Starting phenix.real_space_refine on Sat Oct 24 01:27:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cxt_45997/10_2026/9cxt_45997.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cxt_45997/10_2026/9cxt_45997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cxt_45997/10_2026/9cxt_45997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cxt_45997/10_2026/9cxt_45997.map" model { file = "/net/cci-nas-00/data/ceres_data/9cxt_45997/10_2026/9cxt_45997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cxt_45997/10_2026/9cxt_45997.cif" } resolution = 3.4 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 7230 2.51 5 N 2013 2.21 5 O 2313 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-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11613 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2445 Classifications: {'peptide': 317} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 297} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1342 Classifications: {'peptide': 165} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 164} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, E, D, F Time building chain proxies: 3.01, per 1000 atoms: 0.26 Number of scatterers: 11613 At special positions: 0 Unit cell: (86.25, 85.1, 144.9, 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 57 16.00 O 2313 8.00 N 2013 7.00 C 7230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.65 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.08 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.02 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.02 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.07 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS C 14 " distance=2.64 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.07 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG CYS E 14 " distance=2.64 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.07 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.08 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.08 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.02 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 22 " " NAG A 402 " - " ASN A 81 " " NAG A 403 " - " ASN A 38 " " NAG A 404 " - " ASN A 165 " " NAG A 405 " - " ASN A 285 " " NAG B 501 " - " ASN B 154 " " NAG C 401 " - " ASN C 22 " " NAG C 402 " - " ASN C 81 " " NAG C 403 " - " ASN C 38 " " NAG C 404 " - " ASN C 165 " " NAG C 405 " - " ASN C 285 " " NAG D 501 " - " ASN D 154 " " NAG E 401 " - " ASN E 22 " " NAG E 402 " - " ASN E 81 " " NAG E 403 " - " ASN E 38 " " NAG E 404 " - " ASN E 165 " " NAG E 405 " - " ASN E 285 " " NAG F 501 " - " ASN F 154 " Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 402.2 milliseconds 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2658 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 36 sheets defined 28.2% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.862A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.781A pdb=" N THR A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 12 Processing helix chain 'B' and resid 37 through 52 Processing helix chain 'B' and resid 75 through 127 Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 158 through 161 Processing helix chain 'B' and resid 162 through 171 removed outlier: 4.006A pdb=" N ASN B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 12 Processing helix chain 'D' and resid 37 through 52 Processing helix chain 'D' and resid 75 through 127 Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'D' and resid 158 through 161 Processing helix chain 'D' and resid 162 through 171 removed outlier: 4.007A pdb=" N ASN D 168 " --> pdb=" O ASP D 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 12 Processing helix chain 'F' and resid 37 through 52 Processing helix chain 'F' and resid 75 through 127 Processing helix chain 'F' and resid 145 through 154 Processing helix chain 'F' and resid 158 through 161 Processing helix chain 'F' and resid 162 through 171 removed outlier: 4.005A pdb=" N ASN F 168 " --> pdb=" O ASP F 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.863A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.782A pdb=" N THR C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER C 193 " --> pdb=" O GLN C 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 3.862A pdb=" N ASP E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL E 78 " --> pdb=" O HIS E 75 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN E 80 " --> pdb=" O ASP E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 116 Processing helix chain 'E' and resid 187 through 195 removed outlier: 3.781A pdb=" N