Starting phenix.real_space_refine on Wed Sep 17 22:24:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cxu_45998/09_2025/9cxu_45998.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cxu_45998/09_2025/9cxu_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cxu_45998/09_2025/9cxu_45998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cxu_45998/09_2025/9cxu_45998.map" model { file = "/net/cci-nas-00/data/ceres_data/9cxu_45998/09_2025/9cxu_45998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cxu_45998/09_2025/9cxu_45998.cif" } 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-2.0-5805/lib/python3.9/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: 2.41, per 1000 atoms: 0.21 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 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=2.02 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 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: 1.06 Conformation dependent library (CDL) restraints added in 559.0 milliseconds Enol-peptide restraints added in 1.7 microseconds 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: 0.55 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: 1.87 Time building geometry restraints manager: 1.38 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: 6924 17.70 - 35.39: 201 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: 2.090 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: 0.040 Set scattering table: 0.030 Process input model: 11.570 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:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 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 aren 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 covalent geometry : bond 0.02094 (11766) covalent geometry : angle 1.71778 (15954) SS BOND : bond 0.25155 ( 18) SS BOND : angle 3.42620 ( 36) hydrogen bonds : bond 0.14412 ( 486) hydrogen bonds : angle 7.23663 ( 1395) link_NAG-ASN : bond 0.05283 ( 12) link_NAG-ASN : angle 2.96589 ( 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 : 0.304 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: 0.7406 time to fit residues: 217.9882 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 : 0.463 ------------------------------------------------------------------------------- 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: 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... Flipped N/Q/H residues before XYZ refinement: 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 = 11740.370| |-----------------------------------------------------------------------------| 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: 0.8319 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 aren 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 covalent geometry : bond 0.00341 (11766) covalent geometry : angle 0.61236 (15954) SS BOND : bond 0.00237 ( 18) SS BOND : angle 1.18929 ( 36) hydrogen bonds : bond 0.05258 ( 486) hydrogen bonds : angle 5.09664 ( 1395) link_NAG-ASN : bond 0.00640 ( 12) link_NAG-ASN : angle 2.77995 ( 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 : 0.536 Fit side-chains revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8067 (ttt90) REVERT: A 111 LEU cc_start: 0.8159 (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: 0.6658 (mm-30) cc_final: 0.6330 (tp30) REVERT: D 12 ASN cc_start: 0.6754 (p0) cc_final: 0.6505 (p0) REVERT: D 57 GLU cc_start: 0.6167 (pt0) cc_final: 0.5588 (tt0) REVERT: D 60 ASN cc_start: 0.7236 (m-40) cc_final: 0.7009 (m110) REVERT: F 39 LYS cc_start: 0.8613 (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: 0.8619 (m-30) cc_final: 0.8408 (m-30) REVERT: C 210 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.7577 (pm20) REVERT: E 111 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7911 (tt) outliers start: 14 outliers final: 4 residues processed: 160 average time/residue: 0.8073 time to fit residues: 137.5950 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 : 0.476 ------------------------------------------------------------------------------- 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: chunk 40 optimal weight: 4.9990 chunk 84 optimal weight: 0.0050 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: 0.9990 chunk 105 optimal weight: 1.9990 chunk 47 optimal weight: 0.0870 chunk 37 optimal weight: 2.9990 overall best weight: 0.5374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN D 49 ASN F 49 ASN F 60 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.147852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126422 restraints weight = 11749.258| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.21 r_work: 0.3336 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11796 Z= 0.115 Angle : 0.533 9.742 16026 Z= 0.283 Chirality : 0.044 0.307 1782 Planarity : 0.004 0.040 2079 Dihedral : 5.710 44.004 1809 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.95 % Allowed : 10.24 % Favored : 88.81 % 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: 0.76 (0.21), residues: 1434 helix: 2.04 (0.27), residues: 363 sheet: 0.35 (0.29), residues: 291 loop : -0.11 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 150 TYR 0.016 0.001 TYR E 195 PHE 0.014 0.001 PHE D 24 TRP 0.009 0.001 TRP F 92 HIS 0.004 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00238 (11766) covalent geometry : angle 0.51891 (15954) SS BOND : bond 0.00162 ( 18) SS BOND : angle 0.92295 ( 36) hydrogen bonds : bond 0.04582 ( 486) hydrogen bonds : angle 4.86540 ( 1395) link_NAG-ASN : bond 0.00239 ( 12) link_NAG-ASN : angle 2.49735 ( 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 148 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8067 (ttt90) REVERT: A 111 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7987 (tt) REVERT: A 210 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8026 (pm20) REVERT: D 57 GLU cc_start: 0.5965 (pt0) cc_final: 0.5392 (tt0) REVERT: D 60 ASN cc_start: 0.7291 (m-40) cc_final: 0.7086 (m110) REVERT: F 39 LYS cc_start: 0.8660 (ttmm) cc_final: 0.8378 (mmmt) REVERT: C 57 ARG cc_start: 0.8765 (ttt90) cc_final: 0.8536 (ttt90) REVERT: C 111 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7942 (tt) REVERT: C 248 ASN cc_start: 0.7875 (p0) cc_final: 0.7429 (p0) REVERT: E 111 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7972 (tt) REVERT: E 194 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7983 (mt) outliers start: 12 outliers final: 2 residues processed: 142 average time/residue: 0.8325 time to fit residues: 125.6677 Evaluate side-chains 128 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 210 GLN Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 194 LEU 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: chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN D 12 ASN F 60 ASN C 18 HIS C 248 ASN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.140194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.117384 restraints weight = 11760.329| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.27 r_work: 0.3237 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 11796 Z= 0.317 Angle : 0.763 12.629 16026 Z= 0.403 Chirality : 0.057 0.506 1782 Planarity : 0.006 0.057 2079 Dihedral : 6.566 48.368 1809 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.38 % Allowed : 9.68 % Favored : 87.94 % 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: 0.11 (0.20), residues: 1434 helix: 1.51 (0.26), residues: 348 sheet: 0.12 (0.30), residues: 261 loop : -0.55 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG C 150 TYR 0.019 0.004 TYR C 98 PHE 0.023 0.004 PHE F 24 TRP 0.015 0.003 TRP B 92 HIS 0.011 0.003 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00732 (11766) covalent geometry : angle 0.74134 (15954) SS BOND : bond 0.00437 ( 18) SS BOND : angle 1.21166 ( 36) hydrogen bonds : bond 0.06315 ( 486) hydrogen bonds : angle 5.28170 ( 1395) link_NAG-ASN : bond 0.00528 ( 12) link_NAG-ASN : angle 3.74282 ( 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 151 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8183 (ttt90) REVERT: A 111 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8169 (tt) REVERT: A 137 ASN cc_start: 0.8438 (m-40) cc_final: 0.8203 (m-40) REVERT: A 210 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8147 (pm20) REVERT: B 17 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7436 (ttp) REVERT: B 143 LYS cc_start: 0.7490 (mmtm) cc_final: 0.7238 (mmtt) REVERT: D 57 GLU cc_start: 0.6142 (pt0) cc_final: 0.5536 (tt0) REVERT: F 39 LYS cc_start: 0.8667 (ttmm) cc_final: 0.8410 (mmmt) REVERT: C 210 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8365 (pt0) REVERT: C 321 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8331 (ptp-110) REVERT: E 78 VAL cc_start: 0.8983 (m) cc_final: 0.8749 (p) REVERT: E 194 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7792 (mt) REVERT: E 321 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8267 (ptp-110) outliers start: 30 outliers final: 10 residues processed: 137 average time/residue: 0.7450 time to fit residues: 109.3136 Evaluate side-chains 133 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 B residue 17 MET Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 212 THR 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: chunk 82 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 26 HIS F 60 ASN F 106 HIS E 188 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.142128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.119407 restraints weight = 11703.073| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.27 r_work: 0.3263 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3309 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= 0.143 Angle : 0.557 8.371 16026 Z= 0.296 Chirality : 0.047 0.397 1782 Planarity : 0.004 0.041 2079 Dihedral : 6.048 47.692 1809 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.03 % Allowed : 11.90 % Favored : 87.06 % 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: 0.29 (0.21), residues: 1434 helix: 1.84 (0.26), residues: 363 sheet: 0.16 (0.29), residues: 261 loop : -0.54 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 150 TYR 0.014 0.002 TYR F 157 PHE 0.012 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 covalent geometry : bond 0.00312 (11766) covalent geometry : angle 0.54188 (15954) SS BOND : bond 0.00190 ( 18) SS BOND : angle 0.89572 ( 36) hydrogen bonds : bond 0.05002 ( 486) hydrogen bonds : angle 4.98267 ( 1395) link_NAG-ASN : bond 0.00485 ( 12) link_NAG-ASN : angle 2.65892 ( 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 136 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8215 (ttt90) REVERT: A 111 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8072 (tt) REVERT: A 137 ASN cc_start: 0.8384 (m-40) cc_final: 0.8166 (m-40) REVERT: A 210 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8059 (pm20) REVERT: A 268 MET cc_start: 0.9289 (ttm) cc_final: 0.8694 (ttm) REVERT: B 143 LYS cc_start: 0.7301 (mmtm) cc_final: 0.7046 (mmtt) REVERT: D 39 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8297 (tttt) REVERT: D 57 GLU cc_start: 0.5972 (pt0) cc_final: 0.5346 (tt0) REVERT: D 127 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7068 (mtt180) REVERT: F 39 LYS cc_start: 0.8643 (ttmm) cc_final: 0.8403 (mmmt) REVERT: C 210 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.7594 (pm20) REVERT: E 78 VAL cc_start: 0.8931 (m) cc_final: 0.8718 (p) REVERT: E 194 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7995 (mt) outliers start: 13 outliers final: 3 residues processed: 130 average time/residue: 0.7810 time to fit residues: 108.3725 Evaluate side-chains 124 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 210 GLN Chi-restraints excluded: chain D residue 127 ARG Chi-restraints excluded: chain F residue 127 ARG Chi-restraints excluded: chain C residue 210 GLN 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: chunk 116 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 111 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 119 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 53 optimal weight: 0.0970 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.143278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.120767 restraints weight = 11739.792| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.27 r_work: 0.3284 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11796 Z= 0.113 Angle : 0.515 7.675 16026 Z= 0.270 Chirality : 0.045 0.417 1782 Planarity : 0.004 0.042 2079 Dihedral : 5.718 48.706 1809 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.11 % Allowed : 12.14 % Favored : 86.75 % 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: 0.50 (0.21), residues: 1434 helix: 2.25 (0.26), residues: 363 sheet: 0.21 (0.30), residues: 261 loop : -0.52 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 150 TYR 0.012 0.001 TYR F 157 PHE 0.018 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 covalent geometry : bond 0.00239 (11766) covalent geometry : angle 0.49943 (15954) SS BOND : bond 0.00178 ( 18) SS BOND : angle 0.79428 ( 36) hydrogen bonds : bond 0.04474 ( 486) hydrogen bonds : angle 4.80645 ( 1395) link_NAG-ASN : bond 0.00440 ( 