Starting phenix.real_space_refine on Wed Sep 17 22:36:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cxt_45997/09_2025/9cxt_45997.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cxt_45997/09_2025/9cxt_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 { model { file = "/net/cci-nas-00/data/ceres_data/9cxt_45997/09_2025/9cxt_45997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cxt_45997/09_2025/9cxt_45997.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cxt_45997/09_2025/9cxt_45997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cxt_45997/09_2025/9cxt_45997.map" } 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-2.0-5805/lib/python3.9/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: 2.77, per 1000 atoms: 0.24 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 C 14 " - pdb=" SG CYS D 137 " distance=2.64 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.64 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.08 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.08 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.02 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 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 281 " - pdb=" SG CYS E 305 " distance=2.02 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.07 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.07 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: 1.14 Conformation dependent library (CDL) restraints added in 544.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.53 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: 2.15 Time building geometry restraints manager: 1.52 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: 7044 17.69 - 35.37: 207 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: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.590 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5734 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 : 2.28 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 aren 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 covalent geometry : bond 0.02106 (11850) covalent geometry : angle 1.71830 (16068) SS BOND : bond 0.25183 ( 18) SS BOND : angle 3.42214 ( 36) hydrogen bonds : bond 0.14409 ( 486) hydrogen bonds : angle 7.23733 ( 1395) link_NAG-ASN : bond 0.05567 ( 18) link_NAG-ASN : angle 2.92861 ( 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 : 0.561 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: 0.1230 time to fit residues: 61.6337 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 : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.185180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.155264 restraints weight = 20073.315| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 3.01 r_work: 0.4095 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 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 aren 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 covalent geometry : bond 0.00434 (11850) covalent geometry : angle 0.75735 (16068) SS BOND : bond 0.00579 ( 18) SS BOND : angle 3.74401 ( 36) hydrogen bonds : bond 0.05157 ( 486) hydrogen bonds : angle 5.31965 ( 1395) link_NAG-ASN : bond 0.01470 ( 18) link_NAG-ASN : angle 3.74617 ( 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 : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 17 MET cc_start: 0.2350 (OUTLIER) cc_final: 0.1684 (mtt) REVERT: F 89 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8727 (mp) REVERT: C 260 MET cc_start: 0.8247 (mmm) cc_final: 0.7860 (mmm) REVERT: E 70 LEU cc_start: 0.8876 (tp) cc_final: 0.8662 (tt) REVERT: E 104 ASP cc_start: 0.7080 (t0) cc_final: 0.6579 (t70) REVERT: E 260 MET cc_start: 0.8244 (mmm) cc_final: 0.7979 (mmm) outliers start: 25 outliers final: 15 residues processed: 215 average time/residue: 0.1161 time to fit residues: 35.8341 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 : 0.474 ------------------------------------------------------------------------------- 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: chunk 103 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 250 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 = 0.4441 r_free = 0.4441 target = 0.177377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.148093 restraints weight = 20290.278| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 2.93 r_work: 0.4010 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11886 Z= 0.219 Angle : 