Starting phenix.real_space_refine on Mon Aug 25 08:13:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u44_41874/08_2025/8u44_41874.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u44_41874/08_2025/8u44_41874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u44_41874/08_2025/8u44_41874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u44_41874/08_2025/8u44_41874.map" model { file = "/net/cci-nas-00/data/ceres_data/8u44_41874/08_2025/8u44_41874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u44_41874/08_2025/8u44_41874.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11763 atoms to isotropic. 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 81 5.16 5 C 10683 2.51 5 N 2922 2.21 5 O 3342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17028 Number of models: 1 Model: "" Number of chains: 5 Chain: "V" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 898 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "X" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2527 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "B" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1394 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} 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 Restraints were copied for chains: S, U, T, W, G, H, I, J Time building chain proxies: 2.47, per 1000 atoms: 0.15 Number of scatterers: 17028 At special positions: 0 Unit cell: (130.625, 124.355, 146.3, 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 81 16.00 O 3342 8.00 N 2922 7.00 C 10683 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 94 " distance=2.04 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.06 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 94 " distance=2.04 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 94 " distance=2.04 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.03 Simple disulfide: pdb=" SG CYS W 23 " - pdb=" SG CYS W 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 277 " distance=2.03 Simple disulfide: pdb=" SG CYS H 52 " - pdb=" SG CYS H 277 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 76 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 76 " distance=2.03 Simple disulfide: pdb=" SG CYS G 97 " - pdb=" SG CYS G 139 " distance=2.03 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 139 " distance=2.03 Simple disulfide: pdb=" SG CYS G 281 " - pdb=" SG CYS G 305 " distance=2.06 Simple disulfide: pdb=" SG CYS H 281 " - pdb=" SG CYS H 305 " distance=2.06 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 148 " distance=2.03 Simple disulfide: pdb=" SG CYS J 144 " - pdb=" SG CYS J 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 501 " - " ASN A 21 " " NAG A 502 " - " ASN A 129 " " NAG A 503 " - " ASN A 289 " " NAG G 501 " - " ASN G 21 " " NAG G 502 " - " ASN G 129 " " NAG G 503 " - " ASN G 289 " " NAG H 501 " - " ASN H 21 " " NAG H 502 " - " ASN H 129 " " NAG H 503 " - " ASN H 289 " Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 505.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 42 sheets defined 18.8% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'V' and resid 85 through 89 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.688A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.750A pdb=" N GLN A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 127 Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 145 through 154 removed outlier: 4.226A pdb=" N MET B 149 " --> pdb=" O ASN B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 170 removed outlier: 4.395A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 89 Processing helix chain 'G' and resid 65 through 71 Processing helix chain 'G' and resid 73 through 77 removed outlier: 3.688A pdb=" N GLU G 77 " --> pdb=" O PRO G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 112 Processing helix chain 'G' and resid 187 through 195 removed outlier: 3.750A pdb=" N GLN G 191 " --> pdb=" O ASN G 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 58 Processing helix chain 'I' and resid 74 through 127 Processing helix chain 'I' and resid 134 through 136 No H-bonds generated for 'chain 'I' and resid 134 through 136' Processing helix chain 'I' and resid 145 through 154 removed outlier: 4.226A pdb=" N MET I 149 " --> pdb=" O ASN I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 170 removed outlier: 4.395A pdb=" N GLU I 164 " --> pdb=" O PRO I 160 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLU I 165 " --> pdb=" O LYS I 161 " (cutoff:3.500A) Processing helix chain 'U' and resid 85 through 89 Processing helix chain 'H' and resid 65 through 71 Processing helix chain 'H' and resid 73 through 77 removed outlier: 3.688A pdb=" N GLU H 77 " --> pdb=" O PRO H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 112 Processing helix chain 'H' and resid 187 through 195 removed outlier: 3.750A pdb=" N GLN H 191 " --> pdb=" O ASN H 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 58 Processing helix chain 'J' and resid 74 through 127 Processing helix chain 'J' and resid 134 through 136 No H-bonds generated for 'chain 'J' and resid 134 through 136' Processing helix chain 'J' and resid 145 through 154 removed outlier: 4.226A pdb=" N MET J 149 " --> pdb=" O ASN J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 170 removed outlier: 4.395A pdb=" N GLU J 164 " --> pdb=" O PRO J 160 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLU J 165 " --> pdb=" O LYS J 161 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'V' and resid 5 through 6 removed outlier: 4.203A pdb=" N ALA V 77 " --> pdb=" O CYS V 22 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR V 76 " --> pdb=" O ASP V 71 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP V 71 " --> pdb=" O THR V 76 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR V 69 " --> pdb=" O TYR V 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'V' and resid 10 through 12 removed outlier: 3.953A