Starting phenix.real_space_refine on Wed Feb 4 23:49:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n5z_49044/02_2026/9n5z_49044.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n5z_49044/02_2026/9n5z_49044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n5z_49044/02_2026/9n5z_49044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n5z_49044/02_2026/9n5z_49044.map" model { file = "/net/cci-nas-00/data/ceres_data/9n5z_49044/02_2026/9n5z_49044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n5z_49044/02_2026/9n5z_49044.cif" } resolution = 3.2 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= 0.017 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 60 5.16 5 C 8621 2.51 5 N 2328 2.21 5 O 2692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13701 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 941 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "B" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 809 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "C" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2530 Classifications: {'peptide': 324} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain: "D" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2523 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 19, 'TRANS': 303} Chain: "E" Number of atoms: 2545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2545 Classifications: {'peptide': 326} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 305} Chain: "F" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1381 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "G" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1381 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "H" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1381 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 3.14, per 1000 atoms: 0.23 Number of scatterers: 13701 At special positions: 0 Unit cell: (104.11, 102.674, 163.704, 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 60 16.00 O 2692 8.00 N 2328 7.00 C 8621 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 213 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS G 137 " distance=2.04 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 277 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 76 " distance=2.03 Simple disulfide: pdb=" SG CYS D 97 " - pdb=" SG CYS D 139 " distance=2.02 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS H 137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.02 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.02 Simple disulfide: pdb=" SG CYS G 144 " - pdb=" SG CYS G 148 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 148 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 401 " - " ASN C 94 " " NAG C 402 " - " ASN C 21 " " NAG C 403 " - " ASN C 33 " " NAG C 404 " - " ASN C 278 " " NAG C 405 " - " ASN C 289 " " NAG D 401 " - " ASN D 94 " " NAG D 402 " - " ASN D 278 " " NAG D 403 " - " ASN D 21 " " NAG D 404 " - " ASN D 289 " " NAG E 401 " - " ASN E 94 " " NAG E 402 " - " ASN E 278 " " NAG E 403 " - " ASN E 289 " " NAG E 404 " - " ASN E 33 " " NAG E 405 " - " ASN E 21 " Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 618.5 milliseconds 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3150 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 40 sheets defined 22.7% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'B' and resid 152 through 156 removed outlier: 3.617A pdb=" N LEU B 155 " --> pdb=" O ASN B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 208 removed outlier: 4.049A pdb=" N GLU B 208 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 70 Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.937A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'D' and resid 65 through 72 Processing helix chain 'D' and resid 104 through 112 removed outlier: 3.628A pdb=" N LEU D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 196 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 187 through 195 Processing helix chain 'F' and resid 37 through 58 Processing helix chain 'F' and resid 75 through 95 Processing helix chain 'F' and resid 96 through 127 removed outlier: 3.595A pdb=" N GLU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 158 through 170 removed outlier: 3.996A pdb=" N TYR F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLU F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 58 Processing helix chain 'G' and resid 71 through 73 No H-bonds generated for 'chain 