0.896 21.622 16158 Z= 0.432 Chirality : 0.052 0.417 1812 Planarity : 0.005 0.055 2085 Dihedral : 7.103 58.825 1935 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.41 % Allowed : 10.00 % Favored : 86.59 % 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 aren not related in a simple way. whole: 0.05 (0.21), residues: 1434 helix: 1.19 (0.26), residues: 363 sheet: -0.13 (0.29), residues: 288 loop : -0.40 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 224 TYR 0.020 0.002 TYR D 162 PHE 0.019 0.002 PHE E 120 TRP 0.011 0.001 TRP F 92 HIS 0.010 0.002 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00503 (11850) covalent geometry : angle 0.80760 (16068) SS BOND : bond 0.01033 ( 18) SS BOND : angle 3.49348 ( 36) hydrogen bonds : bond 0.04651 ( 486) hydrogen bonds : angle 5.26539 ( 1395) link_NAG-ASN : bond 0.00631 ( 18) link_NAG-ASN : angle 6.16790 ( 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 197 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 17 MET cc_start: 0.2256 (mtm) cc_final: 0.1664 (mtt) REVERT: F 79 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8527 (m-30) REVERT: C 260 MET cc_start: 0.8321 (mmm) cc_final: 0.8049 (mmm) REVERT: C 268 MET cc_start: 0.7929 (ttp) cc_final: 0.7710 (ttp) REVERT: E 260 MET cc_start: 0.8298 (mmm) cc_final: 0.8043 (mmm) outliers start: 43 outliers final: 26 residues processed: 188 average time/residue: 0.1034 time to fit residues: 29.1599 Evaluate side-chains 148 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 266 SER 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 65 GLN 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 219 SER 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: chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 0.0470 chunk 93 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 69 optimal weight: 0.0050 chunk 66 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 overall best weight: 0.5692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** C 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.177337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.147706 restraints weight = 20260.501| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 2.92 r_work: 0.4005 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11886 Z= 0.166 Angle : 0.847 25.162 16158 Z= 0.410 Chirality : 0.052 0.609 1812 Planarity : 0.005 0.053 2085 Dihedral : 6.877 53.817 1935 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.78 % Allowed : 10.95 % Favored : 86.27 % 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 aren not related in a simple way. whole: 0.07 (0.22), residues: 1434 helix: 1.62 (0.27), residues: 354 sheet: -0.15 (0.32), residues: 258 loop : -0.57 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 224 TYR 0.017 0.001 TYR F 94 PHE 0.017 0.002 PHE B 24 TRP 0.010 0.001 TRP B 14 HIS 0.004 0.001 HIS F 159 Details of bonding type rmsd covalent geometry : bond 0.00353 (11850) covalent geometry : angle 0.76034 (16068) SS BOND : bond 0.00893 ( 18) SS BOND : angle 4.91349 ( 36) hydrogen bonds : bond 0.04182 ( 486) hydrogen bonds : angle 5.07841 ( 1395) link_NAG-ASN : bond 0.01710 ( 18) link_NAG-ASN : angle 5.16481 ( 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 184 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.477 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: B 124 ARG cc_start: 0.6775 (mmp-170) cc_final: 0.6090 (ptp-170) REVERT: D 17 MET cc_start: 0.2350 (mtm) cc_final: 0.1729 (mtt) REVERT: D 167 LEU cc_start: 0.7192 (pp) cc_final: 0.6881 (pp) REVERT: F 79 ASP cc_start: 0.8760 (OUTLIER) cc_final: 0.8505 (m-30) REVERT: C 260 MET cc_start: 0.8321 (mmm) cc_final: 0.8025 (mmm) REVERT: C 268 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7604 (ttp) REVERT: E 260 MET cc_start: 0.8380 (mmm) cc_final: 0.8138 (mmt) outliers start: 35 outliers final: 24 residues processed: 171 average time/residue: 0.0951 time to fit residues: 25.2966 Evaluate side-chains 151 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 9 PHE Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 87 THR 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 79 ASP 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 268 MET Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 202 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 131 optimal weight: 0.0270 chunk 1 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 29 optimal weight: 0.0670 chunk 52 