THR E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER E 193 " --> pdb=" O GLN E 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.444A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN A 53 " --> pdb=" O CYS A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.760A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.023A pdb=" N ASP A 101 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.023A pdb=" N ASP A 101 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB1, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.405A pdb=" N ALA A 138 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 11.123A pdb=" N GLY A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB3, first strand: chain 'A' and resid 286 through 288 removed outlier: 4.410A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 31 through 36 Processing sheet with id=AB5, first strand: chain 'F' and resid 31 through 36 Processing sheet with id=AB6, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AB7, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB8, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB9, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.441A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.758A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 100 through 101 removed outlier: 7.022A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 100 through 101 removed outlier: 7.022A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC5, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.403A pdb=" N ALA C 138 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N GLY C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC7, first strand: chain 'C' and resid 286 through 288 removed outlier: 4.410A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AC9, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD1, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD2, first strand: chain 'E' and resid 51 through 54 removed outlier: 6.441A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N CYS E 277 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN E 53 " --> pdb=" O CYS E 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.759A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 100 through 101 removed outlier: 7.023A pdb=" N ASP E 101 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N TRP E 234 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 100 through 101 removed outlier: 7.023A pdb=" N ASP E 101 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N TRP E 234 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD7, first strand: chain 'E' and resid 136 through 141 removed outlier: 7.406A pdb=" N ALA E 138 " --> pdb=" O GLY E 144 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N GLY E 144 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD9, first strand: chain 'E' and resid 286 through 288 removed outlier: 4.408A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) 516 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2669 1.32 - 1.46: 3996 1.46 - 1.60: 5103 1.60 - 1.74: 13 1.74 - 1.88: 69 Bond restraints: 11850 Sorted by residual: bond pdb=" CB ASN C 250 " pdb=" CG ASN C 250 " ideal model delta sigma weight residual 1.516 1.391 0.125 2.50e-02 1.60e+03 2.51e+01 bond pdb=" CG PHE F 171 " pdb=" CD2 PHE F 171 " ideal model delta sigma weight residual 1.384 1.489 -0.105 2.10e-02 2.27e+03 2.49e+01 bond pdb=" CB ASN E 250 " pdb=" CG ASN E 250 " ideal model delta sigma weight residual 1.516 1.392 0.124 2.50e-02 1.60e+03 2.47e+01 bond pdb=" CB ASN A 250 " pdb=" CG ASN A 250 " ideal model delta sigma weight residual 1.516 1.392 0.124 2.50e-02 1.60e+03 2.47e+01 bond pdb=" CG PHE B 171 " pdb=" CD2 PHE B 171 " ideal model delta sigma weight residual 1.384 1.488 -0.104 2.10e-02 2.27e+03 2.44e+01 ... (remaining 11845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 14321 2.61 - 5.22: 1529 5.22 - 7.83: 183 7.83 - 10.44: 32 10.44 - 13.05: 3 Bond angle restraints: 16068 Sorted by residual: angle pdb=" N ILE B 10 " pdb=" CA ILE B 10 " pdb=" C ILE B 10 " ideal model delta sigma weight residual 111.90 103.33 8.57 8.10e-01 1.52e+00 1.12e+02 angle pdb=" N ILE F 10 " pdb=" CA ILE F 10 " pdb=" C ILE F 10 " ideal model delta sigma weight residual 111.90 103.37 8.53 8.10e-01 1.52e+00 1.11e+02 angle pdb=" N ILE D 10 " pdb=" CA ILE D 10 " pdb=" C ILE D 10 " ideal model delta sigma weight residual 111.90 103.45 8.45 8.10e-01 1.52e+00 1.09e+02 angle pdb=" C ILE C 214 " pdb=" N PRO C 215 " pdb=" CA PRO C 215 " ideal model delta sigma weight residual 119.78 128.14 -8.36 1.03e+00 9.43e-01 6.59e+01 angle pdb=" C ILE E 214 " pdb=" N PRO E 215 " pdb=" CA PRO E 215 " ideal model delta sigma weight residual 119.78 128.12 -8.34 1.03e+00 9.43e-01 6.55e+01 ... (remaining 16063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 7042 17.69 - 35.37: 209 35.37 - 53.06: 48 53.06 - 70.74: 27 70.74 - 88.43: 21 Dihedral angle restraints: 7347 sinusoidal: 3201 harmonic: 4146 Sorted by residual: dihedral pdb=" C LEU E 111 " pdb=" N LEU E 111 " pdb=" CA LEU E 111 " pdb=" CB LEU E 111 " ideal model delta harmonic sigma weight residual -122.60 -113.94 -8.66 0 2.50e+00 1.60e-01 1.20e+01 dihedral pdb=" C LEU C 111 " pdb=" N LEU C 111 " pdb=" CA LEU C 111 " pdb=" CB LEU C 111 " ideal model delta harmonic sigma weight residual -122.60 -113.99 -8.61 0 2.50e+00 1.60e-01 1.19e+01 dihedral pdb=" C LEU A 111 " pdb=" N LEU A 111 " pdb=" CA LEU A 111 " pdb=" CB LEU A 111 " ideal model delta harmonic sigma weight residual -122.60 -114.05 -8.55 0 2.50e+00 1.60e-01 1.17e+01 ... (remaining 7344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1388 0.113 - 0.225: 355 0.225 - 0.338: 49 0.338 - 0.451: 15 0.451 - 0.564: 5 Chirality restraints: 1812 Sorted by residual: chirality pdb=" C1 NAG C 403 " pdb=" ND2 ASN C 38 " pdb=" C2 NAG C 403 " pdb=" O5 NAG C 403 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.94e+00 chirality pdb=" C1 NAG A 403 " pdb=" ND2 ASN A 38 " pdb=" C2 NAG A 403 " pdb=" O5 NAG A 403 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.89e+00 chirality pdb=" C1 NAG E 403 " pdb=" ND2 ASN E 38 " pdb=" C2 NAG E 403 " pdb=" O5 NAG E 403 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.86e+00 ... (remaining 1809 not shown) Planarity restraints: 2103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 405 " 0.217 2.00e-02 2.50e+03 1.85e-01 4.26e+02 pdb=" C7 NAG C 405 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG C 405 " 0.150 2.00e-02 2.50e+03 pdb=" N2 NAG C 405 " -0.312 2.00e-02 2.50e+03 pdb=" O7 NAG C 405 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 405 " -0.217 2.00e-02 2.50e+03 1.84e-01 4.23e+02 pdb=" C7 NAG E 405 " 0.057 2.00e-02 2.50e+03 pdb=" C8 NAG E 405 " -0.150 2.00e-02 2.50e+03 pdb=" N2 NAG E 405 " 0.311 2.00e-02 2.50e+03 pdb=" O7 NAG E 405 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 405 " -0.216 2.00e-02 2.50e+03 1.84e-01 4.21e+02 pdb=" C7 NAG A 405 " 0.057 2.00e-02 2.50e+03 pdb=" C8 NAG A 405 " -0.150 2.00e-02 2.50e+03 pdb=" N2 NAG A 405 " 0.310 2.00e-02 2.50e+03 pdb=" O7 NAG A 405 " -0.001 2.00e-02 2.50e+03 ... (remaining 2100 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 9 2.42 - 3.04: 7281 3.04 - 3.66: 17209 3.66 - 4.28: 28204 4.28 - 4.90: 45824 Nonbonded interactions: 98527 Sorted by model distance: nonbonded pdb=" NE ARG A 220 " pdb=" OE1 GLN C 210 " model vdw 1.802 3.120 nonbonded pdb=" NE ARG C 220 " pdb=" OE1 GLN E 210 " model vdw 1.804 3.120 nonbonded pdb=" OE1 GLN A 210 " pdb=" NE ARG E 220 " model vdw 1.804 3.120 nonbonded pdb=" OD1 ASP C 73 " pdb=" ND1 HIS C 75 " model vdw 1.846 3.120 nonbonded pdb=" OD1 ASP E 73 " pdb=" ND1 HIS E 75 " model vdw 1.847 3.120 ... (remaining 98522 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.020 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 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: 0.5929 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 : 0.023 0.616 11886 Z= 1.213 Angle : 1.729 13.047 16158 Z= 1.173 Chirality : 0.107 0.564 1812 Planarity : 0.013 0.185 2085 Dihedral : 11.230 88.427 4635 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.19), residues: 1434 helix: 0.30 (0.23), residues: 348 sheet: 1.88 (0.32), residues: 180 loop : 0.02 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG B 163 TYR 0.027 0.007 TYR E 195 PHE 0.036 0.009 PHE F 171 TRP 0.020 0.006 TRP E 84 HIS 0.010 0.003 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.02106 / 1.11 (11850) covalent geometry : angle 1.71830 / 1.17 (16068) SS BOND : bond 0.25183 / 15.67 ( 18) SS BOND : angle 3.42214 / 2.19 ( 36) hydrogen bonds : bond 0.14409 / 9.94 ( 486) hydrogen bonds : angle 7.23733 / 5.02 ( 1395) link_NAG-ASN : bond 0.05567 / 3.77 ( 18) link_NAG-ASN : angle 2.92861 / 1.99 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 0.358 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 outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.1045 time to fit residues: 53.0684 Evaluate side-chains 163 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN B 64 HIS B 106 HIS D 64 HIS D 106 HIS F 64 HIS F 106 HIS ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 ASN E 171 ASN E 250 ASN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.185183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.155179 