'G' and resid 71 through 73' Processing helix chain 'G' and resid 74 through 127 removed outlier: 3.810A pdb=" N GLU G 105 " --> pdb=" O LEU G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 155 Processing helix chain 'G' and resid 158 through 169 removed outlier: 3.744A pdb=" N TYR G 162 " --> pdb=" O ASP G 158 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU G 164 " --> pdb=" O PRO G 160 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLU G 165 " --> pdb=" O LYS G 161 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 57 Processing helix chain 'H' and resid 75 through 127 removed outlier: 4.018A pdb=" N ASN H 104 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU H 105 " --> pdb=" O LEU H 101 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU H 108 " --> pdb=" O ASN H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 155 Processing helix chain 'H' and resid 159 through 161 No H-bonds generated for 'chain 'H' and resid 159 through 161' Processing helix chain 'H' and resid 162 through 171 removed outlier: 3.793A pdb=" N GLU H 171 " --> pdb=" O LYS H 167 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 22 removed outlier: 3.512A pdb=" N MET A 83 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 73 " --> pdb=" O THR A 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.773A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 39 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 98 removed outlier: 4.491A pdb=" N ILE A 115 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 130 through 131 removed outlier: 3.504A pdb=" N ILE B 146 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 197 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 170 through 173 removed outlier: 6.893A pdb=" N TRP B 160 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 170 through 173 removed outlier: 6.893A pdb=" N TRP B 160 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 16 through 17 Processing sheet with id=AA8, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AA9, first strand: chain 'C' and resid 40 through 41 Processing sheet with id=AB1, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 7.067A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 140 Processing sheet with id=AB4, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AB5, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.543A pdb=" N LYS C 211 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 229 through 237 Processing sheet with id=AB7, first strand: chain 'C' and resid 287 through 288 removed outlier: 3.675A pdb=" N GLY C 303 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR F 64 " --> pdb=" O GLY C 303 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 16 through 17 Processing sheet with id=AB9, first strand: chain 'D' and resid 25 through 26 Processing sheet with id=AC1, first strand: chain 'D' and resid 39 through 41 Processing sheet with id=AC2, first strand: chain 'D' and resid 43 through 44 removed outlier: 3.734A pdb=" N GLU D 44 " --> pdb=" O PHE D 294 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 59 through 60 removed outlier: 7.149A pdb=" N LEU D 59 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE D 87 " --> pdb=" O ILE D 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 116C through 118 Processing sheet with id=AC5, first strand: chain 'D' and resid 130 through 131 Processing sheet with id=AC6, first strand: chain 'D' and resid 136 through 141 removed outlier: 7.673A pdb=" N ALA D 138 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 9.969A pdb=" N ALA D 144 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 151 through 153 Processing sheet with id=AC8, first strand: chain 'D' and resid 164 through 169 removed outlier: 3.531A pdb=" N VAL D 204 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS D 211 " --> pdb=" O VAL D 204 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 281 through 282 Processing sheet with id=AD1, first strand: chain 'E' and resid 13 through 17 removed outlier: 3.715A pdb=" N HIS H 26 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY H 33 " --> pdb=" O HIS H 26 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AD3, first strand: chain 'E' and resid 40 through 41 Processing sheet with id=AD4, first strand: chain 'E' and resid 43 through 44 removed outlier: 3.622A pdb=" N GLU E 44 " --> pdb=" O PHE E 294 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.969A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE