Starting phenix.real_space_refine on Sat Oct 24 00:42:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cxu_45998/10_2026/9cxu_45998.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cxu_45998/10_2026/9cxu_45998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cxu_45998/10_2026/9cxu_45998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cxu_45998/10_2026/9cxu_45998.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cxu_45998/10_2026/9cxu_45998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cxu_45998/10_2026/9cxu_45998.map" } resolution = 2.3 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= 0.065 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 7182 2.51 5 N 2007 2.21 5 O 2283 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11529 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} Link IDs: {'TRANS': 164} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 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: 2.58, per 1000 atoms: 0.22 Number of scatterers: 11529 At special positions: 0 Unit cell: (87.4, 83.95, 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 2283 8.00 N 2007 7.00 C 7182 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=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.07 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS C 14 " distance=2.64 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.07 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG CYS E 14 " distance=2.64 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.07 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.08 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.02 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.08 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.02 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 81 " " NAG A 402 " - " ASN A 165 " " NAG A 403 " - " ASN A 285 " " NAG B 501 " - " ASN B 154 " " NAG C 401 " - " ASN C 81 " " NAG C 402 " - " ASN C 165 " " NAG C 403 " - " ASN C 285 " " NAG D 501 " - " ASN D 154 " " NAG E 401 " - " ASN E 81 " " NAG E 402 " - " ASN E 165 " " NAG E 403 " - " ASN E 285 " " NAG F 501 " - " ASN F 154 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 506.4 milliseconds 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2658 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 36 sheets defined 28.2% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 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: 5.064A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 3.702A 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: 3.782A pdb=" N THR A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.329A 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: 4.005A 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: 4.006A 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: 4.006A 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: 3.862A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.065A 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: 3.781A pdb=" N THR C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.329A 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: 5.065A pdb=" N VAL E 78 " --> pdb=" O HIS E 75 " (cutoff:3.500A) removed outlier: 3.702A 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: 4.329A 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: 6.442A 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: 3.686A 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: 6.758A 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: 7.022A pdb=" N ASP A 101 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.523A 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: 7.022A pdb=" N ASP A 101 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N TRP A 234 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 7.774A 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: 11.124A 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: 6.167A 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: 7.021A 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: 5.022A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.523A 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: 7.021A 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: 7.774A 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: 7.406A pdb=" N ALA C 138 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 