restraints weight = 20070.255| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 3.03 r_work: 0.4093 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11886 Z= 0.201 Angle : 0.805 12.489 16158 Z= 0.414 Chirality : 0.049 0.277 1812 Planarity : 0.006 0.054 2085 Dihedral : 6.335 46.583 1935 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.98 % Allowed : 8.97 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.21), residues: 1434 helix: 1.46 (0.26), residues: 357 sheet: 0.49 (0.29), residues: 276 loop : -0.22 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 224 TYR 0.029 0.002 TYR E 195 PHE 0.016 0.002 PHE E 174 TRP 0.012 0.001 TRP F 14 HIS 0.007 0.002 HIS E 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (11850) covalent geometry : angle 0.75735 / 0.40 (16068) SS BOND : bond 0.00579 / 0.44 ( 18) SS BOND : angle 3.74401 / 2.44 ( 36) hydrogen bonds : bond 0.05157 / 3.55 ( 486) hydrogen bonds : angle 5.31965 / 3.67 ( 1395) link_NAG-ASN : bond 0.01470 / 1.10 ( 18) link_NAG-ASN : angle 3.74617 / 1.98 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 17 MET cc_start: 0.2362 (OUTLIER) cc_final: 0.1697 (mtt) REVERT: F 89 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8728 (mp) REVERT: C 260 MET cc_start: 0.8250 (mmm) cc_final: 0.7862 (mmm) REVERT: E 70 LEU cc_start: 0.8876 (tp) cc_final: 0.8662 (tt) REVERT: E 104 ASP cc_start: 0.7084 (t0) cc_final: 0.6582 (t70) REVERT: E 260 MET cc_start: 0.8246 (mmm) cc_final: 0.7980 (mmm) outliers start: 25 outliers final: 15 residues processed: 215 average time/residue: 0.1029 time to fit residues: 32.0826 Evaluate side-chains 144 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 202 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [103, 64, 58, 50, 84, 123, 82, 45, 7, 69, 37] chunk 103 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.176054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.146866 restraints weight = 20277.745| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 2.86 r_work: 0.4001 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11886 Z= 0.226 Angle : 0.913 20.984 16158 Z= 0.437 Chirality : 0.053 0.361 1812 Planarity : 0.006 0.055 2085 Dihedral : 7.160 59.833 1935 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.73 % Allowed : 9.52 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.21), residues: 1434 helix: 0.86 (0.26), residues: 381 sheet: -0.09 (0.31), residues: 258 loop : -0.43 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 224 TYR 0.017 0.002 TYR D 162 PHE 0.021 0.002 PHE E 120 TRP 0.011 0.002 TRP F 92 HIS 0.012 0.002 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.23 (11850) covalent geometry : angle 0.83211 / 0.42 (16068) SS BOND : bond 0.00866 / 0.55 ( 18) SS BOND : angle 2.87858 / 2.17 ( 36) hydrogen bonds : bond 0.04653 / 3.17 ( 486) hydrogen bonds : angle 5.32932 / 3.68 ( 1395) link_NAG-ASN : bond 0.00709 / 0.54 ( 18) link_NAG-ASN : angle 6.15230 / 4.00 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 0.470 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: D 17 MET cc_start: 0.2303 (OUTLIER) cc_final: 0.1693 (mtt) REVERT: F 79 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8541 (m-30) REVERT: C 197 GLN cc_start: 0.6404 (tp-100) cc_final: 0.6203 (tp40) REVERT: C 260 MET cc_start: 0.8359 (mmm) cc_final: 0.8085 (mmm) REVERT: C 268 MET cc_start: 0.7968 (ttp) cc_final: 0.7739 (ttp) REVERT: E 260 MET cc_start: 0.8335 (mmm) cc_final: 0.8055 (mmm) outliers start: 47 outliers final: 28 residues processed: 195 average time/residue: 0.0901 time to fit residues: 26.5996 Evaluate side-chains 151 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain B residue 9 PHE Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 266 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [11, 87, 93, 33, 67, 43, 51, 69, 66, 116, 84] chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** 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 = 0.4373 r_free = 0.4373 target = 0.171135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.141323 restraints weight = 20542.422| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.84 r_work: 0.3930 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 11886 Z= 0.229 Angle : 0.854 14.864 16158 Z= 0.419 Chirality : 0.050 0.193 1812 Planarity : 0.005 0.056 2085 Dihedral : 6.773 55.114 1935 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.89 % Allowed : 10.48 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.22), residues: 1434 helix: 0.92 (0.26), residues: 378 sheet: -0.70 (0.30), residues: 270 loop : -0.66 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 