E 268 " --> pdb=" O ILE E 87 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 116C through 118 removed outlier: 3.618A pdb=" N GLU E 116C" --> pdb=" O ALA E 259 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E 259 " --> pdb=" O GLU E 116C" (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 136 through 141 removed outlier: 4.353A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 151 through 153 Processing sheet with id=AD9, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AE1, first strand: chain 'E' and resid 286 through 288 removed outlier: 3.576A pdb=" N THR E 283 " --> pdb=" O GLY E 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN E 282 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE E 302 " --> pdb=" O GLN E 282 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR H 64 " --> pdb=" O GLY E 303 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 130 through 134 removed outlier: 3.556A pdb=" N ILE F 133 " --> pdb=" O CYS F 137 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N CYS F 137 " --> pdb=" O ILE F 133 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 131 through 132 Processing sheet with id=AE4, first strand: chain 'H' and resid 131 through 134 removed outlier: 5.293A pdb=" N GLU H 132 " --> pdb=" O GLU H 139 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU H 139 " --> pdb=" O GLU H 132 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY H 134 " --> pdb=" O CYS H 137 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4419 1.34 - 1.46: 3424 1.46 - 1.59: 6098 1.59 - 1.71: 1 1.71 - 1.83: 79 Bond restraints: 14021 Sorted by residual: bond pdb=" CA ASN C 289 " pdb=" CB ASN C 289 " ideal model delta sigma weight residual 1.539 1.636 -0.097 4.88e-02 4.20e+02 3.91e+00 bond pdb=" C CYS E 305 " pdb=" N PRO E 306 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.84e+00 bond pdb=" CB LYS D 46 " pdb=" CG LYS D 46 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.59e+00 bond pdb=" CA ARG C 55 " pdb=" CB ARG C 55 " ideal model delta sigma weight residual 1.530 1.556 -0.026 1.69e-02 3.50e+03 2.39e+00 bond pdb=" CB GLU F 164 " pdb=" CG GLU F 164 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.25e+00 ... (remaining 14016 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 18546 2.40 - 4.81: 404 4.81 - 7.21: 49 7.21 - 9.61: 11 9.61 - 12.01: 2 Bond angle restraints: 19012 Sorted by residual: angle pdb=" C LYS D 32 " pdb=" N ASN D 33 " pdb=" CA ASN D 33 " ideal model delta sigma weight residual 122.46 128.20 -5.74 1.41e+00 5.03e-01 1.66e+01 angle pdb=" CA ARG C 55 " pdb=" CB ARG C 55 " pdb=" CG ARG C 55 " ideal model delta sigma weight residual 114.10 122.01 -7.91 2.00e+00 2.50e-01 1.56e+01 angle pdb=" CA MET F 59 " pdb=" CB MET F 59 " pdb=" CG MET F 59 " ideal model delta sigma weight residual 114.10 121.73 -7.63 2.00e+00 2.50e-01 1.45e+01 angle pdb=" CA CYS E 305 " pdb=" CB CYS E 305 " pdb=" SG CYS E 305 " ideal model delta sigma weight residual 114.40 122.67 -8.27 2.30e+00 1.89e-01 1.29e+01 angle pdb=" CA LEU E 112 " pdb=" CB LEU E 112 " pdb=" CG LEU E 112 " ideal model delta sigma weight residual 116.30 128.31 -12.01 3.50e+00 8.16e-02 1.18e+01 ... (remaining 19007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 7722 17.57 - 35.14: 647 35.14 - 52.72: 132 52.72 - 70.29: 26 70.29 - 87.86: 12 Dihedral angle restraints: 8539 sinusoidal: 3598 harmonic: 4941 Sorted by residual: dihedral pdb=" CB CYS D 64 " pdb=" SG CYS D 64 " pdb=" SG CYS D 76 " pdb=" CB CYS D 76 " ideal model delta sinusoidal sigma weight residual -86.00 1.86 -87.86 1 1.00e+01 1.00e-02 9.24e+01 dihedral pdb=" CB CYS E 64 " pdb=" SG CYS E 64 " pdb=" SG CYS E 76 " pdb=" CB CYS E 76 " ideal model delta sinusoidal sigma weight residual 93.00 6.67 86.33 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" CB CYS D 52 " pdb=" SG CYS D 52 " pdb=" SG CYS D 277 " pdb=" CB CYS D 277 " ideal model delta sinusoidal sigma weight residual 93.00 8.18 84.82 1 1.00e+01 1.00e-02 8.73e+01 ... (remaining 8536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2032 0.123 - 0.247: 56 0.247 - 0.370: 5 0.370 - 0.494: 0 0.494 - 0.617: 1 Chirality restraints: 2094 Sorted by residual: chirality pdb=" C1 NAG E 402 " pdb=" ND2 ASN E 278 " pdb=" C2 NAG E 402 " pdb=" O5 NAG E 402 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.52e+00 chirality pdb=" CB ILE E 120 " pdb=" CA ILE E 120 " pdb=" CG1 ILE E 120 " pdb=" CG2 ILE E 120 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB ILE D 120 " pdb=" CA