18753) SS BOND : bond 0.00401 ( 15) SS BOND : angle 1.91202 ( 30) hydrogen bonds : bond 0.05112 ( 458) hydrogen bonds : angle 5.83692 ( 1293) link_BETA1-4 : bond 0.00397 ( 3) link_BETA1-4 : angle 1.06536 ( 9) link_BETA1-6 : bond 0.00433 ( 1) link_BETA1-6 : angle 1.54644 ( 3) link_NAG-ASN : bond 0.00537 ( 21) link_NAG-ASN : angle 2.96691 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 245 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 57 LYS cc_start: 0.7595 (mtmm) cc_final: 0.7090 (mttt) REVERT: L 53 ASN cc_start: 0.7209 (m-40) cc_final: 0.6896 (m110) REVERT: A 46 LYS cc_start: 0.7600 (mmtt) cc_final: 0.7282 (mmmt) REVERT: A 78 GLU cc_start: 0.7071 (pm20) cc_final: 0.6720 (pt0) REVERT: A 138 SER cc_start: 0.6482 (OUTLIER) cc_final: 0.6171 (m) REVERT: A 284 ASP cc_start: 0.7654 (t0) cc_final: 0.7339 (t0) REVERT: A 293 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7323 (mm-30) REVERT: a 24 TYR cc_start: 0.7807 (m-80) cc_final: 0.7332 (m-80) REVERT: a 82 LYS cc_start: 0.8587 (tttp) cc_final: 0.8310 (ttmt) REVERT: a 159 TYR cc_start: 0.7046 (t80) cc_final: 0.6631 (t80) REVERT: C 11 ASP cc_start: 0.7905 (m-30) cc_final: 0.7650 (m-30) REVERT: C 46 LYS cc_start: 0.7811 (tptp) cc_final: 0.7565 (tptt) REVERT: C 84 SER cc_start: 0.7922 (m) cc_final: 0.7655 (t) REVERT: C 147 PRO cc_start: 0.5875 (Cg_endo) cc_final: 0.5581 (Cg_exo) REVERT: c 116 LYS cc_start: 0.5282 (mmtt) cc_final: 0.4891 (mmmt) REVERT: B 204 ASN cc_start: 0.7852 (m-40) cc_final: 0.6706 (p0) REVERT: B 237 MET cc_start: 0.8430 (ttm) cc_final: 0.8123 (ttm) REVERT: b 82 LYS cc_start: 0.8587 (tptp) cc_final: 0.8350 (tptp) REVERT: b 98 LEU cc_start: 0.9180 (mm) cc_final: 0.8969 (mm) REVERT: b 109 ASP cc_start: 0.8454 (t0) cc_final: 0.7969 (t0) outliers start: 61 outliers final: 50 residues processed: 289 average time/residue: 0.1173 time to fit residues: 50.1889 Evaluate side-chains 278 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 227 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain a residue 15 THR Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 313 CYS Chi-restraints excluded: chain c residue 18 VAL Chi-restraints excluded: chain c residue 22 TYR Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 98 LEU Chi-restraints excluded: chain c residue 148 CYS Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain b residue 18 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 86 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 108 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 25 HIS a 95 ASN ** C 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 26 HIS c 142 HIS c 169 ASN b 72 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.166414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.146145 restraints weight = 19211.487| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.21 r_work: 0.3727 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 13876 Z= 0.225 Angle : 0.684 15.452 18858 Z= 0.353 Chirality : 0.044 0.291 2111 Planarity : 0.004 0.039 2382 Dihedral : 5.992 55.276 2314 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.38 % Allowed : 15.75 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.56 (0.20), residues: 1641 helix: 0.52 (0.26), residues: 360 sheet: -1.73 (0.29), residues: 299 loop : -1.43 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG b 123 TYR 0.032 0.002 TYR B 88 PHE 0.022 0.002 PHE H 100 TRP 0.021 0.002 TRP B 160 HIS 0.012 0.001 HIS c 142 Details of bonding type rmsd covalent geometry : bond 0.00517 (13836) covalent geometry : angle 0.65965 (18753) SS BOND : bond 0.00497 ( 15) SS BOND : angle 1.50540 ( 30) hydrogen bonds : bond 0.05353 ( 458) hydrogen bonds : angle 5.96519 ( 1293) link_BETA1-4 : bond 0.00377 ( 3) link_BETA1-4 : angle 1.23036 ( 9) link_BETA1-6 : bond 0.00363 ( 1) link_BETA1-6 : angle 1.43243 ( 3) link_NAG-ASN : bond 0.00571 ( 21) link_NAG-ASN : angle 3.02060 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 