Starting phenix.real_space_refine on Sun Apr 5 15:59:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mb5_63766/04_2026/9mb5_63766.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mb5_63766/04_2026/9mb5_63766.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mb5_63766/04_2026/9mb5_63766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mb5_63766/04_2026/9mb5_63766.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mb5_63766/04_2026/9mb5_63766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mb5_63766/04_2026/9mb5_63766.map" } resolution = 3.31 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= 0.001 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 7179 2.51 5 N 1967 2.21 5 O 2227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11427 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2515 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain: "B" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2515 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain: "C" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2515 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain: "D" Number of atoms: 1255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1255 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 1, 'TRANS': 152} Chain: "E" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1207 Classifications: {'peptide': 149} Link IDs: {'TRANS': 148} Chain: "F" Number of atoms: 1252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1252 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 152} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "D" 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: "E" 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: "F" 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: 2.62, per 1000 atoms: 0.23 Number of scatterers: 11427 At special positions: 0 Unit cell: (86.92, 88.56, 145.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2227 8.00 N 1967 7.00 C 7179 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS D 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 67 " distance=2.02 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS E 137 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 67 " distance=2.02 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 303 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 67 " distance=2.02 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 303 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 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 NAG-ASN " NAG A 401 " - " ASN A 11 " " NAG A 402 " - " ASN A 23 " " NAG A 403 " - " ASN A 195 " " NAG B 402 " - " ASN B 23 " " NAG B 403 " - " ASN B 195 " " NAG C 401 " - " ASN C 11 " " NAG C 402 " - " ASN C 23 " " NAG C 403 " - " ASN C 195 " " NAG D 301 " - " ASN D 154 " " NAG E 301 " - " ASN E 154 " " NAG F 301 " - " ASN F 154 " Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 435.3 milliseconds 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2624 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 33 sheets defined 25.1% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.593A pdb=" N LEU A 71 " --> pdb=" O ASP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 184 through 192 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 71 removed outlier: 3.630A pdb=" N LEU B 71 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 106 Processing helix chain 'B' and resid 184 through 192 removed outlier: 3.627A pdb=" N GLN B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 63 Processing helix chain 'C' and resid 67 through 71 removed outlier: 3.577A pdb=" N LEU C 71 " --> pdb=" O ASP C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 106 Processing helix chain 'C' and resid 184 through 192 Processing helix chain 'D' and resid 37 through 58 Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 74 through 126 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'E' and resid 37 through 58 Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 74 through 124 Processing helix chain 'E' and resid 145 through 154 Processing helix chain 'F' and resid 37 through 58 Processing helix chain 'F' and resid 74 through 126 Processing helix chain 'F' and resid 145 through 155 removed outlier: 3.560A pdb=" N MET F 149 " --> pdb=" O ASP F 145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 32 through 34 removed outlier: 3.794A pdb=" N HIS D 25 " --> pdb=" O CYS A 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 16 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.584A pdb=" N LEU A 314 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 40 through 44 removed outlier: 6.788A pdb=" N LEU A 41 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N CYS A 275 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 53 removed outlier: 6.890A pdb=" N LEU A 50 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE A 79 " --> pdb=" O MET A 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 94 through 95 removed outlier: 6.560A pdb=" N GLU A 94 " --> pdb=" O TYR A 229 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N TRP A 231 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 172 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 258 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER A 110 