11.123A 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: 4.411A 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: 3.685A 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: 6.758A 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: 6.523A 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: 7.774A 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: 11.123A 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: 4.410A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) 516 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 1.15 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: 2698 1.32 - 1.46: 3957 1.46 - 1.60: 5030 1.60 - 1.74: 12 1.74 - 1.88: 69 Bond restraints: 11766 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=" CB ASN E 250 " pdb=" CG ASN E 250 " ideal model delta sigma weight residual 1.516 1.391 0.125 2.50e-02 1.60e+03 2.50e+01 bond pdb=" CG PHE F 171 " pdb=" CD2 PHE F 171 " ideal model delta sigma weight residual 1.384 1.488 -0.104 2.10e-02 2.27e+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 2.46e+01 bond pdb=" CG PHE D 171 " pdb=" CD2 PHE D 171 " ideal model delta sigma weight residual 1.384 1.488 -0.104 2.10e-02 2.27e+03 2.44e+01 ... (remaining 11761 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 14212 2.60 - 5.21: 1521 5.21 - 7.81: 185 7.81 - 10.42: 33 10.42 - 13.02: 3 Bond angle restraints: 15954 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 111.90 103.39 8.51 8.10e-01 1.52e+00 1.10e+02 angle pdb=" N ILE F 10 " pdb=" CA ILE F 10 " pdb=" C ILE F 10 " ideal model delta sigma weight residual 111.90 103.45 8.45 8.10e-01 1.52e+00 1.09e+02 angle pdb=" N ILE D 10 " pdb=" CA ILE D 10 " pdb=" C ILE D 10 " ideal model delta sigma weight residual 111.90 103.47 8.43 8.10e-01 1.52e+00 1.08e+02 angle pdb=" C ILE A 214 " pdb=" N PRO A 215 " pdb=" CA PRO A 215 " ideal model delta sigma weight residual 119.78 128.18 -8.40 1.03e+00 9.43e-01 6.66e+01 angle pdb=" C ILE C 214 " pdb=" N PRO C 215 " pdb=" CA PRO C 215 " ideal model delta sigma weight residual 119.78 128.15 -8.37 1.03e+00 9.43e-01 6.60e+01 ... (remaining 15949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 6922 17.70 - 35.39: 203 35.39 - 53.09: 48 53.09 - 70.79: 27 70.79 - 88.48: 21 Dihedral angle restraints: 7221 sinusoidal: 3075 harmonic: 4146 Sorted by residual: 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 -113.92 -8.68 0 2.50e+00 1.60e-01 1.20e+01 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 -113.92 -8.68 0 2.50e+00 1.60e-01 1.20e+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 -113.95 -8.65 0 2.50e+00 1.60e-01 1.20e+01 ... (remaining 7218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1210 0.090 - 0.181: 447 0.181 - 0.271: 101 0.271 - 0.361: 15 0.361 - 0.452: 9 Chirality restraints: 1782 Sorted by residual: chirality pdb=" C2 NAG A 401 " pdb=" C1 NAG A 401 " pdb=" C3 NAG A 401 " pdb=" N2 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.49 -2.94 0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" C2 NAG E 401 " pdb=" C1 NAG E 401 " pdb=" C3 NAG E 401 " pdb=" N2 NAG E 401 " both_signs ideal model delta sigma weight residual False -2.49 -2.94 0.45 2.00e-01 2.50e+01 5.07e+00 chirality pdb=" C2 NAG B 501 " pdb=" C1 NAG B 501 " pdb=" C3 NAG B 501 " pdb=" N2 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.49 -2.94 0.45 2.00e-01 2.50e+01 5.05e+00 ... (remaining 1779 not shown) Planarity restraints: 2091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 403 " 0.216 2.00e-02 2.50e+03 1.84e-01 4.23e+02 pdb=" C7 NAG C 403 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG C 403 " 0.150 2.00e-02 2.50e+03 pdb=" N2 NAG C 403 " -0.311 2.00e-02 2.50e+03 pdb=" O7 NAG C 403 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 403 " -0.216 2.00e-02 2.50e+03 1.84e-01 4.23e+02 pdb=" C7 NAG E 403 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG E 403 " -0.150 2.00e-02 2.50e+03 pdb=" N2 NAG E 403 " 0.311 2.00e-02 2.50e+03 pdb=" O7 NAG E 403 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 403 " -0.216 2.00e-02 2.50e+03 1.84e-01 4.22e+02 pdb=" C7 NAG A 403 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG A 403 " -0.150 2.00e-02 2.50e+03 pdb=" N2 NAG A 403 " 0.311 2.00e-02 2.50e+03 pdb=" O7 NAG A 403 " -0.001 2.00e-02 2.50e+03 ... (remaining 2088 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 9 2.42 - 3.04: 7230 3.04 - 3.66: 17143 3.66 - 4.28: 28019 4.28 - 4.90: 45651 Nonbonded interactions: 98052 Sorted by model distance: nonbonded pdb=" NE ARG C 220 " pdb=" OE1 GLN E 210 " model vdw 1.802 3.120 nonbonded pdb=" NE ARG A 220 " pdb=" OE1 GLN C 210 " model vdw 1.802 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 1.845 3.120 nonbonded pdb=" OD1 ASP A 73 " pdb=" ND1 HIS A 75 " model vdw 1.847 3.120 ... (remaining 98047 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: 3.060 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.490 Find NCS groups from input model: 0.090 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:8.