247 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 57 LYS cc_start: 0.7756 (mtmm) cc_final: 0.7283 (mttt) REVERT: L 53 ASN cc_start: 0.7409 (m-40) cc_final: 0.6834 (m110) REVERT: A 46 LYS cc_start: 0.7681 (mmtt) cc_final: 0.7352 (mmmt) REVERT: A 78 GLU cc_start: 0.7163 (pm20) cc_final: 0.6711 (pt0) REVERT: A 138 SER cc_start: 0.6761 (OUTLIER) cc_final: 0.6447 (m) REVERT: A 284 ASP cc_start: 0.7740 (t0) cc_final: 0.7441 (t0) REVERT: A 293 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7466 (mm-30) REVERT: a 24 TYR cc_start: 0.7878 (m-80) cc_final: 0.7434 (m-80) REVERT: a 82 LYS cc_start: 0.8646 (tttp) cc_final: 0.8364 (ttmt) REVERT: a 159 TYR cc_start: 0.7117 (t80) cc_final: 0.6863 (t80) REVERT: C 46 LYS cc_start: 0.7852 (tptp) cc_final: 0.7570 (tptt) REVERT: C 84 SER cc_start: 0.7960 (m) cc_final: 0.7709 (t) REVERT: C 147 PRO cc_start: 0.5960 (Cg_endo) cc_final: 0.5637 (Cg_exo) REVERT: c 116 LYS cc_start: 0.5196 (mmtt) cc_final: 0.4784 (mmmt) REVERT: c 139 GLU cc_start: 0.6504 (mm-30) cc_final: 0.6059 (mm-30) REVERT: c 167 LYS cc_start: 0.8063 (mtpp) cc_final: 0.7343 (ptmm) REVERT: B 204 ASN cc_start: 0.7932 (m-40) cc_final: 0.6721 (p0) REVERT: B 237 MET cc_start: 0.8364 (ttm) cc_final: 0.8127 (ttm) REVERT: B 279 ASP cc_start: 0.7558 (m-30) cc_final: 0.7320 (m-30) REVERT: b 82 LYS cc_start: 0.8564 (tptp) cc_final: 0.8330 (tptp) REVERT: b 98 LEU cc_start: 0.9210 (mm) cc_final: 0.8970 (mm) REVERT: b 109 ASP cc_start: 0.8429 (t0) cc_final: 0.7968 (t0) outliers start: 64 outliers final: 49 residues processed: 291 average time/residue: 0.1164 time to fit residues: 49.8309 Evaluate side-chains 277 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 227 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain a residue 15 THR Chi-restraints excluded: chain a residue 43 ASN Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 313 CYS Chi-restraints excluded: chain c residue 18 VAL Chi-restraints excluded: chain c residue 22 TYR Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 102 LEU Chi-restraints excluded: chain c residue 148 CYS Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain b residue 18 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 78 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 43 optimal weight: 0.0870 chunk 149 optimal weight: 4.9990 chunk 72 optimal weight: 0.3980 chunk 128 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 95 ASN ** C 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 142 HIS B 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.172513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.153096 restraints weight = 19046.075| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.11 r_work: 0.3784 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13876 Z= 0.142 Angle : 0.631 15.987 18858 Z= 0.322 Chirality : 0.042 0.212 2111 Planarity : 0.004 0.041 2382 Dihedral : 5.760 54.774 2314 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.70 % Allowed : 16.85 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.43 (0.20), residues: 1641 helix: 0.70 (0.26), residues: 360 sheet: -1.63 (0.30), residues: 286 loop : -1.39 (0.18), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 323 TYR 0.019 0.001 TYR B 263 PHE 0.021 0.002 PHE A 127 TRP 0.019 0.001 TRP A 70 HIS 0.012 0.001 HIS c 142 Details of bonding type rmsd covalent geometry : bond 0.00317 (13836) covalent geometry : angle 0.60817 (18753) SS BOND : bond 0.00266 ( 15) SS BOND : angle 1.28475 ( 30) hydrogen bonds : bond 0.04992 ( 458) hydrogen bonds : angle 5.84911 ( 1293) link_BETA1-4 : bond 0.00420 ( 3) link_BETA1-4 : angle 0.98039 ( 9) link_BETA1-6 : bond 0.00338 ( 1) link_BETA1-6 : angle 1.57813 ( 3) link_NAG-ASN : bond 0.00412 ( 21) link_NAG-ASN : angle 2.85899 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 241 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 57 LYS cc_start: 0.7544 (mtmm) cc_final: 0.7171 (mttt) REVERT: H 