12) link_NAG-ASN : angle 2.62553 ( 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 131 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8215 (ttt90) REVERT: A 137 ASN cc_start: 0.8314 (m-40) cc_final: 0.8097 (m-40) REVERT: A 268 MET cc_start: 0.9308 (ttm) cc_final: 0.8717 (ttm) REVERT: B 39 LYS cc_start: 0.8599 (ttmm) cc_final: 0.7890 (tptp) REVERT: B 143 LYS cc_start: 0.7326 (mmtm) cc_final: 0.7117 (mmtt) REVERT: D 127 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7012 (mtt180) REVERT: F 39 LYS cc_start: 0.8644 (ttmm) cc_final: 0.8382 (mmmt) REVERT: C 210 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.7563 (pm20) REVERT: C 321 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8406 (ptp-110) REVERT: E 78 VAL cc_start: 0.8892 (m) cc_final: 0.8675 (p) REVERT: E 194 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8046 (mt) REVERT: E 321 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8234 (ptp-110) outliers start: 14 outliers final: 4 residues processed: 125 average time/residue: 0.8156 time to fit residues: 108.7799 Evaluate side-chains 121 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 D residue 110 LEU Chi-restraints excluded: chain D residue 127 ARG 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 280 GLU Chi-restraints excluded: chain E residue 321 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 102 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.142835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.120340 restraints weight = 11740.902| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.27 r_work: 0.3279 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3451 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= 0.128 Angle : 0.534 9.341 16026 Z= 0.280 Chirality : 0.047 0.534 1782 Planarity : 0.004 0.042 2079 Dihedral : 5.885 57.741 1809 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.87 % Allowed : 12.46 % Favored : 86.67 % 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: 0.53 (0.21), residues: 1434 helix: 2.36 (0.26), residues: 363 sheet: -0.01 (0.28), residues: 297 loop : -0.46 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 141 TYR 0.013 0.001 TYR F 157 PHE 0.018 0.002 PHE F 24 TRP 0.009 0.001 TRP F 92 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00278 (11766) covalent geometry : angle 0.51580 (15954) SS BOND : bond 0.00174 ( 18) SS BOND : angle 0.77131 ( 36) hydrogen bonds : bond 0.04579 ( 486) hydrogen bonds : angle 4.78852 ( 1395) link_NAG-ASN : bond 0.00585 ( 12) link_NAG-ASN : angle 2.92935 ( 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 125 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8191 (ttt90) REVERT: A 137 ASN cc_start: 0.8333 (m-40) cc_final: 0.8102 (m-40) REVERT: A 268 MET cc_start: 0.9301 (ttm) cc_final: 0.8715 (ttm) REVERT: B 39 LYS cc_start: 0.8603 (ttmm) cc_final: 0.7863 (tptp) REVERT: B 143 LYS cc_start: 0.7303 (mmtm) cc_final: 0.7098 (mmtt) REVERT: D 39 LYS cc_start: 0.8649 (ttmm) cc_final: 0.8395 (tppp) REVERT: D 127 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7059 (mtt180) REVERT: F 39 LYS cc_start: 0.8637 (ttmm) cc_final: 0.8399 (mmmt) REVERT: C 210 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.7583 (pm20) REVERT: C 321 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8433 (ptp-110) REVERT: E 78 VAL cc_start: 0.8921 (m) cc_final: 0.8710 (p) REVERT: E 194 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8044 (mt) REVERT: E 321 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8221 (ptp-110) outliers start: 11 outliers final: 4 residues processed: 122 average time/residue: 0.7812 time to fit residues: 101.9692 Evaluate side-chains 120 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 D residue 110 LEU Chi-restraints excluded: chain D residue 127 ARG 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 280 GLU Chi-restraints excluded: chain E residue 321 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 18 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 56 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: F 159 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.141378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.118882 restraints weight = 11733.351| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.27 r_work: 0.3258 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11796 Z= 0.171 Angle : 0.594 10.590 16026 Z= 0.313 