pdb=" N THR V 118 " --> pdb=" O GLU V 10 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS V 12 " --> pdb=" O THR V 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'V' and resid 47 through 49 Processing sheet with id=AA4, first strand: chain 'X' and resid 4 through 7 removed outlier: 4.545A pdb=" N VAL X 19 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE X 75 " --> pdb=" O VAL X 19 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE X 21 " --> pdb=" O LEU X 73 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS X 23 " --> pdb=" O PHE X 71 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE X 71 " --> pdb=" O CYS X 23 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP X 70 " --> pdb=" O SER X 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'X' and resid 53 through 54 removed outlier: 6.647A pdb=" N TRP X 35 " --> pdb=" O LEU X 47 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR X 85 " --> pdb=" O HIS X 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA7, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA8, first strand: chain 'A' and resid 88 through 89 Processing sheet with id=AA9, first strand: chain 'A' and resid 100 through 102 removed outlier: 7.305A pdb=" N HIS A 101 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N TRP A 234 " --> pdb=" O HIS A 101 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 178 " --> pdb=" O THR A 235 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=AB2, first strand: chain 'A' and resid 167 through 170 removed outlier: 3.797A pdb=" N ASP A 241 " --> pdb=" O ASN A 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AB4, first strand: chain 'A' and resid 294 through 295 removed outlier: 3.524A pdb=" N GLN A 295 " --> pdb=" O LYS A 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AB6, first strand: chain 'S' and resid 5 through 6 removed outlier: 4.202A pdb=" N ALA S 77 " --> pdb=" O CYS S 22 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR S 76 " --> pdb=" O ASP S 71 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP S 71 " --> pdb=" O THR S 76 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR S 69 " --> pdb=" O TYR S 78 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.953A pdb=" N THR S 118 " --> pdb=" O GLU S 10 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS S 12 " --> pdb=" O THR S 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 47 through 49 Processing sheet with id=AB9, first strand: chain 'T' and resid 4 through 7 removed outlier: 4.546A pdb=" N VAL T 19 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE T 75 " --> pdb=" O VAL T 19 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE T 21 " --> pdb=" O LEU T 73 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N CYS T 23 " --> pdb=" O PHE T 71 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE T 71 " --> pdb=" O CYS T 23 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP T 70 " --> pdb=" O SER T 67 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'T' and resid 53 through 54 removed outlier: 6.646A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR T 85 " --> pdb=" O HIS T 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 25 through 26 Processing sheet with id=AC3, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AC4, first strand: chain 'G' and resid 88 through 89 Processing sheet with id=AC5, first strand: chain 'G' and resid 100 through 102 removed outlier: 7.306A pdb=" N HIS G 101 " --> pdb=" O TYR G 232 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N TRP G 234 " --> pdb=" O HIS G 101 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL G 178 " --> pdb=" O THR G 235 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 151 through 152 Processing sheet with id=AC7, first strand: chain 'G' and resid 167 through 170 removed outlier: 3.797A pdb=" N ASP G 241 " --> pdb=" O ASN G 170 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 286 through 287 Processing sheet with id=AC9, first strand: chain 'G' and resid 294 through 295 removed outlier: 3.525A pdb=" N GLN G 295 " --> pdb=" O LYS G 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'I' and resid 130 through 132 Processing sheet with id=AD2, first strand: chain 'U' and resid 5 through 6 removed outlier: 4.202A pdb=" N ALA U 77 " --> pdb=" O CYS U 22 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR U 76 " --> pdb=" O ASP U 71 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP U 71 " --> pdb=" O THR U 76 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR U 69 " --> pdb=" O TYR U 78 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'U' and resid 10 through 12 removed outlier: 3.952A pdb=" N THR U 118 " --> pdb=" O GLU U 10 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS U 12 " --> pdb=" O THR U 118 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'U' and resid 47 through 49 Processing sheet with id=AD5, first strand: chain 'W' and resid 4 through 7 removed outlier: 4.545A pdb=" N VAL W 19 " --> pdb=" O ILE W 75 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE W 75 " --> pdb=" O VAL W 19 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE W 21 " --> pdb=" O LEU W 73 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N CYS W 23 " --> pdb=" O PHE W 71 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE W 71 " --> pdb=" O CYS W 23 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP W 70 " --> pdb=" O SER W 67 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'W' and resid 53 through 54 removed outlier: 6.646A pdb=" N TRP W 35 " --> pdb=" O LEU W 47 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR W 85 " --> pdb=" O HIS W 38 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 25 through 26 Processing sheet with id=AD8, first strand: chain 'H' and resid 39 through 41 Processing sheet with id=AD9, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AE1, first strand: chain 'H' and resid 100 through 102 removed outlier: 7.305A pdb=" N HIS H 101 " --> pdb=" O TYR H 232 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N TRP H 234 " --> pdb=" O HIS H 101 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL H 178 " --> pdb=" O THR H 235 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 151 through 152 Processing sheet with id=AE3, first strand: chain 'H' and resid 167 through 170 removed outlier: 3.797A pdb=" N ASP H 241 " --> pdb=" O ASN H 170 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 286 through 287 Processing sheet with id=AE5, first strand: chain 'H' and resid 294 through 295 removed outlier: 3.525A pdb=" N GLN H 295 " --> pdb=" O LYS H 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'J' and resid 130 through 132 492 hydrogen bonds defined for protein. 