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 94 through 95 removed outlier: 6.560A pdb=" N GLU A 94 " --> pdb=" O TYR A 229 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N TRP A 231 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE A 176 " --> pdb=" O PRO A 251 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 178 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 133 through 138 removed outlier: 4.822A pdb=" N CYS A 136 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 143 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 161 through 166 removed outlier: 3.742A pdb=" N VAL A 199 " --> pdb=" O PHE A 210 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 285 through 286 removed outlier: 3.653A pdb=" N LEU A 286 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS A 279 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AB4, first strand: chain 'B' and resid 6 through 7 removed outlier: 3.720A pdb=" N GLY B 6 " --> pdb=" O GLY E 23 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY E 23 " --> pdb=" O GLY B 6 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 15 through 16 Processing sheet with id=AB6, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.621A pdb=" N VAL B 30 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 33 through 34 Processing sheet with id=AB8, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.133A pdb=" N SER B 43 " --> pdb=" O THR B 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 50 through 51 removed outlier: 6.654A pdb=" N LEU B 50 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 93 through 95 removed outlier: 6.426A pdb=" N GLU B 94 " --> pdb=" O TYR B 229 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N TRP B 231 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP B 177 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 172 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 114 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS B 258 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER B 110 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 93 through 95 removed outlier: 6.426A pdb=" N GLU B 94 " --> pdb=" O TYR B 229 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N TRP B 231 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP B 177 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE B 176 " --> pdb=" O PRO B 251 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 133 through 138 removed outlier: 4.765A pdb=" N CYS B 136 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER B 143 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 161 through 166 removed outlier: 3.743A pdb=" N VAL B 201 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 285 through 286 removed outlier: 3.792A pdb=" N CYS B 279 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 31 through 36 removed outlier: 3.585A pdb=" N HIS F 25 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR C 2 " --> pdb=" O ARG F 27 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 15 through 16 Processing sheet with id=AC8, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.740A pdb=" N LEU C 314 " --> pdb=" O VAL C 30 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AD1, first strand: chain 'C' and resid 50 through 51 removed outlier: 6.755A pdb=" N LEU C 50 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 108 through 114 removed outlier: 3.735A pdb=" N SER C 110 " --> pdb=" O LYS C 258 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE C 176 " --> pdb=" O PRO C 251 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 108 through 114 removed outlier: 3.735A pdb=" N SER C 110 " --> pdb=" O LYS C 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP C 177 " --> pdb=" O TYR C 230 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 133 through 138 removed outlier: 4.888A pdb=" N CYS C 136 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER C 143 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 161 through 166 removed outlier: 3.721A pdb=" N LEU C 161 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA C 244 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 199 " --> pdb=" O PHE C 210 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE C 210 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 285 through 286 removed outlier: 3.754A pdb=" N CYS C 279 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR F 64 " --> pdb=" O GLY C 301 " (cutoff:3.500A) 451 hydrogen bonds defined for protein. 1269 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: 1.73 Time building geometry restraints manager: 0.82 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: 3704 1.34 - 1.46: 2793 1.46 - 1.58: 5118 1.58 - 1.70: 1 1.70 - 1.82: 72 Bond restraints: 11688 Sorted by residual: bond pdb=" C1 NAG C 403 " pdb=" O5 NAG C 403 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C1 NAG A 402 " pdb=" O5 NAG A 402 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" CA SER B 12 " pdb=" CB SER B 12 " ideal model delta sigma weight residual 1.530 1.476 0.054 1.69e-02 3.50e+03 1.01e+01 bond pdb=" N ASN B 10 " pdb=" CA ASN B 10 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.40e-02 5.10e+03 7.51e+00 bond pdb=" N ASN B 11 " pdb=" CA ASN B 11 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.47e+00 ... (remaining 