Chirality : 0.051 0.597 1782 Planarity : 0.005 0.043 2079 Dihedral : 6.055 51.162 1809 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.03 % Allowed : 12.46 % Favored : 86.51 % 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: 0.38 (0.21), residues: 1434 helix: 2.21 (0.26), residues: 363 sheet: -0.09 (0.28), residues: 297 loop : -0.55 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 150 TYR 0.015 0.002 TYR F 157 PHE 0.019 0.002 PHE F 24 TRP 0.009 0.002 TRP F 92 HIS 0.004 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00387 (11766) covalent geometry : angle 0.57281 (15954) SS BOND : bond 0.00193 ( 18) SS BOND : angle 0.83990 ( 36) hydrogen bonds : bond 0.05043 ( 486) hydrogen bonds : angle 4.91996 ( 1395) link_NAG-ASN : bond 0.00587 ( 12) link_NAG-ASN : angle 3.28650 ( 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 124 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8227 (ttt90) REVERT: A 137 ASN cc_start: 0.8364 (m-40) cc_final: 0.8120 (m-40) REVERT: A 210 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7772 (pm20) REVERT: A 268 MET cc_start: 0.9269 (ttm) cc_final: 0.8675 (ttm) REVERT: B 39 LYS cc_start: 0.8625 (ttmm) cc_final: 0.7869 (tptp) REVERT: B 143 LYS cc_start: 0.7343 (mmtm) cc_final: 0.7012 (mmtt) REVERT: D 39 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8415 (tppp) REVERT: D 127 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7219 (mtt180) REVERT: F 39 LYS cc_start: 0.8637 (ttmm) cc_final: 0.8407 (mmmt) REVERT: C 210 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: C 321 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8414 (ptp-110) REVERT: E 78 VAL cc_start: 0.8945 (m) cc_final: 0.8742 (p) REVERT: E 194 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8047 (mt) REVERT: E 321 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8237 (ptp-110) outliers start: 13 outliers final: 5 residues processed: 119 average time/residue: 0.7723 time to fit residues: 98.3108 Evaluate side-chains 123 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 31 ASP 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 280 GLU Chi-restraints excluded: chain E residue 321 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.141467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.119143 restraints weight = 11606.843| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.25 r_work: 0.3261 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11796 Z= 0.164 Angle : 0.581 10.961 16026 Z= 0.305 Chirality : 0.050 0.585 1782 Planarity : 0.004 0.042 2079 Dihedral : 5.915 49.699 1809 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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 aren not related in a simple way. whole: 0.41 (0.21), residues: 1434 helix: 2.31 (0.26), residues: 363 sheet: -0.11 (0.28), residues: 297 loop : -0.55 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 150 TYR 0.013 0.002 TYR F 157 PHE 0.017 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 covalent geometry : bond 0.00370 (11766) covalent geometry : angle 0.56191 (15954) SS BOND : bond 0.00193 ( 18) SS BOND : angle 0.82119 ( 36) hydrogen bonds : bond 0.04959 ( 486) hydrogen bonds : angle 4.90827 ( 1395) link_NAG-ASN : bond 0.00580 ( 12) link_NAG-ASN : angle 3.12474 ( 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 122 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8205 (ttt90) REVERT: A 137 ASN cc_start: 0.8365 (m-40) cc_final: 0.8121 (m-40) REVERT: A 210 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7747 (pm20) REVERT: A 268 MET cc_start: 0.9272 (ttm) cc_final: 0.8689 (ttm) REVERT: B 39 LYS cc_start: 0.8615 (ttmm) cc_final: 0.7864 (tptp) REVERT: B 143 LYS cc_start: 0.7352 (mmtm) cc_final: 0.7021 (mmtt) REVERT: D 39 LYS cc_start: 0.8677 (ttmm) cc_final: 0.8416 (tppp) REVERT: D 42 GLN cc_start: 0.8371 (tp-100) cc_final: 0.8142 (tp40) REVERT: D 127 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7140 (mtt180) REVERT: F 39 LYS cc_start: 0.8631 (ttmm) cc_final: 0.8398 (mmmt) REVERT: C 210 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: C 321 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8405 (ptp-110) REVERT: E 78 VAL cc_start: 0.8926 (m) cc_final: 0.8723 (p) REVERT: E 194 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.8020 (mt) REVERT: E 210 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8162 (pt0) REVERT: E 321 