1314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5580 1.35 - 1.47: 4354 1.47 - 1.59: 7364 1.59 - 1.72: 0 1.72 - 1.84: 114 Bond restraints: 17412 Sorted by residual: bond pdb=" N GLY B 1 " pdb=" CA GLY B 1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.03e+00 bond pdb=" N GLY I 1 " pdb=" CA GLY I 1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.03e+00 bond pdb=" N GLY J 1 " pdb=" CA GLY J 1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.02e+00 bond pdb=" N GLU V 1 " pdb=" CA GLU V 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N GLU S 1 " pdb=" CA GLU S 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 ... (remaining 17407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 22620 2.32 - 4.65: 813 4.65 - 6.97: 132 6.97 - 9.30: 18 9.30 - 11.62: 3 Bond angle restraints: 23586 Sorted by residual: angle pdb=" CA TYR A 256 " pdb=" CB TYR A 256 " pdb=" CG TYR A 256 " ideal model delta sigma weight residual 113.90 121.94 -8.04 1.80e+00 3.09e-01 1.99e+01 angle pdb=" CA TYR G 256 " pdb=" CB TYR G 256 " pdb=" CG TYR G 256 " ideal model delta sigma weight residual 113.90 121.94 -8.04 1.80e+00 3.09e-01 1.99e+01 angle pdb=" CA TYR H 256 " pdb=" CB TYR H 256 " pdb=" CG TYR H 256 " ideal model delta sigma weight residual 113.90 121.93 -8.03 1.80e+00 3.09e-01 1.99e+01 angle pdb=" CB LEU J 99 " pdb=" CG LEU J 99 " pdb=" CD1 LEU J 99 " ideal model delta sigma weight residual 110.70 122.32 -11.62 3.00e+00 1.11e-01 1.50e+01 angle pdb=" CB LEU B 99 " pdb=" CG LEU B 99 " pdb=" CD1 LEU B 99 " ideal model delta sigma weight residual 110.70 122.32 -11.62 3.00e+00 1.11e-01 1.50e+01 ... (remaining 23581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 9288 16.96 - 33.91: 944 33.91 - 50.87: 175 50.87 - 67.82: 48 67.82 - 84.78: 36 Dihedral angle restraints: 10491 sinusoidal: 4284 harmonic: 6207 Sorted by residual: dihedral pdb=" CB CYS J 144 " pdb=" SG CYS J 144 " pdb=" SG CYS J 148 " pdb=" CB CYS J 148 " ideal model delta sinusoidal sigma weight residual -86.00 -159.24 73.24 1 1.00e+01 1.00e-02 6.83e+01 dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS B 148 " pdb=" CB CYS B 148 " ideal model delta sinusoidal sigma weight residual -86.00 -159.22 73.22 1 1.00e+01 1.00e-02 6.83e+01 dihedral pdb=" CB CYS I 144 " pdb=" SG CYS I 144 " pdb=" SG CYS I 148 " pdb=" CB CYS I 148 " ideal model delta sinusoidal sigma weight residual -86.00 -159.21 73.21 1 1.00e+01 1.00e-02 6.83e+01 ... (remaining 10488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1656 0.047 - 0.094: 625 0.094 - 0.141: 210 0.141 - 0.189: 62 0.189 - 0.236: 9 Chirality restraints: 2562 Sorted by residual: chirality pdb=" CA GLU J 103 " pdb=" N GLU J 103 " pdb=" C GLU J 103 " pdb=" CB GLU J 103 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA GLU I 103 " pdb=" N GLU I 103 " pdb=" C GLU I 103 " pdb=" CB GLU I 103 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA GLU B 103 " pdb=" N GLU B 103 " pdb=" C GLU B 103 " pdb=" CB GLU B 103 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 2559 not shown) Planarity restraints: 3066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 124 " 0.050 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO H 125 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO H 125 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO H 125 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 124 " -0.050 5.00e-02 4.00e+02 7.62e-02 9.29e+00 pdb=" N PRO A 125 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE G 124 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO G 125 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO G 125 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 125 " 0.041 5.00e-02 4.00e+02 ... (remaining 3063 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 981 2.71 - 3.26: 17350 3.26 - 3.81: 27762 3.81 - 4.35: 35154 4.35 - 4.90: 59713 Nonbonded interactions: 140960 Sorted by model distance: nonbonded pdb=" NE2 GLN W 90 " pdb=" O PRO W 95 " model vdw 2.169 3.120 nonbonded pdb=" NE2 GLN X 90 " pdb=" O PRO X 95 " model vdw 2.169 3.120 nonbonded pdb=" NE2 GLN T 90 " pdb=" O PRO T 95 " model vdw 2.169 3.120 nonbonded pdb=" O SER H 22 " pdb=" ND2 ASN H 322 " model vdw 2.232 3.120 nonbonded pdb=" O SER A 22 " pdb=" ND2 ASN A 322 " model vdw 2.232 3.120 ... (remaining 140955 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: 0.04 Found NCS groups: ncs_group { reference = chain 'V' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'X' selection = chain 'T' selection = chain 'W' } ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'J' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.430 Find NCS groups from input model: 0.130 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17442 Z= 0.257 Angle : 1.015 11.622 23655 Z= 0.531 Chirality : 0.058 0.236 2562 Planarity : 0.006 0.076 3057 Dihedral : 14.786 84.781 6474 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.70 (0.17), residues: 2145 helix: 0.11 (0.26), residues: 378 sheet: -2.20 (0.23), residues: 510 loop : -2.29 (0.16), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG V 36 TYR 0.027 0.002 TYR V 92 PHE 0.024 0.003 PHE B 70 