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 78 optimal weight: 0.2980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.177915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.148580 restraints weight = 20205.040| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 2.84 r_work: 0.4019 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11886 Z= 0.138 Angle : 0.768 17.853 16158 Z= 0.372 Chirality : 0.052 0.573 1812 Planarity : 0.005 0.046 2085 Dihedral : 6.621 59.959 1935 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.17 % Allowed : 11.27 % Favored : 85.56 % 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 aren not related in a simple way. whole: 0.20 (0.22), residues: 1434 helix: 1.93 (0.27), residues: 354 sheet: -0.12 (0.33), residues: 258 loop : -0.58 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 321 TYR 0.016 0.001 TYR D 94 PHE 0.016 0.001 PHE B 24 TRP 0.011 0.001 TRP E 222 HIS 0.003 0.001 HIS D 159 Details of bonding type rmsd covalent geometry : bond 0.00301 (11850) covalent geometry : angle 0.68886 (16068) SS BOND : bond 0.00944 ( 18) SS BOND : angle 4.01038 ( 36) hydrogen bonds : bond 0.03933 ( 486) hydrogen bonds : angle 5.01418 ( 1395) link_NAG-ASN : bond 0.01038 ( 18) link_NAG-ASN : angle 4.97956 ( 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 183 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 0.506 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 197 GLN cc_start: 0.6174 (tp-100) cc_final: 0.5627 (mm-40) REVERT: D 17 MET cc_start: 0.2351 (mtm) cc_final: 0.1742 (mtt) REVERT: D 167 LEU cc_start: 0.7182 (pp) cc_final: 0.6853 (pp) REVERT: C 260 MET cc_start: 0.8367 (mmm) cc_final: 0.8061 (mmm) REVERT: C 268 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7586 (ttp) REVERT: E 114 SER cc_start: 0.8859 (OUTLIER) cc_final: 0.8545 (t) REVERT: E 260 MET cc_start: 0.8426 (mmm) cc_final: 0.8114 (mmt) outliers start: 40 outliers final: 29 residues processed: 167 average time/residue: 0.0964 time to fit residues: 24.8651 Evaluate side-chains 155 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 114 SER 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 275 ASP 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 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 160 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 114 SER 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 112 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4377 r_free = 0.4377 target = 0.171849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.142127 restraints weight = 20562.118| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 2.85 r_work: 0.3945 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 11886 Z= 0.217 Angle : 0.867 18.759 16158 Z= 0.414 Chirality : 0.054 0.606 1812 Planarity : 0.005 0.064 2085 Dihedral : 6.781 51.001 1935 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.89 % Allowed : 11.59 % Favored : 84.52 % 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 aren not related in a simple way. whole: -0.12 (0.22), residues: 1434 helix: 1.50 (0.27), residues: 366 sheet: -0.49 (0.32), residues: 240 loop : -0.66 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 150 TYR 0.029 0.002 TYR D 162 PHE 0.019 0.002 PHE C 120 TRP 0.012 0.002 TRP A 84 HIS 0.007 0.001 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00505 (11850) covalent geometry : angle 0.78082 (16068) SS BOND : bond 0.00626 ( 18) SS BOND : angle 3.82389 ( 36) hydrogen bonds : bond 0.04265 ( 486) hydrogen bonds : angle 5.27449 ( 1395) link_NAG-ASN : bond 0.00954 ( 18) link_NAG-ASN : angle 5.82426 ( 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 185 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 136 time to evaluate : 0.521 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 141 ARG cc_start: 0.6426 (ttm-80) cc_final: 0.6153 (ttp-170) REVERT: A 168 MET cc_start: 0.7164 (mpp) cc_final: 0.6620 (mmm) REVERT: B 124 ARG cc_start: 0.6819 (mmp-170) cc_final: 0.6209 (ptm160) REVERT: D 17 MET cc_start: 0.2640 (OUTLIER) cc_final: 0.2013 (mtt) REVERT: D 143 LYS cc_start: 0.6877 (mmmt) cc_final: 0.6476 (mmtp) REVERT: D 167 LEU cc_start: 0.7182 (pp) cc_final: 0.6855 (pp) REVERT: F 79 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8499 (m-30) REVERT: C 174 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8535 (p90) REVERT: C 260 MET cc_start: 0.8388 (mmm) cc_final: 0.7997 (mmm) REVERT: E 141 ARG cc_start: 