ILE D 120 " pdb=" CG1 ILE D 120 " pdb=" CG2 ILE D 120 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 2091 not shown) Planarity restraints: 2460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU H 105 " -0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C GLU H 105 " 0.067 2.00e-02 2.50e+03 pdb=" O GLU H 105 " -0.025 2.00e-02 2.50e+03 pdb=" N ARG H 106 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 73 " 0.039 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO C 74 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP E 127 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.12e+00 pdb=" N PRO E 128 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO E 128 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 128 " -0.032 5.00e-02 4.00e+02 ... (remaining 2457 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.05: 8390 3.05 - 3.51: 13920 3.51 - 3.97: 22876 3.97 - 4.44: 26585 4.44 - 4.90: 42818 Nonbonded interactions: 114589 Sorted by model distance: nonbonded pdb=" N VAL D 155 " pdb=" O VAL D 155 " model vdw 2.585 2.496 nonbonded pdb=" N SER D 206 " pdb=" O SER D 206 " model vdw 2.592 2.496 nonbonded pdb=" N ASN B 151 " pdb=" O ASN B 151 " model vdw 2.598 2.496 nonbonded pdb=" N SER C 206 " pdb=" O SER C 206 " model vdw 2.601 2.496 nonbonded pdb=" N PHE E 147 " pdb=" O PHE E 147 " model vdw 2.605 2.496 ... (remaining 114584 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 10 through 324 or resid 401 through 405)) selection = chain 'D' selection = (chain 'E' and (resid 10 through 324 or resid 401 through 405)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 10.250 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.710 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 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 : 0.004 0.097 14054 Z= 0.196 Angle : 0.863 12.014 19092 Z= 0.444 Chirality : 0.056 0.617 2094 Planarity : 0.007 0.080 2446 Dihedral : 13.249 80.289 5332 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.92 (0.19), residues: 1704 helix: -0.42 (0.26), residues: 349 sheet: -1.51 (0.32), residues: 259 loop : -1.55 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG C 315 TYR 0.030 0.002 TYR D 105 PHE 0.036 0.003 PHE E 203 TRP 0.022 0.002 TRP E 69 HIS 0.012 0.002 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00447 (14021) covalent geometry : angle 0.84204 (19012) SS BOND : bond 0.00415 ( 19) SS BOND : angle 1.95888 ( 38) hydrogen bonds : bond 0.17159 ( 458) hydrogen bonds : angle 8.95175 ( 1251) link_NAG-ASN : bond 0.00991 ( 14) link_NAG-ASN : angle 3.73081 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 95 ASN cc_start: 0.6730 (m110) cc_final: 0.6528 (m110) REVERT: G 123 ARG cc_start: 0.7118 (ptm-80) cc_final: 0.6742 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.1159 time to fit residues: 45.8208 Evaluate side-chains 206 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.0010 chunk 66 optimal weight: 0.0980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN C 197 ASN E 231 ASN ** E 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN H 62 GLN ** H 104 ASN ** 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 = 0.4062 r_free = 0.4062 target = 0.166091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.146835 restraints weight = 19621.296| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.23 r_work: 0.3715 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14054 Z= 0.124 Angle : 0.604 9.032 19092 Z= 0.310 Chirality : 0.045 0.223 2094 Planarity : 0.005 0.053 2446 Dihedral : 5.948 79.819 2165 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.61 % Allowed : 8.64 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.53 (0.19), residues: 1704 helix: 0.06 (0.26), residues: 359 sheet: -1.45 (0.31), residues: 258 loop : -1.31 (0.17), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 315 TYR 0.032 0.001 TYR G 141 PHE 0.016 0.002 PHE E 118 TRP 0.015 0.001 TRP E 69 HIS 0.004 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00270 (14021) covalent geometry : angle 0.58865 (19012) SS BOND : bond 0.00339 ( 19) SS BOND : angle 1.46204 ( 38) hydrogen bonds : bond 0.04772 ( 458) hydrogen bonds : angle 6.42091 ( 1251) link_NAG-ASN : bond 0.00617 ( 14) link_NAG-ASN : angle 2.61989 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 244 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8146 (mtm110) cc_final: 0.7566 (mtm110) REVERT: E 27 ASP cc_start: 0.7287 (m-30) cc_final: 0.6882 (p0) REVERT: F 97 GLU