TRP 0.026 0.002 TRP G 69 HIS 0.005 0.001 HIS J 142 Details of bonding type rmsd covalent geometry : bond 0.00603 (17412) covalent geometry : angle 1.00882 (23586) SS BOND : bond 0.01135 ( 21) SS BOND : angle 2.51843 ( 42) hydrogen bonds : bond 0.15114 ( 492) hydrogen bonds : angle 8.66761 ( 1314) link_NAG-ASN : bond 0.00363 ( 9) link_NAG-ASN : angle 1.80758 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 113 GLN cc_start: 0.7953 (pt0) cc_final: 0.7612 (pm20) REVERT: X 55 GLN cc_start: 0.8407 (tp-100) cc_final: 0.8043 (tp-100) REVERT: X 100 GLN cc_start: 0.7988 (mm110) cc_final: 0.7343 (mp10) REVERT: B 17 MET cc_start: 0.6903 (mmm) cc_final: 0.6164 (tpp) REVERT: S 113 GLN cc_start: 0.8062 (pt0) cc_final: 0.7581 (pp30) REVERT: T 53 ASN cc_start: 0.8697 (m-40) cc_final: 0.8476 (m110) REVERT: T 55 GLN cc_start: 0.8438 (tp-100) cc_final: 0.8022 (tp-100) REVERT: T 100 GLN cc_start: 0.8130 (mm110) cc_final: 0.7607 (mp10) REVERT: I 42 GLN cc_start: 0.7949 (tp-100) cc_final: 0.7723 (tp40) REVERT: U 113 GLN cc_start: 0.8025 (pt0) cc_final: 0.7667 (pm20) REVERT: W 100 GLN cc_start: 0.7911 (mm110) cc_final: 0.7330 (mp10) REVERT: J 17 MET cc_start: 0.6739 (mmm) cc_final: 0.6306 (tpp) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.1211 time to fit residues: 64.5847 Evaluate side-chains 199 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN B 114 ASN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN G 199 ASN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 ASN I 114 ASN I 125 GLN I 169 ASN ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 114 ASN ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 169 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.080819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.069592 restraints weight = 65925.390| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.56 r_work: 0.3530 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17442 Z= 0.166 Angle : 0.638 11.162 23655 Z= 0.334 Chirality : 0.048 0.185 2562 Planarity : 0.005 0.053 3057 Dihedral : 5.570 59.317 2523 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.92 % Allowed : 9.76 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.18), residues: 2145 helix: 0.50 (0.27), residues: 384 sheet: -2.11 (0.23), residues: 522 loop : -2.17 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 220 TYR 0.015 0.001 TYR A 17 PHE 0.016 0.001 PHE U 53 TRP 0.011 0.001 TRP U 45 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00374 (17412) covalent geometry : angle 0.63182 (23586) SS BOND : bond 0.00254 ( 21) SS BOND : angle 1.94122 ( 42) hydrogen bonds : bond 0.04461 ( 492) hydrogen bonds : angle 6.70266 ( 1314) link_NAG-ASN : bond 0.00317 ( 9) link_NAG-ASN : angle 1.37397 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 225 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 MET cc_start: 0.7604 (tpp) cc_final: 0.7401 (tpp) REVERT: B 17 MET cc_start: 0.7179 (mmm) cc_final: 0.6967 (tpp) REVERT: B 27 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7646 (tm-30) REVERT: S 13 LYS cc_start: 0.7673 (tptt) cc_final: 0.7378 (tptt) REVERT: S 78 TYR cc_start: 0.6760 (m-80) cc_final: 0.6426 (m-80) REVERT: S 113 GLN cc_start: 0.8384 (pt0) cc_final: 0.7799 (pm20) REVERT: T 55 GLN cc_start: 0.8881 (tp-100) cc_final: 0.8368 (tp-100) REVERT: U 13 LYS cc_start: 0.7809 (tptt) cc_final: 0.7528 (tptt) REVERT: U 113 GLN cc_start: 0.8459 (pt0) cc_final: 0.7669 (pp30) REVERT: H 274 MET cc_start: 0.7609 (tpp) cc_final: 0.7376 (tpp) outliers start: 17 outliers final: 7 residues processed: 235 average time/residue: 0.1171 time to fit residues: 42.2181 Evaluate side-chains 185 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 178 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain H residue 256 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 79 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 204 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 42 optimal weight: 0.0570 chunk 4 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 overall best weight: 4.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 6 GLN ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 GLN G 183 HIS ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN H 183 HIS H 199 ASN ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.074452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.062370 restraints weight = 68574.925| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.98 r_work: 0.3275 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 17442 Z= 0.304 Angle : 0.738 8.943 23655 Z= 0.387 Chirality : 0.049 0.196 2562 Planarity : 0.005 0.048 3057 Dihedral : 5.914 50.811 2523 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.10 % Allowed : 16.02 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.17), residues: 2145 helix: 0.49 (0.26), residues: 366 sheet: -1.86 (0.26), residues: 423 loop : -2.11 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 106 TYR 0.013 0.002 TYR A 17 PHE 0.023 0.003 PHE U 53 TRP 0.011 0.002 TRP H 153 HIS 0.005 0.002 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00676 (17412) covalent geometry : angle 0.73135 (23586) SS BOND : bond 0.00449 ( 21) SS BOND : angle 2.13390 ( 42) hydrogen bonds : bond 0.04767 ( 492) hydrogen bonds : angle 6.60909 ( 1314) link_NAG-ASN : bond 0.00379 ( 9) link_NAG-ASN : angle 1.73198 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 0.501 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: V 53 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.6614 (m-10) REVERT: V 108 MET cc_start: 0.7222 (tpp) cc_final: 0.6869 (tpp) REVERT: B 17 MET cc_start: 0.7229 (mmm) cc_final: 0.6813 (tpp) REVERT: B 27 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7649 (tm-30) REVERT: B 98 LEU cc_start: 0.9057 (mm) cc_final: 0.8753 (mm) REVERT: S 53 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.6630 (m-10) REVERT: G 268 ILE cc_start: 0.6824 (OUTLIER) cc_final: 