224 TYR 0.018 0.002 TYR B 94 PHE 0.019 0.002 PHE E 120 TRP 0.013 0.002 TRP E 84 HIS 0.007 0.002 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.23 (11850) covalent geometry : angle 0.79947 / 0.40 (16068) SS BOND : bond 0.01249 / 0.79 ( 18) SS BOND : angle 3.96452 / 2.44 ( 36) hydrogen bonds : bond 0.04467 / 3.08 ( 486) hydrogen bonds : angle 5.48479 / 3.84 ( 1395) link_NAG-ASN : bond 0.01112 / 0.71 ( 18) link_NAG-ASN : angle 4.21042 / 2.74 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 136 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.6402 (ttm-80) cc_final: 0.6070 (ttp-170) REVERT: D 17 MET cc_start: 0.2800 (OUTLIER) cc_final: 0.1984 (mtt) REVERT: D 167 LEU cc_start: 0.7452 (pp) cc_final: 0.7149 (pp) REVERT: F 79 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8514 (m-30) REVERT: F 89 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8816 (mp) REVERT: C 260 MET cc_start: 0.8327 (mmm) cc_final: 0.7852 (mmm) REVERT: E 141 ARG cc_start: 0.6383 (ttm-80) cc_final: 0.5823 (ttp-170) REVERT: E 260 MET cc_start: 0.8515 (mmm) cc_final: 0.8208 (mmm) outliers start: 49 outliers final: 34 residues processed: 172 average time/residue: 0.0911 time to fit residues: 24.0345 Evaluate side-chains 151 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain B residue 9 PHE Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 322 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [131, 1, 113, 42, 61, 72, 29, 52, 89, 137, 78] chunk 131 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 0.0970 chunk 89 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** 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 = 0.4383 r_free = 0.4383 target = 0.172369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.142173 restraints weight = 20277.721| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.88 r_work: 0.3945 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11886 Z= 0.157 Angle : 0.720 10.348 16158 Z= 0.358 Chirality : 0.047 0.307 1812 Planarity : 0.005 0.047 2085 Dihedral : 6.395 57.147 1935 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.33 % Allowed : 11.59 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.22), residues: 1434 helix: 1.45 (0.27), residues: 360 sheet: -0.47 (0.30), residues: 282 loop : -0.66 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 224 TYR 0.013 0.001 TYR D 162 PHE 0.017 0.002 PHE B 24 TRP 0.009 0.001 TRP E 222 HIS 0.005 0.001 HIS E 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (11850) covalent geometry : angle 0.68492 / 0.35 (16068) SS BOND : bond 0.00694 / 0.45 ( 18) SS BOND : angle 3.04808 / 1.81 ( 36) hydrogen bonds : bond 0.04040 / 2.77 ( 486) hydrogen bonds : angle 5.34996 / 3.73 ( 1395) link_NAG-ASN : bond 0.00384 / 0.28 ( 18) link_NAG-ASN : angle 3.02567 / 1.94 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.6449 (ttm-80) cc_final: 0.6154 (ttp-170) REVERT: D 17 MET cc_start: 0.2496 (mtm) cc_final: 0.1825 (mtt) REVERT: D 167 LEU cc_start: 0.7216 (pp) cc_final: 0.6881 (pp) REVERT: C 174 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8471 (p90) REVERT: C 208 ARG cc_start: 0.7462 (mtt90) cc_final: 0.7232 (mtm-85) REVERT: C 260 MET cc_start: 0.8457 (mmm) cc_final: 0.8070 (mmm) REVERT: E 141 ARG cc_start: 0.6358 (ttm-80) cc_final: 0.5882 (ttp-170) outliers start: 42 outliers final: 31 residues processed: 174 average time/residue: 0.0940 time to fit residues: 24.4395 Evaluate side-chains 150 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 222 TRP Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain B residue 9 PHE Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 222 TRP Chi-restraints excluded: chain E residue 275 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [112, 50, 108, 25, 32, 6, 7, 61, 136, 33, 86] chunk 112 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 108 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** 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 = 0.4382 r_free = 0.4382 target = 0.171914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.142181 restraints weight = 20485.585| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.82 r_work: 0.3953 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.5560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11886 Z= 0.159 Angle : 0.752 14.107 16158 Z= 0.364 Chirality : 0.048 0.439 1812 Planarity : 0.005 0.050 2085 Dihedral : 6.267 58.086 1935 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.33 % Allowed : 12.14 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.22), residues: 1434 helix: 1.50 (0.27), residues: 366 sheet: -0.51 (0.30), residues: 282 loop : -0.72 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 124 TYR 0.029 0.002 TYR D 162 PHE 0.020 0.002 PHE D 24 TRP 0.009 0.001 TRP B 14 HIS 0.004 0.001 HIS E 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (11850) covalent geometry : angle 0.70975 / 0.35 (16068) SS BOND : bond 0.00594 / 0.39 ( 18) SS BOND : angle 2.59959 / 1.57 ( 36) hydrogen bonds : bond 0.04014 / 2.75 ( 486) hydrogen bonds : angle 5.17331 / 3.58 ( 1395) link_NAG-ASN : bond 0.00658 / 0.48 ( 18) link_NAG-ASN : angle 3.84341 / 2.48 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.6415 (ttm-80) cc_final: 0.6110 (ttp-170) REVERT: A 168 MET cc_start: 0.7137 (mpp) cc_final: 0.6730 (mmm) REVERT: D 17 MET cc_start: 0.2723 (mtm) cc_final: 0.1762 (mtt) REVERT: D 143 LYS cc_start: 0.6843 (mmmt) cc_final: 0.6416 (mmtp) REVERT: D 167 LEU cc_start: 0.7184 (pp) cc_final: 0.6839 (pp) REVERT: C 68 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: C 174 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8444 (p90) REVERT: C 260 MET cc_start: 0.8371 (mmm) cc_final: 0.7977 (mmm) REVERT: E 141 ARG cc_start: 0.6419 (ttm-80) cc_final: 0.5949 (ttp-170) outliers start: 42 outliers final: 32 residues processed: 164 average time/residue: 0.0937 time to fit residues: 23.1585 Evaluate side-chains 151 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 222 TRP Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain B residue 9 PHE Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 222 TRP Chi-restraints excluded: chain E residue 275 ASP Chi-restraints excluded: chain E residue 322 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [52, 76, 136, 75, 108, 85, 129, 110, 115, 65, 30] chunk 52 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.170511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.140640 restraints weight = 20332.099| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.86 r_work: 0.3929 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 11886 Z= 0.174 Angle : 0.726 11.920 16158 Z= 0.356 Chirality : 0.048 0.515 1812 Planarity : 0.005 0.048 2085 Dihedral : 6.107 52.082 1935 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.33 % Allowed : 13.10 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.22), residues: 1434 helix: 1.52 (0.27), residues: 366 sheet: -0.58 (0.30), residues: 282 loop : -0.80 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 224 TYR 0.040 0.002 TYR D 162 PHE 0.024 0.002 PHE B 24 TRP 0.010 0.001 TRP B 14 HIS 0.009 0.001 HIS F 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (11850) covalent geometry : angle 0.68910 / 0.35 (16068) SS BOND : bond 0.00411 / 0.28 ( 18) SS BOND : angle 2.27951 / 1.39 ( 36) hydrogen bonds : bond 0.04051 / 2.78 ( 486) hydrogen bonds : angle 5.28717 / 3.66 ( 1395) link_NAG-ASN : bond 0.00664 / 0.50 ( 18) link_NAG-ASN : angle 3.58152 / 2.28 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.6433 (ttm-80) cc_final: 0.6087 (ttp-170) REVERT: A 168 MET cc_start: 0.7120 (mpp) cc_final: 0.6665 (mmm) REVERT: D 17 MET cc_start: 0.3022 (mtm) cc_final: 0.2110 (mtt) REVERT: D 167 LEU cc_start: 0.7165 (pp) cc_final: 0.6797 (pp) REVERT: F 79 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8419 (m-30) REVERT: C 68 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7472 (m-30) REVERT: C 174 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8471 (p90) REVERT: C 260 MET cc_start: 0.8410 (mmm) cc_final: 0.7760 (mmm) REVERT: E 141 ARG cc_start: 0.6396 (ttm-80) cc_final: 0.6058 (ttp-170) outliers start: 42 outliers final: 33 residues processed: 167 average time/residue: 0.0874 time to fit residues: 22.4919 Evaluate side-chains 155 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 222 TRP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain B residue 9 PHE Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 222 TRP Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 275 ASP Chi-restraints excluded: chain E residue 322 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [32, 120, 13, 82, 15, 135, 66, 94, 62, 137, 6] chunk 32 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 94 optimal weight: 0.0980 chunk 62 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.170986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.141311 restraints weight = 20345.919| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.87 r_work: 0.3930 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.6001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11886 Z= 0.158 Angle : 0.786 25.252 16158 Z= 0.381 Chirality : 0.049 0.578 1812 Planarity : 0.005 0.049 2085 Dihedral : 6.164 51.453 1935 