0.6439 (ttm-80) cc_final: 0.5929 (ttp-170) REVERT: E 260 MET cc_start: 0.8446 (mmm) cc_final: 0.8193 (mmm) outliers start: 49 outliers final: 34 residues processed: 168 average time/residue: 0.1017 time to fit residues: 25.9320 Evaluate side-chains 155 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 266 SER Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain B residue 9 PHE Chi-restraints excluded: chain B residue 73 VAL 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 17 MET 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 98 LEU Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 38 ASN 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 277 CYS 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 268 MET Chi-restraints excluded: chain E residue 275 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 52 optimal weight: 0.4980 chunk 76 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 129 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 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** C 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.172851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.145454 restraints weight = 19948.495| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 2.43 r_work: 0.3951 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3831 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11886 Z= 0.163 Angle : 0.869 22.676 16158 Z= 0.411 Chirality : 0.054 0.711 1812 Planarity : 0.005 0.054 2085 Dihedral : 6.116 49.300 1935 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.10 % Allowed : 13.25 % Favored : 83.65 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.22), residues: 1434 helix: 1.62 (0.27), residues: 366 sheet: -0.33 (0.33), residues: 234 loop : -0.75 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 224 TYR 0.043 0.002 TYR D 162 PHE 0.020 0.002 PHE B 24 TRP 0.008 0.001 TRP E 222 HIS 0.008 0.001 HIS F 142 Details of bonding type rmsd covalent geometry : bond 0.00361 (11850) covalent geometry : angle 0.75352 (16068) SS BOND : bond 0.00421 ( 18) SS BOND : angle 4.32335 ( 36) hydrogen bonds : bond 0.03926 ( 486) hydrogen bonds : angle 5.20473 ( 1395) link_NAG-ASN : bond 0.01758 ( 18) link_NAG-ASN : angle 6.65545 ( 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 172 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.449 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: A 141 ARG cc_start: 0.6468 (ttm-80) cc_final: 0.6212 (ttp-170) REVERT: A 168 MET cc_start: 0.7187 (mpp) cc_final: 0.6804 (mmm) REVERT: D 17 MET cc_start: 0.3256 (mtm) cc_final: 0.2912 (mtt) REVERT: D 49 ASN cc_start: 0.5818 (m-40) cc_final: 0.5504 (m-40) REVERT: D 167 LEU cc_start: 0.7110 (pp) cc_final: 0.6738 (pp) REVERT: F 79 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8462 (m-30) REVERT: F 89 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8871 (mp) REVERT: F 124 ARG cc_start: 0.6637 (mmp-170) cc_final: 0.6407 (mmp-170) REVERT: C 260 MET cc_start: 0.8301 (mmm) cc_final: 0.7836 (mmm) REVERT: E 141 ARG cc_start: 0.6451 (ttm-80) cc_final: 0.6056 (ttp-170) REVERT: E 260 MET cc_start: 0.8470 (mmm) cc_final: 0.8242 (mmm) outliers start: 39 outliers final: 30 residues processed: 160 average time/residue: 0.1099 time to fit residues: 25.9111 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 : 0.453 ------------------------------------------------------------------------------- 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 275 ASP Chi-restraints excluded: chain A residue 287 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 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 79 ASP Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain E residue 38 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 32 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 13 optimal weight: 0.2980 chunk 82 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 135 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 137 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 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** C 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.172744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.145323 restraints weight = 19952.719| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.45 r_work: 0.3949 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3829 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 11886 Z= 0.156 Angle : 