0.6396 (tt) REVERT: I 27 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7690 (tm-30) REVERT: U 53 PHE cc_start: 0.7180 (OUTLIER) cc_final: 0.5947 (m-10) REVERT: U 85 ARG cc_start: 0.7285 (mtm110) cc_final: 0.7043 (mtm110) REVERT: H 258 PHE cc_start: 0.8305 (m-10) cc_final: 0.7891 (m-10) REVERT: J 27 GLN cc_start: 0.8171 (tm-30) cc_final: 0.7740 (tm-30) outliers start: 39 outliers final: 22 residues processed: 232 average time/residue: 0.1041 time to fit residues: 37.8149 Evaluate side-chains 194 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 53 PHE Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 62 PHE Chi-restraints excluded: chain U residue 89 THR Chi-restraints excluded: chain H residue 158 ASN Chi-restraints excluded: chain H residue 256 TYR Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 268 ILE Chi-restraints excluded: chain J residue 120 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 115 optimal weight: 4.9990 chunk 114 optimal weight: 0.5980 chunk 164 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 137 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 ASN I 169 ASN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 50 ASN ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 169 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.075009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.063248 restraints weight = 67951.354| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.73 r_work: 0.3323 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 17442 Z= 0.268 Angle : 0.700 8.191 23655 Z= 0.365 Chirality : 0.048 0.204 2562 Planarity : 0.005 0.048 3057 Dihedral : 5.591 37.815 2523 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.97 % Allowed : 18.34 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.12 (0.18), residues: 2145 helix: 0.56 (0.27), residues: 366 sheet: -1.75 (0.26), residues: 447 loop : -1.93 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 82 TYR 0.014 0.002 TYR U 92 PHE 0.024 0.002 PHE A 121 TRP 0.011 0.001 TRP V 45 HIS 0.006 0.002 HIS H 184 Details of bonding type rmsd covalent geometry : bond 0.00600 (17412) covalent geometry : angle 0.69428 (23586) SS BOND : bond 0.00392 ( 21) SS BOND : angle 1.96864 ( 42) hydrogen bonds : bond 0.04600 ( 492) hydrogen bonds : angle 6.37677 ( 1314) link_NAG-ASN : bond 0.00299 ( 9) link_NAG-ASN : angle 1.61189 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 186 time to evaluate : 0.738 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: V 12 LYS cc_start: 0.8368 (mtmm) cc_final: 0.7971 (tptp) REVERT: V 19 ARG cc_start: 0.8199 (mmm-85) cc_final: 0.7641 (tpp80) REVERT: V 53 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.6218 (m-80) REVERT: V 108 MET cc_start: 0.7341 (tpp) cc_final: 0.6894 (tpp) REVERT: X 90 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.7190 (pt0) REVERT: B 27 GLN cc_start: 0.8287 (tm-30) cc_final: 0.8000 (tm-30) REVERT: B 98 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8776 (mm) REVERT: S 53 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.6419 (m-10) REVERT: G 268 ILE cc_start: 0.6942 (OUTLIER) cc_final: 0.6603 (tt) REVERT: G 274 MET cc_start: 0.8368 (tpp) cc_final: 0.8150 (tpp) REVERT: I 27 GLN cc_start: 0.8061 (tm-30) cc_final: 0.7526 (tm-30) REVERT: U 53 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.6039 (m-10) REVERT: H 258 PHE cc_start: 0.8171 (m-10) cc_final: 0.7677 (m-10) REVERT: J 27 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7633 (tm-30) REVERT: J 98 LEU cc_start: 0.8975 (mm) cc_final: 0.8699 (mm) outliers start: 55 outliers final: 34 residues processed: 234 average time/residue: 0.1202 time to fit residues: 44.9766 Evaluate side-chains 206 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 53 PHE Chi-restraints excluded: chain V residue 67 THR Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain X residue 90 GLN Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain S residue 67 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 62 PHE Chi-restraints excluded: chain W residue 90 GLN Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 256 TYR Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain J residue 120 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 11 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN I 169 ASN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 55 GLN ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 169 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.076100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.064340 restraints weight = 66886.490| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.72 r_work: 0.3352 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17442 Z= 0.186 Angle : 0.641 7.902 23655 Z= 0.332 Chirality : 0.047 0.180 2562 Planarity : 0.004 0.049 3057 Dihedral : 5.079 34.902 2523 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.21 % Allowed : 20.50 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.18), residues: 2145 helix: 0.84 (0.27), residues: 366 sheet: -1.45 (0.28), residues: 417 loop : -1.85 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 82 TYR 0.011 0.001 TYR U 92 PHE 0.038 0.002 PHE A 121 TRP 0.012 0.001 TRP V 111 HIS 0.005 0.001 HIS I 142 Details of bonding type rmsd covalent geometry : bond 0.00418 (17412) covalent geometry : angle 0.63520 (23586) SS BOND : bond 0.00313 ( 21) SS BOND : angle 1.81177 ( 42) hydrogen bonds : bond 0.04198 ( 492) hydrogen bonds : angle 6.07275 ( 1314) link_NAG-ASN : bond 0.00215 ( 9) link_NAG-ASN : angle 1.42060 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 0.695 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: V 12 LYS cc_start: 0.8369 (mtmm) cc_final: 0.8015 (tptp) REVERT: V 108 MET cc_start: 0.7360 (tpp) cc_final: 0.6863 (tpp) REVERT: B 27 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7947 (tm-30) REVERT: B 98 LEU cc_start: 0.9003 (mm) cc_final: 0.8759 (mm) REVERT: S 53 