11683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 15130 1.51 - 3.03: 586 3.03 - 4.54: 106 4.54 - 6.05: 11 6.05 - 7.56: 8 Bond angle restraints: 15841 Sorted by residual: angle pdb=" CA PRO C 159 " pdb=" N PRO C 159 " pdb=" CD PRO C 159 " ideal model delta sigma weight residual 112.00 105.93 6.07 1.40e+00 5.10e-01 1.88e+01 angle pdb=" C PRO D 160 " pdb=" N LYS D 161 " pdb=" CA LYS D 161 " ideal model delta sigma weight residual 121.54 129.10 -7.56 1.91e+00 2.74e-01 1.57e+01 angle pdb=" C SER B 12 " pdb=" N THR B 13 " pdb=" CA THR B 13 " ideal model delta sigma weight residual 121.92 128.60 -6.68 1.73e+00 3.34e-01 1.49e+01 angle pdb=" C ASP B 1 " pdb=" N THR B 2 " pdb=" CA THR B 2 " ideal model delta sigma weight residual 122.33 116.28 6.05 1.68e+00 3.54e-01 1.30e+01 angle pdb=" C TYR E 22 " pdb=" N GLY E 23 " pdb=" CA GLY E 23 " ideal model delta sigma weight residual 122.03 117.75 4.28 1.28e+00 6.10e-01 1.12e+01 ... (remaining 15836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.61: 6431 24.61 - 49.22: 569 49.22 - 73.83: 94 73.83 - 98.44: 10 98.44 - 123.05: 4 Dihedral angle restraints: 7108 sinusoidal: 3003 harmonic: 4105 Sorted by residual: dihedral pdb=" CB CYS C 42 " pdb=" SG CYS C 42 " pdb=" SG CYS C 275 " pdb=" CB CYS C 275 " ideal model delta sinusoidal sigma weight residual -86.00 -14.51 -71.49 1 1.00e+01 1.00e-02 6.55e+01 dihedral pdb=" C2 NAG A 402 " pdb=" C1 NAG A 402 " pdb=" O5 NAG A 402 " pdb=" C5 NAG A 402 " ideal model delta sinusoidal sigma weight residual -62.96 60.09 -123.05 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" C1 NAG C 403 " pdb=" C5 NAG C 403 " pdb=" O5 NAG C 403 " pdb=" C6 NAG C 403 " ideal model delta sinusoidal sigma weight residual 171.16 -73.86 -114.98 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 7105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1493 0.066 - 0.132: 236 0.132 - 0.197: 15 0.197 - 0.263: 3 0.263 - 0.329: 1 Chirality restraints: 1748 Sorted by residual: chirality pdb=" C1 NAG D 301 " pdb=" ND2 ASN D 154 " pdb=" C2 NAG D 301 " pdb=" O5 NAG D 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C1 NAG B 402 " pdb=" ND2 ASN B 23 " pdb=" C2 NAG B 402 " pdb=" O5 NAG B 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C1 NAG C 403 " pdb=" ND2 ASN C 195 " pdb=" C2 NAG C 403 " pdb=" O5 NAG C 403 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1745 not shown) Planarity restraints: 2039 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 11 " -0.002 2.00e-02 2.50e+03 2.78e-02 9.63e+00 pdb=" CG ASN C 11 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN C 11 " 0.033 2.00e-02 2.50e+03 pdb=" ND2 ASN C 11 " -0.030 2.00e-02 2.50e+03 pdb=" C1 NAG C 401 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 12 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.33e+00 pdb=" C SER B 12 " -0.050 2.00e-02 2.50e+03 pdb=" O SER B 12 " 0.019 2.00e-02 2.50e+03 pdb=" N THR B 13 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 8 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.41e+00 pdb=" C HIS B 8 " 0.044 2.00e-02 2.50e+03 pdb=" O HIS B 8 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA B 9 " -0.015 2.00e-02 2.50e+03 ... (remaining 2036 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2143 2.76 - 3.30: 10169 3.30 - 3.83: 18367 3.83 - 4.37: 20445 4.37 - 4.90: 37429 Nonbonded interactions: 88553 Sorted by model distance: nonbonded pdb=" NE2 GLN B 189 " pdb=" OE1 GLN B 193 " model vdw 2.231 3.120 nonbonded pdb=" O SER B 77 " pdb=" OG SER B 263 " model vdw 2.243 3.040 nonbonded pdb=" OE1 GLU A 172 " pdb=" NZ LYS A 259 " model vdw 2.244 3.120 nonbonded pdb=" O HIS A 37 " pdb=" ND1 HIS A 37 " model vdw 2.246 3.120 nonbonded pdb=" N GLN D 30 " pdb=" OE1 GLN D 30 " model vdw 2.262 3.120 ... (remaining 88548 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' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 9 through 125 or (resid 126 and (name N or name CA or name \ C or name O or name CB )) or resid 127 through 157 or resid 301)) selection = (chain 'E' and (resid 9 through 125 or (resid 126 and (name N or name CA or name \ C or name O or name CB )) or resid 127 through 301)) selection = (chain 'F' and (resid 9 through 157 or resid 301)) } 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: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.590 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 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 : 0.007 0.090 11716 Z= 0.333 Angle : 0.708 10.211 15908 Z= 0.382 Chirality : 0.048 0.329 1748 Planarity : 0.005 0.053 2028 Dihedral : 17.913 123.055 4433 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.62 % Favored : 95.24 % Rotamer: Outliers : 0.56 % Allowed : 27.40 % Favored : 72.04 % 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: -0.35 (0.22), residues: 1408 helix: 2.03 (0.27), residues: 323 sheet: 0.26 (0.37), residues: 222 loop : -1.34 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 27 TYR 0.026 0.003 TYR C 145 PHE 0.027 0.003 PHE C 210 TRP 0.018 0.002 TRP A 123 HIS 0.008 0.002 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00730 (11688) covalent geometry : angle 0.69355 (15841) SS BOND : bond 0.00351 ( 17) SS BOND : angle 1.15375 ( 34) hydrogen bonds : bond 0.19786 ( 425) hydrogen bonds : angle 7.11217 ( 1269) link_NAG-ASN : bond 0.00539 ( 11) link_NAG-ASN : angle 