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.17 % Allowed : 13.57 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.22), residues: 1434 helix: 1.61 (0.27), residues: 366 sheet: -0.56 (0.32), residues: 252 loop : -0.93 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 124 TYR 0.042 0.002 TYR B 162 PHE 0.020 0.002 PHE B 24 TRP 0.008 0.001 TRP E 222 HIS 0.006 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (11850) covalent geometry : angle 0.74284 / 0.37 (16068) SS BOND : bond 0.00892 / 0.54 ( 18) SS BOND : angle 3.39333 / 1.86 ( 36) hydrogen bonds : bond 0.03983 / 2.76 ( 486) hydrogen bonds : angle 5.19538 / 3.60 ( 1395) link_NAG-ASN : bond 0.00831 / 0.56 ( 18) link_NAG-ASN : angle 3.60270 / 2.27 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.7010 (mpp) cc_final: 0.6641 (mmm) REVERT: A 312 ASN cc_start: 0.8137 (m-40) cc_final: 0.7683 (p0) REVERT: B 124 ARG cc_start: 0.6430 (mmp-170) cc_final: 0.6097 (ptp-170) REVERT: D 167 LEU cc_start: 0.6813 (pp) cc_final: 0.6427 (pp) REVERT: C 68 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7506 (m-30) REVERT: C 174 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8244 (p90) REVERT: C 260 MET cc_start: 0.8428 (mmm) cc_final: 0.8038 (mmm) REVERT: E 141 ARG cc_start: 0.6454 (ttm-80) cc_final: 0.6211 (ttp-170) REVERT: E 312 ASN cc_start: 0.8080 (m-40) cc_final: 0.7773 (p0) outliers start: 40 outliers final: 33 residues processed: 162 average time/residue: 0.0820 time to fit residues: 20.6144 Evaluate side-chains 155 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 222 TRP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain B residue 9 PHE Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 222 TRP Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 275 ASP Chi-restraints excluded: chain E residue 322 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [2, 12, 97, 62, 115, 100, 61, 41, 50, 108, 88] chunk 2 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 97 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 chunk 115 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 108 optimal weight: 0.0050 chunk 88 optimal weight: 0.6980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** 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 = 0.4376 r_free = 0.4376 target = 0.171460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.142354 restraints weight = 20305.620| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 2.81 r_work: 0.3943 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.6176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11886 Z= 0.150 Angle : 0.818 24.923 16158 Z= 0.391 Chirality : 0.049 0.571 1812 Planarity : 0.005 0.048 2085 Dihedral : 6.169 55.369 1935 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.70 % Allowed : 13.81 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.22), residues: 1434 helix: 1.59 (0.27), residues: 366 sheet: -0.38 (0.35), residues: 222 loop : -0.98 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 224 TYR 0.043 0.002 TYR B 162 PHE 0.020 0.002 PHE B 24 TRP 0.008 0.001 TRP E 222 HIS 0.006 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (11850) covalent geometry : angle 0.73768 / 0.37 (16068) SS BOND : bond 0.00843 / 0.51 ( 18) SS BOND : angle 3.69133 / 1.98 ( 36) hydrogen bonds : bond 0.03925 / 2.72 ( 486) hydrogen bonds : angle 5.25031 / 3.61 ( 1395) link_NAG-ASN : bond 0.00720 / 0.52 ( 18) link_NAG-ASN : angle 5.38693 / 4.09 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.6973 (mpp) cc_final: 0.6612 (mmm) REVERT: A 312 ASN cc_start: 0.7898 (m-40) cc_final: 0.7511 (p0) REVERT: B 56 ILE cc_start: 0.7404 (pp) cc_final: 0.7110 (mm) REVERT: B 124 ARG cc_start: 0.6768 (mmp-170) cc_final: 0.6272 (ptp-170) REVERT: D 56 ILE cc_start: 0.7503 (pp) cc_final: 0.7247 (mm) REVERT: F 89 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8802 (mp) REVERT: F 143 LYS cc_start: 0.6265 (mmmt) cc_final: 0.5564 (mmmt) REVERT: C 68 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7545 (m-30) REVERT: C 174 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8164 (p90) REVERT: C 260 MET cc_start: 0.8412 (mmm) cc_final: 0.8033 (mmm) REVERT: C 312 ASN cc_start: 0.7822 (m-40) cc_final: 0.7408 (p0) REVERT: E 141 ARG cc_start: 0.6463 (ttm-80) cc_final: 0.6212 (ttp-170) REVERT: E 312 ASN cc_start: 0.8040 (m-40) cc_final: 0.7750 (p0) outliers start: 34 outliers final: 28 residues processed: 151 average time/residue: 0.0812 time to fit residues: 19.1602 Evaluate side-chains 149 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 222 TRP Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain B residue 9 PHE Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 