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.6912 (m-10) REVERT: T 55 GLN cc_start: 0.9080 (tp40) cc_final: 0.8861 (tp-100) REVERT: G 268 ILE cc_start: 0.6829 (OUTLIER) cc_final: 0.6545 (tt) REVERT: G 274 MET cc_start: 0.8383 (tpp) cc_final: 0.8108 (tpp) REVERT: I 27 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7525 (tm-30) REVERT: U 53 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.5760 (m-10) REVERT: H 258 PHE cc_start: 0.8128 (m-10) cc_final: 0.7614 (m-10) REVERT: J 17 MET cc_start: 0.7356 (tpp) cc_final: 0.7153 (tpp) REVERT: J 27 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7603 (tm-30) REVERT: J 98 LEU cc_start: 0.8954 (mm) cc_final: 0.8701 (mm) outliers start: 41 outliers final: 28 residues processed: 233 average time/residue: 0.1187 time to fit residues: 44.4808 Evaluate side-chains 204 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 67 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain S residue 67 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 62 PHE Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 89 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 256 TYR Chi-restraints excluded: chain J residue 120 GLU Chi-restraints excluded: chain J residue 126 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 25 optimal weight: 7.9990 chunk 166 optimal weight: 10.0000 chunk 172 optimal weight: 8.9990 chunk 181 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 175 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.075555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.063683 restraints weight = 67136.870| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.77 r_work: 0.3334 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17442 Z= 0.217 Angle : 0.664 8.264 23655 Z= 0.344 Chirality : 0.047 0.181 2562 Planarity : 0.004 0.051 3057 Dihedral : 5.094 34.758 2523 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.13 % Allowed : 20.06 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.18), residues: 2145 helix: 0.82 (0.27), residues: 366 sheet: -1.35 (0.27), residues: 435 loop : -1.82 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 82 TYR 0.013 0.002 TYR U 92 PHE 0.038 0.002 PHE A 121 TRP 0.010 0.001 TRP V 111 HIS 0.004 0.001 HIS H 184 Details of bonding type rmsd covalent geometry : bond 0.00486 (17412) covalent geometry : angle 0.65791 (23586) SS BOND : bond 0.00381 ( 21) SS BOND : angle 1.94760 ( 42) hydrogen bonds : bond 0.04276 ( 492) hydrogen bonds : angle 6.16063 ( 1314) link_NAG-ASN : bond 0.00252 ( 9) link_NAG-ASN : angle 1.44018 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 183 time to evaluate : 0.723 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: V 12 LYS cc_start: 0.8339 (mtmm) cc_final: 0.8016 (tptm) REVERT: V 68 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8827 (mm) REVERT: V 108 MET cc_start: 0.7361 (tpp) cc_final: 0.6864 (tpp) REVERT: X 32 TYR cc_start: 0.8061 (m-80) cc_final: 0.7827 (m-80) REVERT: B 27 GLN cc_start: 0.8294 (tm-30) cc_final: 0.7965 (tm-30) REVERT: B 98 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8814 (mm) REVERT: S 53 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.6853 (m-10) REVERT: G 268 ILE cc_start: 0.6911 (OUTLIER) cc_final: 0.6601 (tt) REVERT: I 27 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7531 (tm-30) REVERT: U 53 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.5910 (m-10) REVERT: U 108 MET cc_start: 0.7126 (tpp) cc_final: 0.6510 (tpp) REVERT: H 258 PHE cc_start: 0.8180 (m-10) cc_final: 0.7677 (m-10) REVERT: J 27 GLN cc_start: 0.8154 (tm-30) cc_final: 0.7460 (tm-30) REVERT: J 98 LEU cc_start: 0.8994 (mm) cc_final: 0.8750 (mm) outliers start: 58 outliers final: 40 residues processed: 232 average time/residue: 0.1135 time to fit residues: 41.7093 Evaluate side-chains 210 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 165 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 67 THR Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain X residue 47 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain S residue 67 THR Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 62 PHE Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 89 THR Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 90 GLN Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 69 TRP Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 256 TYR Chi-restraints excluded: chain J residue 120 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 111 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 209 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 ASN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 ASN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 GLN ** 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 = 0.3769 r_free = 0.3769 target = 0.075609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.063824 restraints weight = 66909.708| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.73 r_work: 0.3341 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17442 Z= 0.205 Angle : 0.654 8.130 23655 Z= 0.337 Chirality : 0.047 0.177 2562 Planarity : 0.004 0.051 3057 Dihedral : 5.019 33.758 2523 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.02 % Allowed : 20.50 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.18), residues: 2145 helix: 0.63 (0.27), residues: 384 sheet: -1.66 (0.26), residues: 468 loop : -1.74 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 82 TYR 0.016 0.002 TYR V 58 PHE 0.037 0.002 PHE A 121 TRP 0.011 0.001 TRP V 111 HIS 0.004 0.001 HIS H 184 Details of bonding type rmsd covalent geometry : bond 0.00461 (17412) covalent geometry : angle 0.64762 (23586) SS BOND : bond 0.00350 ( 21) SS BOND : angle 2.03795 ( 42) hydrogen bonds : bond 0.04186 ( 492) hydrogen bonds : angle 6.04989 ( 1314) link_NAG-ASN : bond 0.00217 ( 9) link_NAG-ASN : angle 1.39649 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 180 