cc_start: 0.7399 (tp30) cc_final: 0.6845 (tt0) outliers start: 9 outliers final: 5 residues processed: 247 average time/residue: 0.1196 time to fit residues: 43.3954 Evaluate side-chains 215 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 210 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain G residue 156 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 111 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 166 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 121 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 153 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 74 ASN C 111 GLN E 231 ASN E 263 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.160440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.140073 restraints weight = 20074.636| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.29 r_work: 0.3640 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14054 Z= 0.194 Angle : 0.650 8.732 19092 Z= 0.335 Chirality : 0.046 0.184 2094 Planarity : 0.005 0.048 2446 Dihedral : 5.990 80.258 2165 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.82 % Allowed : 10.59 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.52 (0.19), residues: 1704 helix: 0.08 (0.26), residues: 360 sheet: -1.21 (0.30), residues: 285 loop : -1.37 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 262 TYR 0.023 0.002 TYR G 141 PHE 0.025 0.002 PHE C 121 TRP 0.008 0.001 TRP C 84 HIS 0.005 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00442 (14021) covalent geometry : angle 0.63564 (19012) SS BOND : bond 0.00479 ( 19) SS BOND : angle 1.67696 ( 38) hydrogen bonds : bond 0.04949 ( 458) hydrogen bonds : angle 6.13668 ( 1251) link_NAG-ASN : bond 0.00531 ( 14) link_NAG-ASN : angle 2.52483 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8265 (mtm110) cc_final: 0.7734 (mtm110) REVERT: D 299 PRO cc_start: 0.7998 (Cg_exo) cc_final: 0.7726 (Cg_endo) REVERT: E 27 ASP cc_start: 0.7279 (m-30) cc_final: 0.6765 (p0) REVERT: H 86 ASP cc_start: 0.7581 (m-30) cc_final: 0.7327 (t0) REVERT: H 104 ASN cc_start: 0.8809 (m-40) cc_final: 0.8565 (m-40) outliers start: 27 outliers final: 19 residues processed: 228 average time/residue: 0.1164 time to fit residues: 39.4999 Evaluate side-chains 215 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 168 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 21 optimal weight: 0.3980 chunk 85 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 95 optimal weight: 0.0970 chunk 103 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.162130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.142453 restraints weight = 19769.102| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.16 r_work: 0.3675 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14054 Z= 0.143 Angle : 0.590 9.061 19092 Z= 0.304 Chirality : 0.044 0.227 2094 Planarity : 0.005 0.047 2446 Dihedral : 5.776 80.250 2165 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.15 % Allowed : 13.29 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.39 (0.19), residues: 1704 helix: 0.21 (0.26), residues: 360 sheet: -1.17 (0.31), residues: 279 loop : -1.28 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 262 TYR 0.021 0.002 TYR G 141 PHE 0.020 0.002 PHE C 121 TRP 0.007 0.001 TRP C 153 HIS 0.003 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00321 (14021) covalent geometry : angle 0.57801 (19012) SS BOND : bond 0.00368 ( 19) SS BOND : angle 1.38372 ( 38) hydrogen bonds : bond 0.04607 ( 458) hydrogen bonds : angle 5.87828 ( 1251) link_NAG-ASN : bond 0.00406 ( 14) link_NAG-ASN : angle 2.34828 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8258 (mtm110) cc_final: 0.7837 (mtm110) REVERT: D 260 MET cc_start: 0.7641 (ttp) cc_final: 0.7208 (ptm) REVERT: E 27 ASP cc_start: 0.7186 (m-30) cc_final: 0.6746 (p0) REVERT: E 120 ILE cc_start: 0.8129 (tt) cc_final: 0.7853 (tt) REVERT: H 86 ASP cc_start: 0.7639 (m-30) cc_final: 0.7393 (t0) outliers start: 17 outliers final: 10 residues processed: 211 average time/residue: 0.1162 time to fit residues: 36.7413 Evaluate side-chains 202 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 192 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain H residue 11 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 147 optimal weight: 0.6980 chunk 149 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 160 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 33 ASN E 231 ASN F 26 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.160297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.140325 