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 0.615 11796 Z= 1.206 Angle : 1.727 13.023 16026 Z= 1.175 Chirality : 0.101 0.452 1782 Planarity : 0.013 0.184 2079 Dihedral : 11.298 88.482 4509 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.19), residues: 1434 helix: 0.32 (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 A 195 PHE 0.036 0.009 PHE F 171 TRP 0.020 0.006 TRP E 84 HIS 0.010 0.003 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.02094 / 1.10 (11766) covalent geometry : angle 1.71778 / 1.17 (15954) SS BOND : bond 0.25155 / 15.64 ( 18) SS BOND : angle 3.42620 / 2.19 ( 36) hydrogen bonds : bond 0.14412 / 9.94 ( 486) hydrogen bonds : angle 7.23663 / 5.01 ( 1395) link_NAG-ASN : bond 0.05283 / 3.95 ( 12) link_NAG-ASN : angle 2.96589 / 1.87 ( 36) *********************** 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 277 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 260 MET cc_start: 0.7890 (mtp) cc_final: 0.7429 (mtp) REVERT: D 57 GLU cc_start: 0.5751 (pt0) cc_final: 0.5383 (tt0) REVERT: D 60 ASN cc_start: 0.7052 (m-40) cc_final: 0.6785 (m110) REVERT: C 168 MET cc_start: 0.8262 (tpp) cc_final: 0.7875 (tpp) REVERT: C 320 MET cc_start: 0.8651 (ptp) cc_final: 0.8212 (ptp) REVERT: E 168 MET cc_start: 0.8302 (tpp) cc_final: 0.8054 (tpp) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.6573 time to fit residues: 194.3120 Evaluate side-chains 141 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 GLN A 132 GLN A 133 ASN A 188 ASN B 42 GLN B 64 HIS B 78 GLN D 64 HIS D 78 GLN F 42 GLN F 60 ASN F 64 HIS F 78 GLN ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN C 188 ASN C 312 ASN E 80 GLN E 132 GLN E 133 ASN E 188 ASN E 312 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.148794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.127335 restraints weight = 11740.374| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.21 r_work: 0.3348 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11796 Z= 0.159 Angle : 0.628 9.064 16026 Z= 0.338 Chirality : 0.046 0.263 1782 Planarity : 0.005 0.037 2079 Dihedral : 6.095 50.420 1809 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.11 % Allowed : 8.17 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.21), residues: 1434 helix: 1.77 (0.26), residues: 354 sheet: 0.42 (0.29), residues: 291 loop : -0.06 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 150 TYR 0.012 0.002 TYR F 157 PHE 0.018 0.002 PHE B 24 TRP 0.011 0.002 TRP D 92 HIS 0.008 0.002 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (11766) covalent geometry : angle 0.61236 / 0.34 (15954) SS BOND : bond 0.00237 / 0.18 ( 18) SS BOND : angle 1.18929 / 0.80 ( 36) hydrogen bonds : bond 0.05258 / 3.64 ( 486) hydrogen bonds : angle 5.09664 / 3.52 ( 1395) link_NAG-ASN : bond 0.00640 / 0.42 ( 12) link_NAG-ASN : angle 2.77995 / 1.80 ( 36) *********************** 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 171 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8066 (ttt90) REVERT: A 111 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7949 (tt) REVERT: A 210 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8059 (pm20) REVERT: B 150 GLU cc_start: 0.6657 (mm-30) cc_final: 0.6329 (tp30) REVERT: D 12 ASN cc_start: 0.6753 (p0) cc_final: 0.6505 (p0) REVERT: D 57 GLU cc_start: 0.6168 (pt0) cc_final: 0.5588 (tt0) REVERT: D 60 ASN cc_start: 0.7237 (m-40) cc_final: 0.7010 (m110) REVERT: F 39 LYS cc_start: 0.8614 (ttmm) cc_final: 0.8234 (tttt) REVERT: C 111 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7901 (tt) REVERT: C 172 ASP cc_start: 0.8620 (m-30) cc_final: 0.8409 (m-30) REVERT: C 210 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.7578 (pm20) REVERT: E 111 