0.824 18.274 16158 Z= 0.395 Chirality : 0.053 0.644 1812 Planarity : 0.005 0.063 2085 Dihedral : 6.049 48.244 1935 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.33 % Allowed : 13.17 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.22), residues: 1434 helix: 1.64 (0.27), residues: 366 sheet: -0.34 (0.34), residues: 234 loop : -0.81 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 321 TYR 0.037 0.002 TYR B 162 PHE 0.028 0.002 PHE D 24 TRP 0.009 0.001 TRP B 21 HIS 0.005 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00360 (11850) covalent geometry : angle 0.72882 (16068) SS BOND : bond 0.00426 ( 18) SS BOND : angle 4.04583 ( 36) hydrogen bonds : bond 0.03936 ( 486) hydrogen bonds : angle 5.17208 ( 1395) link_NAG-ASN : bond 0.01174 ( 18) link_NAG-ASN : angle 5.85252 ( 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 177 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 0.462 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: A 141 ARG cc_start: 0.6499 (ttm-80) cc_final: 0.6231 (ttp-170) REVERT: A 168 MET cc_start: 0.7040 (mpp) cc_final: 0.6736 (mmm) REVERT: D 17 MET cc_start: 0.3436 (mtm) cc_final: 0.3100 (mtt) REVERT: D 167 LEU cc_start: 0.6777 (pp) cc_final: 0.6375 (pp) REVERT: C 260 MET cc_start: 0.8356 (mmm) cc_final: 0.7890 (mmm) REVERT: E 141 ARG cc_start: 0.6390 (ttm-80) cc_final: 0.6060 (ttp-170) REVERT: E 260 MET cc_start: 0.8487 (mmm) cc_final: 0.8266 (mmm) REVERT: E 312 ASN cc_start: 0.8150 (m-40) cc_final: 0.7749 (p0) outliers start: 42 outliers final: 32 residues processed: 167 average time/residue: 0.1087 time to fit residues: 26.9671 Evaluate side-chains 157 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 114 SER 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 275 ASP 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 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 98 LEU Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 322 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 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: chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 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 = 0.4355 r_free = 0.4355 target = 0.172143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.144528 restraints weight = 19905.614| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.44 r_work: 0.3941 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3821 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.6030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11886 Z= 0.162 Angle : 0.830 18.070 16158 Z= 0.397 Chirality : 0.051 0.623 1812 Planarity : 0.005 0.062 2085 Dihedral : 6.114 49.683 1935 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.10 % Allowed : 14.29 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.22), residues: 1434 helix: 1.60 (0.27), residues: 366 sheet: -0.37 (0.34), residues: 234 loop : -0.86 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 321 TYR 0.045 0.002 TYR B 162 PHE 0.022 0.002 PHE B 24 TRP 0.009 0.001 TRP B 92 HIS 0.007 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00377 (11850) covalent geometry : angle 0.74743 (16068) SS BOND : bond 0.00527 ( 18) SS BOND : angle 3.88535 ( 36) hydrogen bonds : bond 0.03947 ( 486) hydrogen bonds : angle 5.28730 ( 1395) link_NAG-ASN : bond 0.01132 ( 18) link_NAG-ASN : angle 5.45899 ( 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 169 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.502 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: A 168 MET cc_start: 0.7042 (mpp) cc_final: 0.6734 (mmm) REVERT: D 17 MET cc_start: 0.3579 (mtm) cc_final: 0.3207 (mtt) REVERT: F 143 LYS cc_start: 0.6500 (mmmt) cc_final: 0.5786 (mmmt) REVERT: C 260 MET cc_start: 0.8324 (mmm) cc_final: 0.7872 (mmm) REVERT: E 141 ARG cc_start: 0.6466 (ttm-80) cc_final: 0.6118 (ttp-170) REVERT: E 260 MET cc_start: 0.8480 (mmm) cc_final: 0.8242 (mmm) REVERT: E 312 ASN cc_start: 0.8129 (m-40) cc_final: 0.7767 (p0) outliers start: 39 outliers final: 33 residues processed: 159 average time/residue: 0.0985 time to fit residues: 23.9869 Evaluate side-chains 151 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 114 SER 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 275 ASP Chi-restraints excluded: chain B residue 9 PHE Chi-restraints excluded: chain B residue 79 ASP 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 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 C