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8177 (ptp-110) outliers start: 14 outliers final: 5 residues processed: 116 average time/residue: 0.7733 time to fit residues: 96.0665 Evaluate side-chains 121 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 194 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 Chi-restraints excluded: chain E residue 321 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.141492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.119109 restraints weight = 11751.982| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.26 r_work: 0.3261 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11796 Z= 0.160 Angle : 0.586 11.201 16026 Z= 0.305 Chirality : 0.050 0.583 1782 Planarity : 0.004 0.042 2079 Dihedral : 5.864 55.634 1809 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.03 % Allowed : 13.02 % 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 aren not related in a simple way. whole: 0.41 (0.21), residues: 1434 helix: 2.32 (0.26), residues: 363 sheet: -0.13 (0.28), residues: 297 loop : -0.55 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 150 TYR 0.014 0.002 TYR F 157 PHE 0.017 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 covalent geometry : bond 0.00361 (11766) covalent geometry : angle 0.56702 (15954) SS BOND : bond 0.00202 ( 18) SS BOND : angle 0.81105 ( 36) hydrogen bonds : bond 0.04937 ( 486) hydrogen bonds : angle 4.89315 ( 1395) link_NAG-ASN : bond 0.00631 ( 12) link_NAG-ASN : angle 3.07851 ( 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 120 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8205 (ttt90) REVERT: A 137 ASN cc_start: 0.8361 (m-40) cc_final: 0.8114 (m-40) REVERT: A 210 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7751 (pm20) REVERT: A 268 MET cc_start: 0.9274 (ttm) cc_final: 0.8692 (ttm) REVERT: B 39 LYS cc_start: 0.8617 (ttmm) cc_final: 0.7868 (tptp) REVERT: B 143 LYS cc_start: 0.7361 (mmtm) cc_final: 0.7032 (mmtt) REVERT: D 39 LYS cc_start: 0.8668 (ttmm) cc_final: 0.8412 (tppp) REVERT: D 42 GLN cc_start: 0.8376 (tp-100) cc_final: 0.8151 (tp40) REVERT: D 127 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7140 (mtt180) REVERT: F 39 LYS cc_start: 0.8630 (ttmm) cc_final: 0.8404 (mmmt) REVERT: C 210 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7597 (pm20) REVERT: C 321 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8410 (ptp-110) REVERT: E 78 VAL cc_start: 0.8930 (m) cc_final: 0.8727 (p) REVERT: E 194 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.8017 (mt) REVERT: E 210 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8164 (pt0) REVERT: E 321 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8160 (ptp-110) outliers start: 13 outliers final: 5 residues processed: 115 average time/residue: 0.7691 time to fit residues: 94.8041 Evaluate side-chains 119 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 194 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 Chi-restraints excluded: chain E residue 321 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 136 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 59 optimal weight: 0.0670 chunk 49 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.142900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.120601 restraints weight = 11737.221| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.27 r_work: 0.3281 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3586 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= 0.121 Angle : 0.538 10.948 16026 Z= 0.278 Chirality : 0.047 0.533 1782 Planarity : 0.004 0.043 2079 Dihedral : 5.486 49.624 1809 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.95 % Allowed : 13.02 % Favored : 86.03 % 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: 0.60 (0.21), residues: 1434 helix: 2.59 (0.26), residues: 363 sheet: -0.06 (0.27), residues: 297 loop : -0.47 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 141 TYR 0.012 0.001 TYR B 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 covalent geometry : bond 0.00261 (11766) covalent geometry : angle 0.51977 (15954) SS BOND : bond 0.00192 ( 18) SS BOND : angle 0.73437 ( 36) hydrogen bonds : bond 0.04495 ( 486) hydrogen bonds : angle 4.74649 ( 1395) link_NAG-ASN : bond 0.00668 ( 12) link_NAG-ASN : angle 2.95787 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4689.95 seconds wall clock time: 80 minutes 58.73 seconds (4858.73 seconds total)