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7910 (tt) outliers start: 14 outliers final: 4 residues processed: 160 average time/residue: 0.6563 time to fit residues: 112.5988 Evaluate side-chains 141 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 111 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [40, 84, 76, 135, 28, 139, 34, 87, 105, 47, 37] chunk 40 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 47 optimal weight: 0.0370 chunk 37 optimal weight: 2.9990 overall best weight: 1.1060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN B 42 GLN D 49 ASN F 49 ASN F 60 ASN F 106 HIS ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.144414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.121157 restraints weight = 11698.110| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.30 r_work: 0.3286 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11796 Z= 0.169 Angle : 0.598 11.248 16026 Z= 0.318 Chirality : 0.047 0.280 1782 Planarity : 0.005 0.043 2079 Dihedral : 5.942 45.720 1809 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.43 % Allowed : 9.68 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.21), residues: 1434 helix: 1.78 (0.27), residues: 363 sheet: 0.34 (0.30), residues: 261 loop : -0.24 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 150 TYR 0.019 0.002 TYR A 195 PHE 0.018 0.002 PHE D 24 TRP 0.010 0.002 TRP F 92 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (11766) covalent geometry : angle 0.58675 / 0.32 (15954) SS BOND : bond 0.00168 / 0.12 ( 18) SS BOND : angle 0.98757 / 0.66 ( 36) hydrogen bonds : bond 0.05133 / 3.58 ( 486) hydrogen bonds : angle 5.00358 / 3.46 ( 1395) link_NAG-ASN : bond 0.00448 / 0.28 ( 12) link_NAG-ASN : angle 2.38704 / 1.49 ( 36) *********************** 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 156 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8134 (ttt90) REVERT: A 111 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8037 (tt) REVERT: A 210 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8059 (pm20) REVERT: B 34 GLN cc_start: 0.8639 (tt0) cc_final: 0.8437 (tt0) REVERT: B 143 LYS cc_start: 0.8208 (mttt) cc_final: 0.8002 (mmtt) REVERT: D 57 GLU cc_start: 0.5962 (pt0) cc_final: 0.5475 (tt0) REVERT: F 39 LYS cc_start: 0.8671 (ttmm) cc_final: 0.8399 (mmmt) REVERT: C 111 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8099 (tt) REVERT: C 210 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7608 (pm20) REVERT: E 194 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8004 (mt) outliers start: 18 outliers final: 7 residues processed: 146 average time/residue: 0.6679 time to fit residues: 104.3121 Evaluate side-chains 130 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 280 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [25, 82, 38, 31, 93, 50, 73, 76, 28, 56, 23] chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 GLN D 12 ASN D 60 ASN F 26 HIS F 60 ASN F 106 HIS C 18 HIS ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.141496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118587 restraints weight = 11760.512| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.29 r_work: 0.3252 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11796 Z= 0.217 Angle : 0.642 11.256 16026 Z= 0.342 Chirality : 0.050 0.361 1782 Planarity : 0.005 0.043 2079 Dihedral : 6.191 48.406 1809 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.14 % Allowed : 10.48 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.20), residues: 1434 helix: 1.59 (0.26), residues: 363 sheet: -0.12 (0.27), residues: 291 loop : -0.60 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 150 TYR 0.016 0.003 TYR E 195 PHE 0.017 0.003 PHE F 24 TRP 0.012 0.002 TRP F 92 HIS 0.008 0.002 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.22 (11766) covalent geometry : angle 0.62442 / 0.34 (15954) SS BOND : bond 0.00254 / 0.18 ( 18) SS BOND : angle 1.00474 / 0.66 ( 36) hydrogen bonds : bond 0.05551 / 3.88 ( 486) hydrogen bonds : angle 5.11652 / 3.54 ( 1395) link_NAG-ASN : bond 0.00550 / 0.33 ( 12) link_NAG-ASN : angle 3.09327 / 1.94 ( 36) *********************** 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 148 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.439 Fit side-chains REVERT: A 57 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8185 (ttt90) REVERT: A 111 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8113 (tt) REVERT: A 210 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8099 (pm20) REVERT: D 57 GLU cc_start: 0.5956 (pt0) cc_final: 0.5452 (tt0) REVERT: F 39 LYS cc_start: 0.8679 (ttmm) cc_final: 0.8418 (mmmt) REVERT: C 111 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8157 (tt) REVERT: C 210 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: E 78 VAL cc_start: 0.8959 (m) cc_final: 0.8705 (p) REVERT: E 121 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8574 (mm) REVERT: E 194 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7644 (mt) REVERT: E 321 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8268 (ptp-110) outliers start: 27 outliers final: 8 residues processed: 135 average time/residue: 0.5985 time to fit residues: 87.1178 Evaluate side-chains 134 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 280 GLU Chi-restraints excluded: chain E residue 321 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [82, 56, 118, 75, 74, 27, 81, 119, 10, 80, 52] chunk 82 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 52 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 60 ASN E 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.143516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.122590 restraints weight = 11711.271| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.19 r_work: 0.3291 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11796 Z= 0.121 Angle : 0.528 8.526 16026 Z= 0.278 Chirality : 0.045 0.398 1782 Planarity : 0.004 0.042 2079 Dihedral : 5.734 47.352 1809 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.11 % Allowed : 11.59 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.21), residues: 1434 helix: 2.08 (0.26), residues: 363 sheet: -0.05 (0.27), residues: 291 loop : -0.63 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 150 TYR 0.013 0.001 TYR F 157 PHE 0.011 0.001 PHE F 24 TRP 0.010 0.001 TRP F 92 HIS 0.003 0.001 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (11766) covalent geometry : angle 0.51344 / 0.28 (15954) SS BOND : bond 0.00176 / 0.13 ( 18) SS BOND : angle 0.82196 / 0.53 ( 36) hydrogen bonds : bond 0.04636 / 3.23 ( 486) hydrogen bonds : angle 4.85869 / 3.35 ( 1395) link_NAG-ASN : bond 0.00534 / 0.34 ( 12) link_NAG-ASN : angle 2.58453 / 1.73 ( 36) *********************** 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 138 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8213 (ttt90) REVERT: A 210 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8040 (pm20) REVERT: B 39 LYS cc_start: 0.8625 (ttmm) cc_final: 0.7907 (tptp) REVERT: B 143 LYS cc_start: 0.7237 (mmtm) cc_final: 0.7025 (mmtt) REVERT: F 39 LYS cc_start: 0.8648 (ttmm) cc_final: 0.8391 (mmmt) REVERT: C 111 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8019 (tt) REVERT: C 321 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8398 (ptp-110) REVERT: E 78 VAL cc_start: 0.8927 (m) cc_final: 0.8690 (p) REVERT: E 194 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8041 (mt) outliers start: 14 outliers final: 2 residues processed: 132 average time/residue: 0.6022 time to fit residues: 85.4288 Evaluate side-chains 123 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 280 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [116, 110, 8, 88, 111, 32, 25, 14, 119, 2, 53] chunk 116 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.140368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117812 restraints weight = 11725.243| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.27 r_work: 0.3243 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11796 Z= 0.233 Angle : 0.655 11.049 16026 Z= 0.346 Chirality : 0.052 0.505 1782 Planarity : 0.005 0.046 2079 Dihedral : 6.300 50.088 1809 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.51 % Allowed : 11.67 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.20), residues: 1434 helix: 1.69 (0.26), residues: 363 sheet: -0.41 (0.27), residues: 303 loop : -0.77 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 150 TYR 0.015 0.003 TYR F 157 PHE 0.022 0.003 PHE F 24 TRP 0.012 0.002 TRP F 92 HIS 0.007 0.002 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.23 (11766) covalent geometry : angle 0.63610 / 0.34 (15954) SS BOND : bond 0.00273 / 0.19 ( 18) SS BOND : angle 0.99395 / 0.66 ( 36) hydrogen bonds : bond 0.05600 / 3.93 ( 486) hydrogen bonds : angle 