82 MET cc_start: 0.7320 (mtp) cc_final: 0.7055 (mtp) REVERT: L 53 ASN cc_start: 0.7367 (m-40) cc_final: 0.6836 (m110) REVERT: A 11 ASP cc_start: 0.6404 (m-30) cc_final: 0.5582 (t0) REVERT: A 46 LYS cc_start: 0.7688 (mmtt) cc_final: 0.7335 (mmmt) REVERT: A 78 GLU cc_start: 0.7122 (pm20) cc_final: 0.6770 (pt0) REVERT: A 138 SER cc_start: 0.6559 (OUTLIER) cc_final: 0.6281 (m) REVERT: A 176 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8836 (mp) REVERT: A 284 ASP cc_start: 0.7673 (t0) cc_final: 0.7369 (t0) REVERT: A 293 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7334 (mm-30) REVERT: a 24 TYR cc_start: 0.7741 (m-80) cc_final: 0.7219 (m-80) REVERT: a 82 LYS cc_start: 0.8503 (tttp) cc_final: 0.7750 (ttmt) REVERT: a 86 ASP cc_start: 0.8263 (m-30) cc_final: 0.7857 (m-30) REVERT: a 159 TYR cc_start: 0.7055 (t80) cc_final: 0.6825 (t80) REVERT: C 46 LYS cc_start: 0.7795 (tptp) cc_final: 0.7478 (tptt) REVERT: C 84 SER cc_start: 0.7925 (m) cc_final: 0.7658 (t) REVERT: C 121 PHE cc_start: 0.7012 (t80) cc_final: 0.6407 (t80) REVERT: C 147 PRO cc_start: 0.5821 (Cg_endo) cc_final: 0.5513 (Cg_exo) REVERT: c 50 ASN cc_start: 0.8056 (t0) cc_final: 0.7764 (t0) REVERT: c 116 LYS cc_start: 0.5248 (mmtt) cc_final: 0.4864 (mmmt) REVERT: B 204 ASN cc_start: 0.7852 (m-40) cc_final: 0.6698 (p0) REVERT: b 82 LYS cc_start: 0.8590 (tptp) cc_final: 0.8386 (tptp) REVERT: b 98 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8956 (mm) REVERT: b 103 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7703 (mm-30) REVERT: b 109 ASP cc_start: 0.8494 (t0) cc_final: 0.8036 (t0) outliers start: 54 outliers final: 44 residues processed: 278 average time/residue: 0.1167 time to fit residues: 47.6608 Evaluate side-chains 270 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 223 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain a residue 15 THR Chi-restraints excluded: chain a residue 133 ILE Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 313 CYS Chi-restraints excluded: chain c residue 22 TYR Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 102 LEU Chi-restraints excluded: chain c residue 148 CYS Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 98 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 54 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 5 optimal weight: 0.0470 chunk 6 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 129 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.9680 ------------------------------------------------------------------------------- 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 95 ASN ** C 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 142 HIS B 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.169817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.149424 restraints weight = 19147.189| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.23 r_work: 0.3758 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13876 Z= 0.167 Angle : 0.649 15.346 18858 Z= 0.334 Chirality : 0.043 0.216 2111 Planarity : 0.004 0.040 2382 Dihedral : 5.710 55.067 2314 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.56 % Allowed : 17.40 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.42 (0.20), residues: 1641 helix: 0.72 (0.26), residues: 360 sheet: -1.57 (0.30), residues: 292 loop : -1.41 (0.18), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 112 TYR 0.020 0.002 TYR B 263 PHE 0.030 0.002 PHE A 127 TRP 0.024 0.001 TRP A 70 HIS 0.012 0.001 HIS c 142 Details of bonding type rmsd covalent geometry : bond 0.00381 (13836) covalent geometry : angle 0.62833 (18753) SS BOND : bond 0.00307 ( 15) SS BOND : angle 1.29295 ( 30) hydrogen bonds : bond 0.05046 ( 458) hydrogen bonds : angle 5.85491 ( 1293) link_BETA1-4 : bond 0.00367 ( 3) link_BETA1-4 : angle 1.03136 ( 9) link_BETA1-6 : bond 0.00285 ( 1) link_BETA1-6 : angle 1.51136 ( 3) link_NAG-ASN : bond 0.00499 ( 21) link_NAG-ASN : angle 2.71747 