restraints weight = 20001.365| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.19 r_work: 0.3640 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14054 Z= 0.175 Angle : 0.611 8.862 19092 Z= 0.315 Chirality : 0.045 0.174 2094 Planarity : 0.005 0.048 2446 Dihedral : 5.824 80.737 2165 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.29 % Allowed : 13.77 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.37 (0.19), residues: 1704 helix: 0.23 (0.26), residues: 363 sheet: -1.20 (0.32), residues: 266 loop : -1.26 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 262 TYR 0.019 0.002 TYR G 141 PHE 0.016 0.002 PHE A 63 TRP 0.008 0.001 TRP C 153 HIS 0.004 0.001 HIS F 25 Details of bonding type rmsd covalent geometry : bond 0.00398 (14021) covalent geometry : angle 0.59879 (19012) SS BOND : bond 0.00433 ( 19) SS BOND : angle 1.44210 ( 38) hydrogen bonds : bond 0.04648 ( 458) hydrogen bonds : angle 5.81421 ( 1251) link_NAG-ASN : bond 0.00397 ( 14) link_NAG-ASN : angle 2.30375 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 5 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6702 (tt) REVERT: D 260 MET cc_start: 0.7727 (ttp) cc_final: 0.7259 (ptm) REVERT: E 112 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7911 (pp) REVERT: F 97 GLU cc_start: 0.7505 (tp30) cc_final: 0.6955 (tt0) REVERT: H 86 ASP cc_start: 0.7705 (m-30) cc_final: 0.7442 (t0) outliers start: 34 outliers final: 22 residues processed: 225 average time/residue: 0.1154 time to fit residues: 38.7451 Evaluate side-chains 220 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 168 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 14 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.160965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.140581 restraints weight = 19767.925| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.29 r_work: 0.3643 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14054 Z= 0.155 Angle : 0.605 10.797 19092 Z= 0.310 Chirality : 0.044 0.162 2094 Planarity : 0.004 0.049 2446 Dihedral : 5.746 80.861 2165 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.16 % Allowed : 14.37 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.28 (0.19), residues: 1704 helix: 0.33 (0.26), residues: 363 sheet: -1.26 (0.33), residues: 245 loop : -1.19 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 262 TYR 0.014 0.002 TYR C 105 PHE 0.025 0.002 PHE C 102 TRP 0.015 0.001 TRP C 153 HIS 0.004 0.001 HIS F 142 Details of bonding type rmsd covalent geometry : bond 0.00352 (14021) covalent geometry : angle 0.59238 (19012) SS BOND : bond 0.00417 ( 19) SS BOND : angle 1.51171 ( 38) hydrogen bonds : bond 0.04541 ( 458) hydrogen bonds : angle 5.74681 ( 1251) link_NAG-ASN : bond 0.00418 ( 14) link_NAG-ASN : angle 2.31294 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 5 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6554 (tt) REVERT: D 120 ILE cc_start: 0.8164 (tt) cc_final: 0.7849 (tt) REVERT: D 139 CYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6769 (m) REVERT: D 260 MET cc_start: 0.7678 (ttp) cc_final: 0.7152 (ptm) REVERT: E 112 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7879 (pp) REVERT: F 97 GLU cc_start: 0.7531 (tp30) cc_final: 0.6968 (tt0) REVERT: F 157 TYR cc_start: 0.7461 (t80) cc_final: 0.7141 (t80) REVERT: H 86 ASP cc_start: 0.7692 (m-30) cc_final: 0.7402 (t0) outliers start: 32 outliers final: 22 residues processed: 226 average time/residue: 0.1188 time to fit residues: 39.8389 Evaluate side-chains 224 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 153 TRP Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 168 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.158270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.138401 restraints weight = 19980.265| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.16 r_work: 0.3626 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14054 Z= 0.189 Angle : 0.633 12.445 19092 Z= 0.322 Chirality : 0.045 0.166 2094 Planarity : 0.005 0.050 2446 Dihedral : 5.917 81.749 2165 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.23 % Allowed : 14.91 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.31 (0.19), residues: 1704 helix: 0.34 (0.26), residues: 363 sheet: -1.18 (0.33), residues: 245 loop : -1.25 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 315 TYR 0.018 0.002 TYR C 232 PHE 0.023 0.002 PHE C 102 TRP 0.010 0.001 TRP C 153 HIS 0.004 