5.10805 / 3.54 ( 1395) link_NAG-ASN : bond 0.00570 / 0.36 ( 12) link_NAG-ASN : angle 3.30291 / 2.12 ( 36) *********************** 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 134 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.446 Fit side-chains REVERT: A 57 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8196 (ttt90) REVERT: A 210 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8112 (pm20) REVERT: A 268 MET cc_start: 0.9294 (ttm) cc_final: 0.8700 (ttm) REVERT: B 143 LYS cc_start: 0.7330 (mmtm) cc_final: 0.7091 (mmtt) REVERT: F 39 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8415 (mmmt) REVERT: C 111 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8176 (tt) REVERT: C 168 MET cc_start: 0.8811 (tpp) cc_final: 0.8488 (tpp) REVERT: C 210 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.7582 (pm20) REVERT: C 321 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8346 (ptp-110) REVERT: E 78 VAL cc_start: 0.8958 (m) cc_final: 0.8749 (p) REVERT: E 194 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8073 (mt) REVERT: E 210 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8212 (pt0) outliers start: 19 outliers final: 6 residues processed: 124 average time/residue: 0.5871 time to fit residues: 78.6184 Evaluate side-chains 126 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 280 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [102, 27, 1, 6, 129, 4, 36, 116, 138, 92, 53] chunk 102 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.142161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.121557 restraints weight = 11741.192| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.17 r_work: 0.3276 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11796 Z= 0.136 Angle : 0.562 10.021 16026 Z= 0.292 Chirality : 0.049 0.608 1782 Planarity : 0.004 0.043 2079 Dihedral : 6.171 54.680 1809 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.11 % Allowed : 12.46 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.20), residues: 1434 helix: 2.18 (0.26), residues: 363 sheet: -0.14 (0.27), residues: 291 loop : -0.77 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 150 TYR 0.014 0.001 TYR F 157 PHE 0.019 0.002 PHE F 24 TRP 0.011 0.001 TRP F 92 HIS 0.003 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (11766) covalent geometry : angle 0.53740 / 0.29 (15954) SS BOND : bond 0.00197 / 0.15 ( 18) SS BOND : angle 0.81825 / 0.53 ( 36) hydrogen bonds : bond 0.04796 / 3.35 ( 486) hydrogen bonds : angle 4.92638 / 3.40 ( 1395) link_NAG-ASN : bond 0.00634 / 0.40 ( 12) link_NAG-ASN : angle 3.48009 / 2.39 ( 36) *********************** 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 133 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8162 (ttt90) REVERT: A 210 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8038 (pm20) REVERT: A 268 MET cc_start: 0.9292 (ttm) cc_final: 0.8719 (ttm) REVERT: B 39 LYS cc_start: 0.8600 (ttmm) cc_final: 0.7873 (tptp) REVERT: B 143 LYS cc_start: 0.7304 (mmtm) cc_final: 0.7087 (mmtt) REVERT: D 39 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8447 (tppp) REVERT: D 127 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8081 (mmm-85) REVERT: F 39 LYS cc_start: 0.8648 (ttmm) cc_final: 0.8409 (mmmt) REVERT: C 111 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8038 (tt) REVERT: C 210 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.7571 (pm20) REVERT: C 321 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8411 (ptp-110) REVERT: E 78 VAL cc_start: 0.8921 (m) cc_final: 0.8713 (p) outliers start: 14 outliers final: 5 residues processed: 127 average time/residue: 0.6258 time to fit residues: 85.3518 Evaluate side-chains 126 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 127 ARG Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 280 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [18, 113, 20, 34, 33, 57, 1, 109, 41, 17, 56] chunk 18 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 0.0020 chunk 109 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.142607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122103 restraints weight = 11758.893| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.17 r_work: 0.3284 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11796 Z= 0.127 Angle : 0.552 10.706 16026 Z= 0.286 Chirality : 0.049 0.610 1782 Planarity : 0.004 0.045 2079 