3.02231 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 239 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 208 LYS cc_start: 0.6663 (ttpt) cc_final: 0.6035 (ttpt) REVERT: C 258 LYS cc_start: 0.8189 (mtpp) cc_final: 0.7750 (ttmm) REVERT: C 302 LYS cc_start: 0.8899 (mtmt) cc_final: 0.8593 (mttp) REVERT: D 17 MET cc_start: 0.6905 (tmm) cc_final: 0.6623 (tmm) REVERT: E 54 SER cc_start: 0.8029 (t) cc_final: 0.7771 (m) REVERT: E 77 MET cc_start: 0.8348 (mmm) cc_final: 0.8010 (mtt) outliers start: 7 outliers final: 4 residues processed: 244 average time/residue: 0.1158 time to fit residues: 39.1699 Evaluate side-chains 239 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 235 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain F residue 149 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.0870 chunk 55 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS B 196 ASN ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN F 129 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.136018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.123148 restraints weight = 15844.836| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.27 r_work: 0.3436 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11716 Z= 0.144 Angle : 0.587 14.701 15908 Z= 0.301 Chirality : 0.044 0.369 1748 Planarity : 0.004 0.032 2028 Dihedral : 9.358 109.190 1783 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.63 % Favored : 97.30 % Rotamer: Outliers : 3.37 % Allowed : 23.88 % Favored : 72.76 % 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: 0.01 (0.22), residues: 1408 helix: 2.32 (0.26), residues: 332 sheet: 0.48 (0.36), residues: 246 loop : -1.18 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 27 TYR 0.013 0.001 TYR A 91 PHE 0.017 0.001 PHE B 144 TRP 0.007 0.001 TRP A 123 HIS 0.006 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00309 (11688) covalent geometry : angle 0.55099 (15841) SS BOND : bond 0.00204 ( 17) SS BOND : angle 0.67315 ( 34) hydrogen bonds : bond 0.04808 ( 425) hydrogen bonds : angle 5.19337 ( 1269) link_NAG-ASN : bond 0.00541 ( 11) link_NAG-ASN : angle 4.43219 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 219 time to evaluate : 0.373 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: A 162 SER cc_start: 0.7600 (t) cc_final: 0.7326 (p) REVERT: A 172 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7588 (mt-10) REVERT: B 44 LEU cc_start: 0.7960 (tp) cc_final: 0.7716 (tp) REVERT: B 215 VAL cc_start: 0.8198 (OUTLIER) cc_final: 0.7960 (m) REVERT: B 277 THR cc_start: 0.8211 (t) cc_final: 0.7969 (p) REVERT: C 172 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7369 (pt0) REVERT: C 205 LYS cc_start: 0.7972 (tptt) cc_final: 0.7702 (tptt) REVERT: C 208 LYS cc_start: 0.6137 (OUTLIER) cc_final: 0.5886 (ttpt) REVERT: C 259 LYS cc_start: 0.8338 (mmtm) cc_final: 0.8077 (mmtm) REVERT: D 51 LYS cc_start: 0.7562 (ttmm) cc_final: 0.7190 (ttmt) REVERT: D 60 ASN cc_start: 0.7653 (p0) cc_final: 0.7439 (p0) REVERT: D 79 ASN cc_start: 0.8559 (m-40) cc_final: 0.8301 (m110) REVERT: D 114 ASN cc_start: 0.7770 (m-40) cc_final: 0.7555 (m110) REVERT: E 54 SER cc_start: 0.7797 (t) cc_final: 0.7431 (m) REVERT: E 77 MET cc_start: 0.8513 (mmm) cc_final: 0.8296 (mtt) REVERT: E 126 LEU cc_start: 0.5610 (tp) cc_final: 0.5314 (tp) REVERT: E 149 MET cc_start: 0.7013 (tpt) cc_final: 0.6773 (tpt) outliers start: 42 outliers final: 24 residues processed: 246 average time/residue: 0.1234 time to fit residues: 41.2519 Evaluate side-chains 235 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 ASP Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 7 TYR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 208 LYS Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 144 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 10 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 127 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN D 95 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.135920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.123023 restraints weight = 15903.535| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.29 r_work: 0.3445 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11716 Z= 0.144 Angle : 0.527 9.937 15908 Z= 0.273 Chirality : 0.043 0.371 1748 Planarity : 0.003 0.034 2028 Dihedral : 8.706 106.992 1775 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.63 % Favored : 97.30 % Rotamer: Outliers : 3.53 % Allowed : 23.80 % Favored : 72.68 % 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: 0.15 (0.22), residues: 1408 helix: 2.49 (0.26), residues: 332 sheet: 0.44 (0.36), residues: 252 loop : -1.08 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 217 TYR 0.012 0.001 TYR B 145 PHE 0.013 0.002 PHE E 110 TRP 0.007 0.001 TRP A 123 HIS 0.006 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00316 (11688) covalent geometry : angle 0.50666 (15841) SS BOND : bond 0.00201 ( 17) SS BOND : angle 0.55450 ( 34) hydrogen bonds : bond 0.04479 ( 425) hydrogen bonds : angle 4.85611 ( 1269) link_NAG-ASN : bond 0.00503 ( 11) link_NAG-ASN : angle 3.19147 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 212 time to evaluate : 0.458 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: B 44 LEU cc_start: 0.7971 (tp) cc_final: 0.7709 (tp) REVERT: B 144 PHE cc_start: 0.8512 (t80) cc_final: 0.8238 (t80) REVERT: B 154 LYS cc_start: 0.7477 (mtpt) cc_final: 0.7129 (ttmt) REVERT: B 208 LYS cc_start: 0.8241 (tttt) cc_final: 0.8013 (tptt) REVERT: B 215 VAL cc_start: 0.8220 (OUTLIER) cc_final: 0.7984 (m) REVERT: C 205 LYS cc_start: 0.8036 (tptt) cc_final: 0.7720 (tptt) REVERT: C 208 LYS cc_start: 0.6194 (OUTLIER) cc_final: 0.5913 (ttpt) REVERT: D 51 LYS cc_start: 0.7530 (ttmm) cc_final: 0.7156 (ttmt) REVERT: E 54 SER cc_start: 0.7764 (t) cc_final: 0.7373 (m) REVERT: E 149 MET cc_start: 0.6965 (tpt) cc_final: 0.6756 (tpt) outliers start: 44 outliers final: 29 residues processed: 238 average time/residue: 0.1188 time to fit residues: 38.4488 Evaluate side-chains 240 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 7 TYR Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 208 LYS Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 149 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 87 optimal weight: 2.9990 chunk 126 optimal weight: 0.0170 chunk 82 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 HIS B 181 HIS ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.132826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.119982 restraints weight = 15961.328| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.27 r_work: 0.3403 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 11716 Z= 0.302 Angle : 0.630 13.684 15908 Z= 0.327 Chirality : 0.047 0.371 1748 Planarity : 0.004 0.043 2028 Dihedral : 8.399 103.909 1775 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.01 % Allowed : 23.64 % Favored : 72.36 % 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: -0.29 (0.22), residues: 1408 helix: 1.99 (0.26), residues: 332 sheet: 0.30 (0.35), residues: 252 loop : -1.35 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 313 TYR 0.022 0.003 TYR A 158 PHE 0.019 0.002 PHE E 110 TRP 0.014 0.002 TRP A 123 HIS 0.008 0.002 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00682 (11688) covalent geometry : angle 0.60528 (15841) SS BOND : bond 0.00332 ( 17) SS BOND : angle 0.96398 ( 34) hydrogen bonds : bond 0.05020 ( 425) hydrogen bonds : angle 4.99642 ( 1269) link_NAG-ASN : bond 0.00587 ( 11) link_NAG-ASN : angle 3.80564 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 219 time to evaluate : 0.412 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: B 44 LEU cc_start: 0.8028 (tp) cc_final: 0.7809 (tp) REVERT: B 208 LYS cc_start: 0.8287 (tttt) cc_final: 0.8054 (tptt) REVERT: B 215 VAL cc_start: 0.8222 (OUTLIER) cc_final: 0.8003 (m) REVERT: C 205 LYS cc_start: 0.8102 (tptt) cc_final: 0.7769 (tptt) REVERT: D 51 LYS cc_start: 0.7679 (ttmm) cc_final: 0.7158 (ttmt) REVERT: D 59 MET cc_start: 0.8049 (tpp) cc_final: 0.7471 (ttp) REVERT: D 77 MET cc_start: 0.8548 (mmm) cc_final: 0.8211 (mtt) REVERT: E 54 SER cc_start: 0.7860 (t) cc_final: 0.7453 (m) REVERT: E 149 MET cc_start: 0.6916 (tpt) cc_final: 0.6646 (tpt) outliers start: 50 outliers final: 39 residues processed: 251 average time/residue: 0.1194 time to fit residues: 40.6519 Evaluate side-chains 251 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 211 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 ASP Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 7 TYR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 208 LYS Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 25 HIS Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 149 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 58 optimal weight: 0.0060 chunk 105 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 127 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 HIS F 158 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.134473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.121647 restraints weight = 15806.131| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.27 r_work: 0.3413 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11716 Z= 0.172 Angle : 0.577 13.548 15908 Z= 0.293 Chirality : 0.044 0.372 1748 Planarity : 0.004 0.040 2028 Dihedral : 8.243 101.699 1775 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.09 % Allowed : 23.16 % Favored : 72.76 % 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: -0.10 (0.22), residues: 1408 helix: 2.26 (0.26), residues: 332 sheet: 0.32 (0.35), residues: 252 loop : -1.26 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 217 TYR 0.015 0.002 TYR B 145 PHE 0.019 0.002 PHE B 144 TRP 0.007 0.001 TRP A 123 HIS 0.010 0.001 HIS D 25 Details of bonding type rmsd covalent geometry : bond 0.00381 (11688) covalent geometry : angle 0.53871 (15841) SS BOND : bond 0.00227 ( 17) SS BOND : angle 0.76500 ( 34) hydrogen bonds : bond 0.04393 ( 425) hydrogen bonds : angle 4.83303 ( 1269) link_NAG-ASN : bond 0.00548 ( 11) link_NAG-ASN : angle 4.52005 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 206 time to evaluate : 0.455 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: A 222 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7231 (mm-30) REVERT: B 23 ASN cc_start: 0.6978 (t0) cc_final: 0.6762 (t0) REVERT: B 144 PHE cc_start: 0.8462 (t80) cc_final: 0.8161 (t80) REVERT: B 208 LYS cc_start: 0.8253 (tttt) cc_final: 0.8042 (tptt) REVERT: B 215 VAL cc_start: 0.8218 (OUTLIER) cc_final: 0.7994 (m) REVERT: B 277 THR cc_start: 0.8277 (t) cc_final: 0.7984 (p) REVERT: C 205 LYS cc_start: 0.8102 (tptt) cc_final: 0.7770 (tptt) REVERT: C 208 LYS cc_start: 0.6351 (OUTLIER) cc_final: 0.6074 (ttpt) REVERT: D 25 HIS cc_start: 0.8150 (OUTLIER) cc_final: 0.7947 (t-90) REVERT: D 51 LYS cc_start: 0.7635 (ttmm) cc_final: 0.7089 (ttmt) REVERT: D 59 MET cc_start: 0.8034 (tpp) cc_final: 0.7485 (ttp) REVERT: D 77 MET cc_start: 0.8527 (mmm) cc_final: 0.8164 (mtt) REVERT: E 54 SER cc_start: 0.7804 (t) cc_final: 0.7391 (m) REVERT: E 149 MET cc_start: 0.6871 (tpt) cc_final: 0.6615 (tpt) outliers start: 51 outliers final: 41 residues processed: 239 average time/residue: 0.1221 time to fit residues: 39.8665 Evaluate side-chains 245 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 201 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain B residue 7 TYR Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 208 LYS Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 25 HIS Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 158 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 2 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.133765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.120901 restraints weight = 15914.889| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.28 r_work: 0.3415 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11716 Z= 0.235 Angle : 0.575 11.705 15908 Z= 0.296 Chirality : 0.045 0.370 1748 Planarity : 0.004 0.041 2028 Dihedral : 8.192 99.563 1775 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.25 % Allowed : 23.48 % Favored : 72.28 % 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: -0.18 (0.22), residues: 1408 helix: 2.19 (0.26), residues: 332 sheet: 0.31 (0.35), residues: 252 loop : -1.31 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 313 TYR 0.017 0.002 TYR C 158 PHE 0.014 0.002 PHE E 110 TRP 0.009 0.002 TRP A 123 HIS 0.011 0.002 HIS D 25 Details of bonding type rmsd covalent geometry : bond 0.00529 (11688) covalent geometry : angle 0.55101 (15841) SS BOND : bond 0.00280 ( 17) SS BOND : angle 0.75844 ( 34) hydrogen bonds : bond 0.04585 ( 425) hydrogen bonds : angle 4.81925 ( 1269) link_NAG-ASN : bond 0.00652 ( 11) link_NAG-ASN : angle 3.62472 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 218 time to evaluate : 0.345 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: A 37 HIS cc_start: 0.8094 (p90) cc_final: 0.7524 (p90) REVERT: A 222 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7253 (mm-30) REVERT: B 23 ASN cc_start: 0.6956 (t0) cc_final: 0.6736 (t0) REVERT: B 208 LYS cc_start: 0.8267 (tttt) cc_final: 0.8066 (tptt) REVERT: B 215 VAL cc_start: 0.8230 (OUTLIER) cc_final: 0.8011 (m) REVERT: C 205 LYS cc_start: 0.8106 (tptt) cc_final: 0.7790 (tptt) REVERT: C 208 LYS cc_start: 0.6425 (OUTLIER) cc_final: 0.6148 (ttpt) REVERT: D 51 LYS cc_start: 0.7647 (ttmm) cc_final: 0.7123 (ttmt) REVERT: D 59 MET cc_start: 0.8074 (tpp) cc_final: 0.7541 (ttp) REVERT: D 77 MET cc_start: 0.8540 (mmm) cc_final: 0.8269 (mtt) REVERT: E 54 SER cc_start: 0.7840 (t) cc_final: 0.7406 (m) REVERT: E 149 MET cc_start: 0.6766 (tpt) cc_final: 0.6471 (tpt) outliers start: 53 outliers final: 43 residues processed: 251 average time/residue: 0.1159 time to fit residues: 39.9352 Evaluate side-chains 261 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 216 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASN Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 7 TYR Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 208 LYS Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 149 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 107 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 126 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS C 156 ASN ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.134467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121653 restraints weight = 15879.280| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.26 r_work: 0.3413 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11716 Z= 0.193 Angle : 0.556 11.399 15908 Z= 0.285 Chirality : 0.044 0.369 1748 Planarity : 0.004 0.040 2028 Dihedral : 8.075 97.584 1775 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.25 % Allowed : 23.00 % Favored : 72.76 % 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: -0.07 (0.22), residues: 1408 helix: 2.37 (0.26), residues: 332 sheet: 0.34 (0.36), residues: 252 loop : -1.27 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 217 TYR 0.014 0.002 TYR C 158 PHE 0.012 0.002 PHE E 110 TRP 0.007 0.001 TRP C 123 HIS 0.006 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00432 (11688) covalent geometry : angle 0.53237 (15841) SS BOND : bond 0.00232 ( 17) SS BOND : angle 0.69857 ( 34) hydrogen bonds : bond 0.04316 ( 425) hydrogen bonds : angle 4.72956 ( 1269) link_NAG-ASN : bond 0.00622 ( 11) link_NAG-ASN : angle 3.49863 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 210 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 HIS cc_start: 0.8103 (p90) cc_final: 0.7647 (p90) REVERT: A 222 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7239 (mm-30) REVERT: A 293 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7653 (pp30) REVERT: B 23 ASN cc_start: 0.6974 (t0) cc_final: 0.6746 (t0) REVERT: B 144 PHE cc_start: 0.8402 (t80) cc_final: 0.8178 (t80) REVERT: B 166 THR cc_start: 0.7764 (t) cc_final: 0.7449 (p) REVERT: B 208 LYS