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 12 LYS cc_start: 0.8328 (mtmm) cc_final: 0.7958 (tptm) REVERT: V 57 ASN cc_start: 0.7757 (t0) cc_final: 0.7489 (t0) REVERT: X 32 TYR cc_start: 0.8001 (m-80) cc_final: 0.7740 (m-80) REVERT: B 27 GLN cc_start: 0.8302 (tm-30) cc_final: 0.7966 (tm-30) REVERT: B 98 LEU cc_start: 0.9016 (mm) cc_final: 0.8809 (mm) REVERT: S 53 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6813 (m-10) REVERT: G 268 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6611 (tt) REVERT: G 274 MET cc_start: 0.8389 (tpp) cc_final: 0.8180 (tpp) REVERT: I 27 GLN cc_start: 0.8156 (tm-30) cc_final: 0.7520 (tm-30) REVERT: U 1 GLU cc_start: 0.2821 (OUTLIER) cc_final: 0.2432 (tp30) REVERT: U 53 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.5791 (m-10) REVERT: U 61 LYS cc_start: 0.8774 (pptt) cc_final: 0.8564 (pptt) REVERT: U 108 MET cc_start: 0.7128 (tpp) cc_final: 0.6532 (tpp) REVERT: W 32 TYR cc_start: 0.8258 (m-80) cc_final: 0.7889 (m-80) REVERT: H 258 PHE cc_start: 0.8169 (m-10) cc_final: 0.7775 (m-10) REVERT: J 98 LEU cc_start: 0.8991 (mm) cc_final: 0.8698 (mm) outliers start: 56 outliers final: 44 residues processed: 231 average time/residue: 0.1167 time to fit residues: 43.2757 Evaluate side-chains 216 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 67 THR Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain S residue 67 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain U residue 1 GLU Chi-restraints excluded: chain U residue 43 LEU Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 82 ASP Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 69 TRP Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 256 TYR Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain J residue 120 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 77 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 57 optimal weight: 0.0870 chunk 181 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 212 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 188 optimal weight: 5.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 GLN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 ASN H 111 GLN ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.078589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.066707 restraints weight = 66386.868| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.86 r_work: 0.3420 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17442 Z= 0.114 Angle : 0.599 8.721 23655 Z= 0.307 Chirality : 0.046 0.173 2562 Planarity : 0.004 0.051 3057 Dihedral : 4.565 28.411 2523 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.62 % Allowed : 22.11 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.18), residues: 2145 helix: 0.83 (0.27), residues: 384 sheet: -1.49 (0.29), residues: 390 loop : -1.75 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 255 TYR 0.014 0.001 TYR G 17 PHE 0.035 0.002 PHE A 121 TRP 0.011 0.001 TRP G 69 HIS 0.004 0.001 HIS I 142 Details of bonding type rmsd covalent geometry : bond 0.00255 (17412) covalent geometry : angle 0.59316 (23586) SS BOND : bond 0.00210 ( 21) SS BOND : angle 1.90938 ( 42) hydrogen bonds : bond 0.03744 ( 492) hydrogen bonds : angle 5.73357 ( 1314) link_NAG-ASN : bond 0.00239 ( 9) link_NAG-ASN : angle 1.09817 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 108 MET cc_start: 0.7404 (tpp) cc_final: 0.7172 (tpp) REVERT: B 98 LEU cc_start: 0.9047 (mm) cc_final: 0.8776 (mm) REVERT: S 43 LEU cc_start: 0.8167 (mm) cc_final: 0.7955 (mt) REVERT: S 57 ASN cc_start: 0.7999 (m-40) cc_final: 0.7720 (t0) REVERT: S 58 TYR cc_start: 0.7080 (m-10) cc_final: 0.6838 (m-10) REVERT: S 68 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8715 (mm) REVERT: S 116 MET cc_start: 0.7900 (mtp) cc_final: 0.7649 (mmm) REVERT: G 274 MET cc_start: 0.8415 (tpp) cc_final: 0.8189 (tpp) REVERT: I 27 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7492 (tm-30) REVERT: U 72 ASP cc_start: 0.8023 (m-30) cc_final: 0.7810 (m-30) REVERT: U 81 VAL cc_start: 0.8275 (t) cc_final: 0.7781 (p) REVERT: U 92 TYR cc_start: 0.6868 (m-10) cc_final: 0.6654 (m-10) REVERT: U 108 MET cc_start: 0.7236 (tpp) cc_final: 0.6567 (tpp) REVERT: W 55 GLN cc_start: 0.8903 (tp-100) cc_final: 0.8606 (tp-100) REVERT: W 105 GLU cc_start: 0.3658 (tp30) cc_final: 0.3416 (tp30) outliers start: 30 outliers final: 19 residues processed: 235 average time/residue: 0.1129 time to fit residues: 42.7988 Evaluate side-chains 200 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 67 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain S residue 67 THR Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 69 TRP Chi-restraints excluded: chain H residue 256 TYR Chi-restraints excluded: chain J residue 120 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 193 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 152 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 116 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 chunk 135 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 57 ASN ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 ASN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 GLN ** 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 = 0.3832 r_free = 0.3832 target = 0.078043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.066209 restraints weight = 66413.107| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.79 r_work: 0.3408 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17442 Z= 0.133 Angle : 0.636 9.789 23655 Z= 0.324 Chirality : 0.046 0.223 2562 Planarity : 0.004 0.053 3057 Dihedral : 4.576 26.957 2523 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.73 % Allowed : 22.71 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.18), residues: 2145 helix: 0.82 (0.27), residues: 384 sheet: -1.06 (0.30), residues: 390 loop : -1.71 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 220 TYR 0.015 0.001 TYR V 92 PHE 0.051 0.002 PHE A 