Dihedral : 6.053 54.202 1809 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.95 % Allowed : 12.70 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.21), residues: 1434 helix: 2.43 (0.26), residues: 363 sheet: -0.11 (0.27), residues: 291 loop : -0.76 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 141 TYR 0.013 0.001 TYR F 157 PHE 0.017 0.001 PHE F 24 TRP 0.011 0.001 TRP F 92 HIS 0.003 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (11766) covalent geometry : angle 0.52881 / 0.28 (15954) SS BOND : bond 0.00188 / 0.14 ( 18) SS BOND : angle 0.78127 / 0.50 ( 36) hydrogen bonds : bond 0.04618 / 3.22 ( 486) hydrogen bonds : angle 4.83661 / 3.34 ( 1395) link_NAG-ASN : bond 0.00685 / 0.43 ( 12) link_NAG-ASN : angle 3.30766 / 2.32 ( 36) *********************** 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 127 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.446 Fit side-chains REVERT: A 57 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8144 (ttt90) REVERT: A 210 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8024 (pm20) REVERT: A 268 MET cc_start: 0.9291 (ttm) cc_final: 0.8727 (ttm) REVERT: B 39 LYS cc_start: 0.8616 (ttmm) cc_final: 0.7907 (tptp) REVERT: B 143 LYS cc_start: 0.7336 (mmtm) cc_final: 0.7134 (mmtt) REVERT: D 39 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8454 (tppp) REVERT: D 127 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7944 (mmm-85) REVERT: F 39 LYS cc_start: 0.8643 (ttmm) cc_final: 0.8409 (mmmt) REVERT: C 111 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8034 (tt) REVERT: C 210 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.7564 (pm20) REVERT: C 321 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8458 (ptp-110) REVERT: E 78 VAL cc_start: 0.8933 (m) cc_final: 0.8718 (p) outliers start: 12 outliers final: 6 residues processed: 122 average time/residue: 0.6594 time to fit residues: 86.5660 Evaluate side-chains 126 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 127 ARG Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 280 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [55, 12, 99, 28, 95, 97, 37, 24, 87, 121, 93] chunk 55 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.141440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.120989 restraints weight = 11643.549| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.17 r_work: 0.3272 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11796 Z= 0.173 Angle : 0.609 11.309 16026 Z= 0.317 Chirality : 0.053 0.644 1782 Planarity : 0.005 0.043 2079 Dihedral : 6.123 53.016 1809 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.11 % Allowed : 12.62 % 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 are not related in a simple way. whole: 0.25 (0.21), residues: 1434 helix: 2.55 (0.26), residues: 348 sheet: -0.34 (0.26), residues: 327 loop : -0.74 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 150 TYR 0.014 0.002 TYR F 157 PHE 0.018 0.002 PHE F 24 TRP 0.010 0.002 TRP F 92 HIS 0.004 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (11766) covalent geometry : angle 0.58171 / 0.31 (15954) SS BOND : bond 0.00211 / 0.16 ( 18) SS BOND : angle 0.85347 / 0.56 ( 36) hydrogen bonds : bond 0.05041 / 3.53 ( 486) hydrogen bonds : angle 4.93597 / 3.41 ( 1395) link_NAG-ASN : bond 0.00702 / 0.46 ( 12) link_NAG-ASN : angle 3.76651 / 2.55 ( 36) *********************** 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 129 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8191 (ttt90) REVERT: A 210 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8069 (pm20) REVERT: A 268 MET cc_start: 0.9268 (ttm) cc_final: 0.8682 (ttm) REVERT: B 39 LYS cc_start: 0.8621 (ttmm) cc_final: 0.7884 (tptp) REVERT: B 143 LYS cc_start: 0.7334 (mmtm) cc_final: 0.7012 (mmtt) REVERT: D 39 LYS cc_start: 0.8705 (ttmm) cc_final: 0.8455 (tppp) REVERT: D 127 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7185 (mtt180) REVERT: F 39 LYS cc_start: 0.8638 (ttmm) cc_final: 0.8412 (mmmt) REVERT: C 111 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8114 (tt) REVERT: C 210 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.7604 (pm20) REVERT: C 321 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8393 (ptp-110) REVERT: E 78 VAL cc_start: 0.8945 (m) cc_final: 0.8734 (p) REVERT: E 210 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8164 (pt0) outliers