cc_start: 0.8255 (tttt) cc_final: 0.8054 (tptt) REVERT: B 215 VAL cc_start: 0.8245 (OUTLIER) cc_final: 0.8033 (m) REVERT: C 205 LYS cc_start: 0.8106 (tptt) cc_final: 0.7793 (tptt) REVERT: D 51 LYS cc_start: 0.7619 (ttmm) cc_final: 0.7079 (ttmt) REVERT: D 59 MET cc_start: 0.8039 (tpp) cc_final: 0.7508 (ttp) REVERT: D 77 MET cc_start: 0.8534 (mmm) cc_final: 0.8286 (mtt) REVERT: E 54 SER cc_start: 0.7802 (t) cc_final: 0.7384 (m) REVERT: E 149 MET cc_start: 0.6786 (tpt) cc_final: 0.6455 (tpt) outliers start: 53 outliers final: 43 residues processed: 244 average time/residue: 0.1206 time to fit residues: 40.1345 Evaluate side-chains 249 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 204 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 7 TYR Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 208 LYS Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 25 HIS Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 149 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 126 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 6 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS C 87 ASN C 156 ASN ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.135371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.122539 restraints weight = 15817.735| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.26 r_work: 0.3437 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11716 Z= 0.137 Angle : 0.528 9.914 15908 Z= 0.271 Chirality : 0.044 0.368 1748 Planarity : 0.004 0.039 2028 Dihedral : 7.963 95.733 1775 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.01 % Allowed : 23.24 % Favored : 72.76 % 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: 0.09 (0.22), residues: 1408 helix: 2.57 (0.26), residues: 332 sheet: 0.41 (0.36), residues: 252 loop : -1.18 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 217 TYR 0.011 0.001 TYR D 119 PHE 0.010 0.001 PHE C 111 TRP 0.005 0.001 TRP C 123 HIS 0.006 0.001 HIS E 25 Details of bonding type rmsd covalent geometry : bond 0.00303 (11688) covalent geometry : angle 0.51174 (15841) SS BOND : bond 0.00196 ( 17) SS BOND : angle 0.62505 ( 34) hydrogen bonds : bond 0.04060 ( 425) hydrogen bonds : angle 4.62426 ( 1269) link_NAG-ASN : bond 0.00538 ( 11) link_NAG-ASN : angle 2.91228 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 216 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 HIS cc_start: 0.8103 (p90) cc_final: 0.7650 (p90) REVERT: A 222 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7233 (mm-30) REVERT: B 23 ASN cc_start: 0.6961 (t0) cc_final: 0.6731 (t0) REVERT: B 144 PHE cc_start: 0.8390 (t80) cc_final: 0.8125 (t80) REVERT: B 166 THR cc_start: 0.7779 (t) cc_final: 0.7444 (p) REVERT: B 215 VAL cc_start: 0.8241 (OUTLIER) cc_final: 0.8025 (m) REVERT: B 277 THR cc_start: 0.8278 (t) cc_final: 0.7995 (p) REVERT: C 205 LYS cc_start: 0.8123 (tptt) cc_final: 0.7808 (tptt) REVERT: C 208 LYS cc_start: 0.6311 (ttpt) cc_final: 0.5921 (ttpt) REVERT: D 51 LYS cc_start: 0.7552 (ttmm) cc_final: 0.6988 (ttmt) REVERT: D 59 MET cc_start: 0.8014 (tpp) cc_final: 0.7506 (ttp) REVERT: D 77 MET cc_start: 0.8523 (mmm) cc_final: 0.8264 (mtt) REVERT: E 54 SER cc_start: 0.7767 (t) cc_final: 0.7346 (m) REVERT: E 149 MET cc_start: 0.6759 (tpt) cc_final: 0.6407 (tpt) outliers start: 50 outliers final: 41 residues processed: 247 average time/residue: 0.1187 time to fit residues: 40.3332 Evaluate side-chains 254 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 212 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASN Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 7 TYR Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 25 HIS Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 149 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 111 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS C 156 ASN ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.133485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.120696 restraints weight = 15828.179| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.24 r_work: 0.3406 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11716 Z= 0.266 Angle : 0.600 13.410 15908 Z= 0.307 Chirality : 0.046 0.366 1748 Planarity : 0.004 0.042 2028 Dihedral : 8.024 94.702 1775 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.09 % Allowed : 23.24 % Favored : 72.68 % 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: -0.12 (0.22), residues: 1408 helix: 2.24 (0.26), residues: 332 sheet: 0.36 (0.35), residues: 252 loop : -1.27 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 226 TYR 0.018 0.002 TYR A 158 PHE 0.015 0.002 PHE E 110 TRP 0.012 0.002 TRP A 60 HIS 0.007 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00600 (11688) covalent geometry : angle 0.57473 (15841) SS BOND : bond 0.00284 ( 17) SS BOND : angle 0.77181 ( 34) hydrogen bonds : bond 0.04599 ( 425) hydrogen bonds : angle 4.74339 ( 1269) link_NAG-ASN : bond 0.00541 ( 11) link_NAG-ASN : angle 3.75572 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 211 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 HIS cc_start: 0.8111 (p90) cc_final: 0.7664 (p90) REVERT: A 222 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7277 (mm-30) REVERT: A 293 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7621 (pp30) REVERT: B 23 ASN cc_start: 0.6980 (t0) cc_final: 