residue 38 ASN Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 277 CYS 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: chunk 103 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 118 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.171051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.143928 restraints weight = 20108.180| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.41 r_work: 0.3933 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3810 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.6232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 11886 Z= 0.175 Angle : 0.831 14.495 16158 Z= 0.402 Chirality : 0.050 0.592 1812 Planarity : 0.005 0.061 2085 Dihedral : 6.622 59.880 1935 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.62 % Allowed : 14.60 % Favored : 82.78 % 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 aren not related in a simple way. whole: -0.43 (0.22), residues: 1434 helix: 1.49 (0.27), residues: 366 sheet: -0.28 (0.36), residues: 204 loop : -1.11 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 124 TYR 0.034 0.002 TYR F 162 PHE 0.022 0.002 PHE B 24 TRP 0.010 0.001 TRP A 84 HIS 0.009 0.002 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00403 (11850) covalent geometry : angle 0.76565 (16068) SS BOND : bond 0.00655 ( 18) SS BOND : angle 3.93599 ( 36) hydrogen bonds : bond 0.04038 ( 486) hydrogen bonds : angle 5.40498 ( 1395) link_NAG-ASN : bond 0.00900 ( 18) link_NAG-ASN : angle 4.65278 ( 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 158 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.487 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: A 168 MET cc_start: 0.7053 (mpp) cc_final: 0.6700 (mmm) REVERT: A 312 ASN cc_start: 0.7653 (m-40) cc_final: 0.7340 (p0) REVERT: B 42 GLN cc_start: 0.7388 (mm-40) cc_final: 0.7050 (mm-40) REVERT: D 17 MET cc_start: 0.3818 (mtm) cc_final: 0.3535 (mtt) REVERT: D 124 ARG cc_start: 0.6625 (mmp-170) cc_final: 0.6220 (ttp-170) REVERT: C 260 MET cc_start: 0.8357 (mmm) cc_final: 0.7925 (mmm) REVERT: E 141 ARG cc_start: 0.6535 (ttm-80) cc_final: 0.6304 (ttp-170) REVERT: E 312 ASN cc_start: 0.8167 (m-40) cc_final: 0.7804 (p0) outliers start: 33 outliers final: 33 residues processed: 148 average time/residue: 0.0966 time to fit residues: 21.8310 Evaluate side-chains 154 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 114 SER 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 275 ASP Chi-restraints excluded: chain B residue 9 PHE Chi-restraints excluded: chain B residue 79 ASP 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 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 167 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 202 VAL 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: chunk 24 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 104 optimal weight: 0.0970 chunk 27 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 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** F 142 HIS C 250 ASN ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.171288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.144038 restraints weight = 20293.082| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.45 r_work: 0.3939 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3820 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.6401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 11886 Z= 0.159 Angle : 0.811 12.879 16158 Z= 0.397 Chirality : 0.049 0.559 1812 Planarity : 0.005 0.060 2085 Dihedral : 6.387 52.083 1935 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.70 % Allowed : 14.92 % Favored : 82.38 % 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 aren not related in a simple way. whole: -0.40 (0.22), residues: 1434 helix: 1.45 (0.27), residues: 366 sheet: -0.52 (0.34), residues: 240 loop : -1.00 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 153 TYR 0.029 0.002 TYR F 162 PHE 0.021 0.002 PHE D 138 TRP 0.009 0.001 TRP A 84 HIS 0.009 0.002 HIS F 142 Details of bonding type rmsd covalent geometry : bond 0.00369 (11850) covalent geometry : angle 0.75339 (16068) SS BOND : bond 0.00384 ( 18) SS BOND : angle 4.02202 ( 36) hydrogen bonds : bond 0.04046 ( 486) hydrogen bonds : angle 5.38001 ( 1395) link_NAG-ASN : bond 0.00767 ( 18) link_NAG-ASN : angle 4.15641 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2844.15 seconds wall clock time: 49 minutes 54.03 seconds (2994.03 seconds total)