121 TRP 0.016 0.001 TRP V 111 HIS 0.003 0.001 HIS H 130 Details of bonding type rmsd covalent geometry : bond 0.00303 (17412) covalent geometry : angle 0.62788 (23586) SS BOND : bond 0.00229 ( 21) SS BOND : angle 2.43040 ( 42) hydrogen bonds : bond 0.03803 ( 492) hydrogen bonds : angle 5.73791 ( 1314) link_NAG-ASN : bond 0.00189 ( 9) link_NAG-ASN : angle 1.07869 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.652 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: V 108 MET cc_start: 0.7470 (tpp) cc_final: 0.7227 (tpp) REVERT: S 43 LEU cc_start: 0.8214 (mm) cc_final: 0.7979 (mt) REVERT: G 274 MET cc_start: 0.8373 (tpp) cc_final: 0.8130 (tpp) REVERT: I 94 TYR cc_start: 0.8610 (t80) cc_final: 0.8326 (t80) REVERT: U 81 VAL cc_start: 0.8211 (t) cc_final: 0.7767 (p) REVERT: U 108 MET cc_start: 0.7174 (tpp) cc_final: 0.6934 (tpp) REVERT: W 55 GLN cc_start: 0.8920 (tp-100) cc_final: 0.8627 (tp-100) REVERT: W 105 GLU cc_start: 0.3681 (tp30) cc_final: 0.3425 (tp30) REVERT: H 258 PHE cc_start: 0.7952 (m-10) cc_final: 0.7565 (m-10) REVERT: J 42 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7915 (tp-100) REVERT: J 98 LEU cc_start: 0.8890 (mm) cc_final: 0.8687 (mm) outliers start: 32 outliers final: 23 residues processed: 216 average time/residue: 0.1002 time to fit residues: 34.5515 Evaluate side-chains 202 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 67 THR Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain X residue 47 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain S residue 67 THR Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 69 TRP Chi-restraints excluded: chain H residue 256 TYR Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 120 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 196 optimal weight: 6.9990 chunk 202 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 127 optimal weight: 6.9990 chunk 147 optimal weight: 0.0370 chunk 141 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 overall best weight: 3.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 57 ASN ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN A 183 HIS ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 GLN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.075616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.063765 restraints weight = 66799.902| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 3.72 r_work: 0.3344 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17442 Z= 0.231 Angle : 0.718 10.578 23655 Z= 0.364 Chirality : 0.048 0.276 2562 Planarity : 0.005 0.052 3057 Dihedral : 5.008 29.412 2523 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.83 % Allowed : 23.09 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.18), residues: 2145 helix: 0.63 (0.27), residues: 381 sheet: -1.13 (0.28), residues: 432 loop : -1.59 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 211 TYR 0.027 0.002 TYR V 92 PHE 0.051 0.002 PHE A 121 TRP 0.013 0.002 TRP V 111 HIS 0.004 0.001 HIS G 184 Details of bonding type rmsd covalent geometry : bond 0.00521 (17412) covalent geometry : angle 0.70990 (23586) SS BOND : bond 0.00359 ( 21) SS BOND : angle 2.51970 ( 42) hydrogen bonds : bond 0.04279 ( 492) hydrogen bonds : angle 5.99734 ( 1314) link_NAG-ASN : bond 0.00256 ( 9) link_NAG-ASN : angle 1.36273 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 57 ASN cc_start: 0.7686 (OUTLIER) cc_final: 0.7406 (t0) REVERT: S 57 ASN cc_start: 0.8108 (m-40) cc_final: 0.7764 (t0) REVERT: G 274 MET cc_start: 0.8391 (tpp) cc_final: 0.8141 (tpp) REVERT: U 108 MET cc_start: 0.7094 (tpp) cc_final: 0.6498 (tpp) REVERT: H 258 PHE cc_start: 0.8184 (m-10) cc_final: 0.7669 (m-10) REVERT: J 42 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7992 (tp-100) REVERT: J 98 LEU cc_start: 0.8978 (mm) cc_final: 0.8734 (mm) outliers start: 34 outliers final: 29 residues processed: 196 average time/residue: 0.1118 time to fit residues: 35.5148 Evaluate side-chains 197 residues out of total 1854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 57 ASN Chi-restraints excluded: chain V residue 67 THR Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain S residue 67 THR Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 69 TRP Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 256 TYR Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain J residue 120 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 9 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 210 optimal weight: 7.9990 chunk 158 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 55 GLN A 111 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 GLN ** 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 = 0.3775 r_free = 0.3775 target = 0.075651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.063747 restraints weight = 66925.124| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 3.74 r_work: 0.3338 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.167 17442 Z= 0.260 Angle : 0.889 59.199 23655 Z= 0.488 Chirality : 0.052 1.010 2562 Planarity : 0.005 0.097 3057 Dihedral : 5.015 29.411 2523 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 1.73 % Allowed : 23.19 % Favored : 75.08 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.18), residues: 2145 helix: 0.64 (0.27), residues: 381 sheet: -1.13 (0.28), residues: 432 loop : -1.59 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 36 TYR 0.021 0.002 TYR B 94 PHE 0.045 0.002 PHE A 121 TRP 0.013 0.002 TRP V 111 HIS 0.004 0.001 HIS H 184 Details of bonding type rmsd covalent geometry : bond 0.00571 (17412) covalent geometry : angle 0.88293 (23586) SS BOND : bond 0.00355 ( 21) SS BOND : angle 2.46417 ( 42) hydrogen bonds : bond 0.04477 ( 492) hydrogen bonds : angle 6.08567 ( 1314) link_NAG-ASN : bond 0.00252 ( 9) link_NAG-ASN : angle 1.36071 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3030.64 seconds wall clock time: 53 minutes 22.73 seconds (3202.73 seconds total)