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 232 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 57 LYS cc_start: 0.7645 (mtmm) cc_final: 0.7202 (mttt) REVERT: H 82 MET cc_start: 0.7293 (mtp) cc_final: 0.7023 (mtp) REVERT: L 53 ASN cc_start: 0.7423 (m-40) cc_final: 0.6826 (m110) REVERT: A 11 ASP cc_start: 0.6614 (m-30) cc_final: 0.5738 (t0) REVERT: A 46 LYS cc_start: 0.7703 (mmtt) cc_final: 0.7345 (mmmt) REVERT: A 78 GLU cc_start: 0.7150 (pm20) cc_final: 0.6793 (pt0) REVERT: A 138 SER cc_start: 0.6655 (OUTLIER) cc_final: 0.6374 (m) REVERT: A 176 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8824 (mp) REVERT: A 250 ILE cc_start: 0.7414 (tt) cc_final: 0.7053 (tt) REVERT: A 284 ASP cc_start: 0.7669 (t0) cc_final: 0.7389 (t0) REVERT: A 293 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7345 (mm-30) REVERT: a 24 TYR cc_start: 0.7802 (m-80) cc_final: 0.7252 (m-80) REVERT: a 82 LYS cc_start: 0.8558 (tttp) cc_final: 0.8307 (ttmt) REVERT: a 159 TYR cc_start: 0.7109 (t80) cc_final: 0.6878 (t80) REVERT: C 46 LYS cc_start: 0.7810 (tptp) cc_final: 0.7515 (tptt) REVERT: C 84 SER cc_start: 0.7970 (m) cc_final: 0.7703 (t) REVERT: C 147 PRO cc_start: 0.5792 (Cg_endo) cc_final: 0.5476 (Cg_exo) REVERT: c 50 ASN cc_start: 0.8047 (t0) cc_final: 0.7692 (t0) REVERT: c 116 LYS cc_start: 0.5265 (mmtt) cc_final: 0.4878 (mmmt) REVERT: c 167 LYS cc_start: 0.8051 (mtpp) cc_final: 0.7323 (ptmm) REVERT: B 204 ASN cc_start: 0.7826 (m-40) cc_final: 0.6724 (p0) REVERT: b 82 LYS cc_start: 0.8593 (tptp) cc_final: 0.8388 (tptp) REVERT: b 98 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8942 (mm) REVERT: b 103 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7765 (mm-30) REVERT: b 109 ASP cc_start: 0.8535 (t0) cc_final: 0.8054 (t0) outliers start: 52 outliers final: 45 residues processed: 266 average time/residue: 0.1165 time to fit residues: 45.7091 Evaluate side-chains 274 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 226 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain a residue 15 THR Chi-restraints excluded: chain a residue 133 ILE Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 313 CYS Chi-restraints excluded: chain c residue 22 TYR Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 102 LEU Chi-restraints excluded: chain c residue 148 CYS Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 98 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 26 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 95 ASN ** C 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN c 142 HIS B 166 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.171821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.152166 restraints weight = 19150.721| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.14 r_work: 0.3757 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13876 Z= 0.155 Angle : 0.643 15.394 18858 Z= 0.328 Chirality : 0.042 0.214 2111 Planarity : 0.004 0.040 2382 Dihedral : 5.731 54.931 2314 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.42 % Allowed : 17.53 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.36 (0.20), residues: 1641 helix: 0.79 (0.26), residues: 360 sheet: -1.56 (0.30), residues: 302 loop : -1.36 (0.18), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 94 TYR 0.020 0.001 TYR B 263 PHE 0.028 0.002 PHE A 127 TRP 0.023 0.001 TRP A 70 HIS 0.012 0.001 HIS c 142 Details of bonding type rmsd covalent geometry : bond 0.00353 (13836) covalent geometry : angle 0.62029 (18753) SS BOND : bond 0.00276 ( 15) SS BOND : angle 1.24539 ( 30) hydrogen bonds : bond 0.04975 ( 458) hydrogen bonds : angle 5.81794 ( 1293) link_BETA1-4 : bond 0.00400 ( 3) link_BETA1-4 : angle 1.02893 ( 9) link_BETA1-6 : bond 0.00192 ( 1) link_BETA1-6 : angle 1.51553 ( 3) link_NAG-ASN : bond 0.00637 ( 21) link_NAG-ASN : angle 2.86935 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3599.57 seconds wall clock time: 62 minutes 46.26 seconds (3766.26 seconds total)