222 TRP Chi-restraints excluded: chain E residue 275 ASP Chi-restraints excluded: chain E residue 322 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [103, 88, 115, 40, 118, 34, 1, 111, 24, 35, 85] chunk 103 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** 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 = 0.4367 r_free = 0.4367 target = 0.170506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.141556 restraints weight = 20754.279| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 2.81 r_work: 0.3938 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.6392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11886 Z= 0.168 Angle : 0.812 19.454 16158 Z= 0.398 Chirality : 0.048 0.548 1812 Planarity : 0.005 0.050 2085 Dihedral : 6.252 50.835 1935 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.78 % Allowed : 14.05 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.22), residues: 1434 helix: 1.47 (0.27), residues: 366 sheet: -0.42 (0.35), residues: 222 loop : -1.12 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 163 TYR 0.030 0.002 TYR F 162 PHE 0.020 0.002 PHE B 24 TRP 0.010 0.001 TRP D 14 HIS 0.007 0.002 HIS B 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (11850) covalent geometry : angle 0.74873 / 0.38 (16068) SS BOND : bond 0.00675 / 0.42 ( 18) SS BOND : angle 3.84829 / 2.10 ( 36) hydrogen bonds : bond 0.04012 / 2.80 ( 486) hydrogen bonds : angle 5.47469 / 3.82 ( 1395) link_NAG-ASN : bond 0.00649 / 0.50 ( 18) link_NAG-ASN : angle 4.51646 / 3.34 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.402 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: A 168 MET cc_start: 0.7020 (mpp) cc_final: 0.6605 (mmm) REVERT: A 312 ASN cc_start: 0.7869 (m-40) cc_final: 0.7479 (p0) REVERT: B 14 TRP cc_start: 0.0855 (m-10) cc_final: 0.0329 (m100) REVERT: B 17 MET cc_start: 0.4035 (ptm) cc_final: 0.3489 (ptp) REVERT: B 56 ILE cc_start: 0.7562 (pp) cc_final: 0.7304 (mm) REVERT: B 124 ARG cc_start: 0.6909 (mmp-170) cc_final: 0.6246 (ptp-170) REVERT: D 17 MET cc_start: 0.2873 (mtt) cc_final: 0.0345 (ptp) REVERT: D 56 ILE cc_start: 0.7515 (pp) cc_final: 0.7312 (mm) REVERT: F 79 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8399 (m-30) REVERT: F 89 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8824 (mp) REVERT: C 68 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7615 (m-30) REVERT: C 174 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8120 (p90) REVERT: C 260 MET cc_start: 0.8430 (mmm) cc_final: 0.8047 (mmm) REVERT: C 312 ASN cc_start: 0.7763 (m-40) cc_final: 0.7387 (p0) REVERT: E 141 ARG cc_start: 0.6485 (ttm-80) cc_final: 0.6192 (ttp-170) REVERT: E 312 ASN cc_start: 0.8016 (m-40) cc_final: 0.7767 (p0) outliers start: 35 outliers final: 31 residues processed: 149 average time/residue: 0.0882 time to fit residues: 20.5634 Evaluate side-chains 147 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 222 TRP Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain B residue 9 PHE Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 222 TRP Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 275 ASP Chi-restraints excluded: chain E residue 322 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [24, 56, 131, 91, 8, 28, 115, 96, 81, 104, 27] chunk 24 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.169871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.140823 restraints weight = 20742.131| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 2.89 r_work: 0.3922 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.6528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11886 Z= 0.166 Angle : 0.829 17.550 16158 Z= 0.403 Chirality : 0.046 0.212 1812 Planarity : 0.005 0.061 2085 Dihedral : 6.516 55.211 1935 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.78 % Allowed : 14.60 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.22), residues: 1434 helix: 1.42 (0.27), residues: 366 sheet: -0.42 (0.35), residues: 222 loop : -1.13 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 163 TYR 0.032 0.002 TYR F 162 PHE 0.018 0.002 PHE B 24 TRP 0.009 0.001 TRP C 84 HIS 0.012 0.002 HIS F 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (11850) covalent geometry : angle 0.76324 / 0.38 (16068) SS BOND : bond 0.00367 / 0.25 ( 18) SS BOND : angle 3.91993 / 2.15 ( 36) hydrogen bonds : bond 0.03999 / 2.80 ( 486) hydrogen bonds : angle 5.44376 / 3.82 ( 1395) link_NAG-ASN : bond 0.00414 / 0.30 ( 18) link_NAG-ASN : angle 4.70390 / 3.31 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2322.39 seconds wall clock time: 40 minutes 52.41 seconds (2452.41 seconds total)