0.6753 (t0) REVERT: B 144 PHE cc_start: 0.8427 (t80) cc_final: 0.8192 (t80) REVERT: B 166 THR cc_start: 0.7799 (t) cc_final: 0.7477 (p) REVERT: B 215 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.8040 (m) REVERT: B 277 THR cc_start: 0.8302 (t) cc_final: 0.8022 (p) REVERT: C 205 LYS cc_start: 0.8109 (tptt) cc_final: 0.7797 (tptt) REVERT: D 51 LYS cc_start: 0.7622 (ttmm) cc_final: 0.7091 (ttmt) REVERT: D 59 MET cc_start: 0.8041 (tpp) cc_final: 0.7497 (ttp) REVERT: E 54 SER cc_start: 0.7849 (t) cc_final: 0.7407 (m) REVERT: E 149 MET cc_start: 0.6733 (tpt) cc_final: 0.6365 (tpt) outliers start: 51 outliers final: 46 residues processed: 241 average time/residue: 0.1198 time to fit residues: 39.6123 Evaluate side-chains 257 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 209 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASN Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 7 TYR Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 208 LYS Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 25 HIS Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 149 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 113 optimal weight: 0.0980 chunk 123 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 107 optimal weight: 0.0970 chunk 111 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS C 156 ASN ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.135523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.122685 restraints weight = 15796.302| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.26 r_work: 0.3443 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11716 Z= 0.130 Angle : 0.532 10.137 15908 Z= 0.273 Chirality : 0.043 0.366 1748 Planarity : 0.004 0.039 2028 Dihedral : 7.798 93.087 1775 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.69 % Allowed : 23.48 % Favored : 72.84 % 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: 0.11 (0.22), residues: 1408 helix: 2.60 (0.27), residues: 332 sheet: 0.38 (0.35), residues: 252 loop : -1.17 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 226 TYR 0.020 0.001 TYR C 158 PHE 0.010 0.001 PHE C 111 TRP 0.004 0.001 TRP C 123 HIS 0.009 0.001 HIS E 25 Details of bonding type rmsd covalent geometry : bond 0.00285 (11688) covalent geometry : angle 0.51563 (15841) SS BOND : bond 0.00186 ( 17) SS BOND : angle 0.61217 ( 34) hydrogen bonds : bond 0.04013 ( 425) hydrogen bonds : angle 4.62005 ( 1269) link_NAG-ASN : bond 0.00534 ( 11) link_NAG-ASN : angle 2.86215 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 206 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 HIS cc_start: 0.8113 (p90) cc_final: 0.7681 (p90) REVERT: A 222 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7254 (mm-30) REVERT: A 249 ILE cc_start: 0.8330 (mm) cc_final: 0.8084 (mt) REVERT: B 23 ASN cc_start: 0.6928 (t0) cc_final: 0.6709 (t0) REVERT: B 144 PHE cc_start: 0.8433 (t80) cc_final: 0.8166 (t80) REVERT: B 166 THR cc_start: 0.7795 (t) cc_final: 0.7459 (p) REVERT: B 215 VAL cc_start: 0.8237 (OUTLIER) cc_final: 0.8022 (m) REVERT: B 277 THR cc_start: 0.8276 (t) cc_final: 0.8006 (p) REVERT: C 205 LYS cc_start: 0.8091 (tptt) cc_final: 0.7772 (tptt) REVERT: C 320 ASN cc_start: 0.8323 (m110) cc_final: 0.8094 (m110) REVERT: D 17 MET cc_start: 0.7103 (tmm) cc_final: 0.6714 (tmm) REVERT: D 51 LYS cc_start: 0.7541 (ttmm) cc_final: 0.6982 (ttmt) REVERT: D 59 MET cc_start: 0.7993 (tpp) cc_final: 0.7480 (ttp) REVERT: E 54 SER cc_start: 0.7759 (t) cc_final: 0.7339 (m) REVERT: E 149 MET cc_start: 0.6704 (tpt) cc_final: 0.6328 (tpt) outliers start: 46 outliers final: 40 residues processed: 234 average time/residue: 0.1200 time to fit residues: 38.6449 Evaluate side-chains 248 residues out of total 1249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASN Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 7 TYR Chi-restraints excluded: chain B residue 8 HIS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 25 HIS Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 149 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 37 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.135275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.122424 restraints weight = 15802.352| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.25 r_work: 0.3438 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11716 Z= 0.151 Angle : 0.544 12.201 15908 Z= 0.275 Chirality : 0.044 0.365 1748 Planarity : 0.004 0.040 2028 Dihedral : 7.779 91.572 1775 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.85 % Allowed : 23.72 % Favored : 72.44 % 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: 0.15 (0.22), residues: 1408 helix: 2.64 (0.26), residues: 332 sheet: 0.38 (0.35), residues: 252 loop : -1.13 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 27 TYR 0.012 0.001 TYR B 145 PHE 0.010 0.001 PHE D 110 TRP 0.005 0.001 TRP C 123 HIS 0.011 0.001 HIS E 25 Details of bonding type rmsd covalent geometry : bond 0.00335 (11688) covalent geometry : angle 0.51912 (15841) SS BOND : bond 0.00204 ( 17) SS BOND : angle 0.62474 ( 34) hydrogen bonds : bond 0.04078 ( 425) hydrogen bonds : angle 4.57644 ( 1269) link_NAG-ASN : bond 0.00655 ( 11) link_NAG-ASN : angle 3.60748 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2603.96 seconds wall clock time: 45 minutes 26.87 seconds (2726.87 seconds total)