start: 14 outliers final: 7 residues processed: 123 average time/residue: 0.6146 time to fit residues: 81.4148 Evaluate side-chains 128 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 127 ARG Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 280 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [48, 38, 131, 72, 64, 21, 89, 136, 61, 133, 82] chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.141858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.121356 restraints weight = 11780.854| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.18 r_work: 0.3277 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11796 Z= 0.154 Angle : 0.587 11.119 16026 Z= 0.305 Chirality : 0.051 0.577 1782 Planarity : 0.004 0.043 2079 Dihedral : 5.895 51.512 1809 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.19 % Allowed : 12.86 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.21), residues: 1434 helix: 2.36 (0.26), residues: 363 sheet: -0.35 (0.26), residues: 327 loop : -0.69 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 150 TYR 0.013 0.002 TYR F 157 PHE 0.018 0.002 PHE F 24 TRP 0.011 0.001 TRP F 92 HIS 0.003 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (11766) covalent geometry : angle 0.56006 / 0.30 (15954) SS BOND : bond 0.00219 / 0.16 ( 18) SS BOND : angle 0.80529 / 0.52 ( 36) hydrogen bonds : bond 0.04857 / 3.40 ( 486) hydrogen bonds : angle 4.88395 / 3.38 ( 1395) link_NAG-ASN : bond 0.00732 / 0.45 ( 12) link_NAG-ASN : angle 3.68277 / 2.48 ( 36) ********************** 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 124 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8157 (ttt90) REVERT: A 70 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8269 (tp) REVERT: A 210 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8037 (pm20) REVERT: A 268 MET cc_start: 0.9267 (ttm) cc_final: 0.8684 (ttm) REVERT: B 39 LYS cc_start: 0.8607 (ttmm) cc_final: 0.7877 (tptp) REVERT: B 143 LYS cc_start: 0.7330 (mmtm) cc_final: 0.7011 (mmtt) REVERT: D 39 LYS cc_start: 0.8708 (ttmm) cc_final: 0.8462 (tppp) REVERT: D 42 GLN cc_start: 0.8374 (tp-100) cc_final: 0.8153 (tp40) REVERT: D 127 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7106 (mtt180) REVERT: F 39 LYS cc_start: 0.8633 (ttmm) cc_final: 0.8411 (mmmt) REVERT: C 111 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8082 (tt) REVERT: C 210 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.7586 (pm20) REVERT: C 321 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8464 (ptp-110) REVERT: E 78 VAL cc_start: 0.8927 (m) cc_final: 0.8713 (p) REVERT: E 210 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8157 (pt0) outliers start: 15 outliers final: 7 residues processed: 118 average time/residue: 0.6399 time to fit residues: 81.4745 Evaluate side-chains 123 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 127 ARG Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 280 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: [136, 82, 118, 38, 87, 126, 36, 59, 49, 2, 7] chunk 136 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 36 optimal weight: 0.0670 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.142288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.121917 restraints weight = 11754.206| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.17 r_work: 0.3284 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11796 Z= 0.142 Angle : 0.573 11.509 16026 Z= 0.297 Chirality : 0.051 0.613 1782 Planarity : 0.004 0.043 2079 Dihedral : 5.635 50.440 1809 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.19 % Allowed : 12.94 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.21), residues: 1434 helix: 2.46 (0.26), residues: 363 sheet: -0.33 (0.26), residues: 327 loop : -0.64 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 141 TYR 0.013 0.002 TYR F 157 PHE 0.017 0.002 PHE F 24 TRP 0.011 0.001 TRP F 92 HIS 0.003 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (11766) covalent geometry : angle 0.54783 / 0.29 (15954) SS BOND : bond 0.00196 / 0.15 ( 18) SS BOND : angle 0.77585 / 0.50 ( 36) hydrogen bonds : bond 0.04750 / 3.32 ( 486) hydrogen bonds : angle 4.80839 / 3.33 ( 1395) link_NAG-ASN : bond 0.00804 / 0.46 ( 12) link_NAG-ASN : angle 3.54939 / 2.37 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4061.41 seconds wall clock time: 70 minutes 3.88 seconds (4203.88 seconds total)