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00433 (14021) covalent geometry : angle 0.62288 (19012) SS BOND : bond 0.00512 ( 19) SS BOND : angle 1.37984 ( 38) hydrogen bonds : bond 0.04651 ( 458) hydrogen bonds : angle 5.80012 ( 1251) link_NAG-ASN : bond 0.00384 ( 14) link_NAG-ASN : angle 2.17987 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 209 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 5 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6708 (tt) REVERT: B 231 LEU cc_start: 0.5927 (OUTLIER) cc_final: 0.5597 (pt) REVERT: C 148 TYR cc_start: 0.6811 (m-80) cc_final: 0.6582 (m-80) REVERT: C 260 MET cc_start: 0.7829 (ttp) cc_final: 0.7579 (ttt) REVERT: C 262 ARG cc_start: 0.7640 (mtm-85) cc_final: 0.7402 (mtm-85) REVERT: D 120 ILE cc_start: 0.8193 (tt) cc_final: 0.7865 (tt) REVERT: D 139 CYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6742 (m) REVERT: D 260 MET cc_start: 0.7722 (ttp) cc_final: 0.7466 (ptm) REVERT: E 112 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7884 (pp) REVERT: F 97 GLU cc_start: 0.7570 (tp30) cc_final: 0.6987 (tt0) outliers start: 33 outliers final: 22 residues processed: 228 average time/residue: 0.1204 time to fit residues: 40.7733 Evaluate side-chains 222 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 153 TRP Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 61 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 81 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.158058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.137703 restraints weight = 19903.351| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.28 r_work: 0.3615 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14054 Z= 0.185 Angle : 0.650 13.158 19092 Z= 0.329 Chirality : 0.045 0.222 2094 Planarity : 0.005 0.050 2446 Dihedral : 5.999 82.196 2165 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.36 % Allowed : 14.84 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.37 (0.19), residues: 1704 helix: 0.37 (0.26), residues: 363 sheet: -1.07 (0.33), residues: 257 loop : -1.36 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 315 TYR 0.017 0.002 TYR C 232 PHE 0.023 0.002 PHE C 102 TRP 0.010 0.001 TRP C 153 HIS 0.004 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00428 (14021) covalent geometry : angle 0.63929 (19012) SS BOND : bond 0.00554 ( 19) SS BOND : angle 1.50974 ( 38) hydrogen bonds : bond 0.04629 ( 458) hydrogen bonds : angle 5.79862 ( 1251) link_NAG-ASN : bond 0.00376 ( 14) link_NAG-ASN : angle 2.17608 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 0.557 Fit side-chains REVERT: A 5 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6724 (tt) REVERT: B 231 LEU cc_start: 0.5949 (OUTLIER) cc_final: 0.5622 (pt) REVERT: C 260 MET cc_start: 0.7861 (ttp) cc_final: 0.7528 (ttt) REVERT: D 139 CYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6704 (m) REVERT: D 260 MET cc_start: 0.7697 (ttp) cc_final: 0.7420 (ptm) REVERT: E 112 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7898 (pp) REVERT: E 261 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7606 (tm-30) REVERT: F 97 GLU cc_start: 0.7619 (tp30) cc_final: 0.6984 (tt0) outliers start: 35 outliers final: 25 residues processed: 229 average time/residue: 0.1139 time to fit residues: 39.1741 Evaluate side-chains 221 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 153 TRP Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 168 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 27 optimal weight: 0.4980 chunk 144 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 ASN E 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.159805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.139516 restraints weight = 19909.879| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.28 r_work: 0.3637 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14054 Z= 0.154 Angle : 0.629 13.694 19092 Z= 0.318 Chirality : 0.045 0.336 2094 Planarity : 0.004 0.048 2446 Dihedral : 5.940 82.285 2165 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.23 % Allowed : 15.52 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.29 (0.19), residues: 1704 helix: 0.43 (0.26), residues: 363 sheet: -1.21 (0.32), residues: 270 loop : -1.24 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 315 TYR 0.017 0.002 TYR B 174 PHE 0.021 0.002 PHE C 102 TRP 0.008 0.001 TRP C 153 HIS 0.003 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00351 (14021) covalent geometry : angle 0.61747 (19012) SS BOND : bond 0.00445 ( 19) SS BOND : angle 1.41612 ( 38) hydrogen bonds : bond 0.04449 ( 458) hydrogen bonds : angle 5.69300 ( 1251) link_NAG-ASN : bond 0.00457 ( 14) link_NAG-ASN : angle 2.38087 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 0.569 Fit side-chains REVERT: A 5 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6775 (tt) REVERT: B 231 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5684 (pt) REVERT: C 260 MET cc_start: 0.7799 (ttp) cc_final: 0.7473 (ttt) REVERT: D 139 CYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6675 (m) REVERT: D 260 MET cc_start: 0.7638 (ttp) cc_final: 0.7370 (ptm) REVERT: E 112 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7862 (pp) REVERT: E 261 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7573 (tm-30) REVERT: F 97 GLU cc_start: 0.7611 (tp30) cc_final: 0.6986 (tt0) outliers start: 33 outliers final: 26 residues processed: 209 average time/residue: 0.1164 time to fit residues: 36.4122 Evaluate side-chains 218 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 153 TRP Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 90 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 86 optimal weight: 0.0980 chunk 138 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.159241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.139471 restraints weight = 19901.065| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.16 r_work: 0.3639 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14054 Z= 0.165 Angle : 0.649 14.141 19092 Z= 0.326 Chirality : 0.047 0.538 2094 Planarity : 0.004 0.049 2446 Dihedral : 6.018 82.527 2165 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.02 % Allowed : 15.79 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.27 (0.19), residues: 1704 helix: 0.47 (0.26), residues: 363 sheet: -1.20 (0.32), residues: 269 loop : -1.24 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 315 TYR 0.018 0.002 TYR C 232 PHE 0.024 0.002 PHE D 118 TRP 0.009 0.001 TRP C 153 HIS 0.004 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00378 (14021) covalent geometry : angle 0.63519 (19012) SS BOND : bond 0.00392 ( 19) SS BOND : angle 1.44752 ( 38) hydrogen bonds : bond 0.04480 ( 458) hydrogen bonds : angle 5.66033 ( 1251) link_NAG-ASN : bond 0.00603 ( 14) link_NAG-ASN : angle 2.67453 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 5 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6827 (tt) REVERT: B 231 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5651 (pt) REVERT: C 260 MET cc_start: 0.7795 (ttp) cc_final: 0.7468 (ttt) REVERT: D 139 CYS cc_start: 0.6951 (OUTLIER) cc_final: 0.6652 (m) REVERT: D 260 MET cc_start: 0.7660 (ttp) cc_final: 0.7417 (ptm) REVERT: E 112 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7874 (pp) REVERT: E 261 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7627 (tm-30) outliers start: 30 outliers final: 25 residues processed: 215 average time/residue: 0.1161 time to fit residues: 37.9110 Evaluate side-chains 226 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 153 TRP Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 139 CYS Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 95 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 152 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.157909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.138123 restraints weight = 19893.987| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.23 r_work: 0.3613 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14054 Z= 0.166 Angle : 0.647 14.001 19092 Z= 0.326 Chirality : 0.046 0.424 2094 Planarity : 0.004 0.049 2446 Dihedral : 5.982 83.056 2165 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.02 % Allowed : 15.99 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.24 (0.19), residues: 1704 helix: 0.47 (0.26), residues: 363 sheet: -1.17 (0.32), residues: 268 loop : -1.22 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 315 TYR 0.022 0.002 TYR C 232 PHE 0.032 0.002 PHE C 102 TRP 0.010 0.001 TRP C 153 HIS 0.003 0.001 HIS F 142 Details of bonding type rmsd covalent geometry : bond 0.00383 (14021) covalent geometry : angle 0.63514 (19012) SS BOND : bond 0.00380 ( 19) SS BOND : angle 1.46681 ( 38) hydrogen bonds : bond 0.04469 ( 458) hydrogen bonds : angle 5.65791 ( 1251) link_NAG-ASN : bond 0.00572 ( 14) link_NAG-ASN : angle 2.43930 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3818.39 seconds wall clock time: 66 minutes 35.17 seconds (3995.17 seconds total)