Starting phenix.real_space_refine on Thu Jul 2 12:36:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ejk_28185/07_2026/8ejk_28185.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejk_28185/07_2026/8ejk_28185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ejk_28185/07_2026/8ejk_28185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejk_28185/07_2026/8ejk_28185.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ejk_28185/07_2026/8ejk_28185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejk_28185/07_2026/8ejk_28185.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ejk_28185/07_2026/8ejk_28185.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ejk_28185/07_2026/8ejk_28185.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 51 5.16 5 C 5462 2.51 5 N 1483 2.21 5 O 1598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8594 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1869 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 227} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2556 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 420 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1768 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 1944 Classifications: {'peptide': 267} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PTRANS': 18, 'TRANS': 248} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'2YB': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.70, per 1000 atoms: 0.20 Number of scatterers: 8594 At special positions: 0 Unit cell: (97.37, 116.63, 132.68, 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 51 16.00 O 1598 8.00 N 1483 7.00 C 5462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 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 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 392.7 milliseconds 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2068 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 37.3% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.921A pdb=" N THR A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.780A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 93 removed outlier: 3.879A pdb=" N GLN A 90 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN A 93 " --> pdb=" O GLN A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 122 Processing helix chain 'A' and resid 137 through 148 Processing helix chain 'A' and resid 151 through 155 removed outlier: 3.558A pdb=" N ASP A 154 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 175 through 195 Processing helix chain 'A' and resid 215 through 235 Processing helix chain 'B' and resid 7 through 26 removed outlier: 3.554A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.597A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 20 Processing helix chain 'C' and resid 29 through 45 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'R' and resid 5 through 35 Proline residue: R 21 - end of helix Processing helix chain 'R' and resid 39 through 69 Proline residue: R 60 - end of helix Processing helix chain 'R' and resid 75 through 77 No H-bonds generated for 'chain 'R' and resid 75 through 77' Processing helix chain 'R' and resid 78 through 110 removed outlier: 3.529A pdb=" N VAL R 84 " --> pdb=" O PRO R 80 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE R 88 " --> pdb=" O VAL R 84 " (cutoff:3.500A) Proline residue: R 89 - end of helix removed outlier: 4.090A pdb=" N GLY R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA R 98 " --> pdb=" O GLY R 94 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 118 Processing helix chain 'R' and resid 119 through 146 removed outlier: 3.624A pdb=" N SER R 123 " --> pdb=" O ARG R 119 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL R 141 " --> pdb=" O HIS R 137 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU R 145 " --> pdb=" O VAL R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 191 Proline residue: R 181 - end of helix removed outlier: 3.740A pdb=" N LEU R 186 " --> pdb=" O ALA R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 212 Processing helix chain 'R' and resid 215 through 227 Processing helix chain 'R' and resid 227 through 236 removed outlier: 3.512A pdb=" N CYS R 236 " --> pdb=" O THR R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 250 removed outlier: 3.786A pdb=" N TYR R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 267 removed outlier: 4.374A pdb=" N ARG R 258 " --> pdb=" O GLY R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 272 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 68 removed outlier: 4.677A pdb=" N VAL A 78 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ARG A 35 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ILE A 99 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A 37 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL A 101 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU A 39 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N ASP A 103 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE A 98 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE A 134 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE A 100 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ASN A 136 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL A 102 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL A 131 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N HIS A 206 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 133 " --> pdb=" O HIS A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.345A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.797A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.031A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.953A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.643A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.732A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.628A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.651A pdb=" N GLY E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 149 removed outlier: 3.706A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 194 through 195 removed outlier: 3.722A pdb=" N ASN E 194 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1206 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: 1.14 Time building geometry restraints manager: 0.81 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: 2808 1.34 - 1.47: 2189 1.47 - 1.59: 3717 1.59 - 1.71: 0 1.71 - 1.83: 70 Bond restraints: 8784 Sorted by residual: bond pdb=" C27 2YB R 401 " pdb=" C28 2YB R 401 " ideal model delta sigma weight residual 1.505 1.392 0.113 2.00e-02 2.50e+03 3.22e+01 bond pdb=" C1 2YB R 401 " pdb=" C2 2YB R 401 " ideal model delta sigma weight residual 1.503 1.392 0.111 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C14 2YB R 401 " pdb=" C15 2YB R 401 " ideal model delta sigma weight residual 1.502 1.392 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C21 2YB R 401 " pdb=" C22 2YB R 401 " ideal model delta sigma weight residual 1.498 1.395 0.103 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C16 2YB R 401 " pdb=" C17 2YB R 401 " ideal model delta sigma weight residual 1.485 1.395 0.090 2.00e-02 2.50e+03 2.04e+01 ... (remaining 8779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 11718 1.92 - 3.83: 174 3.83 - 5.75: 29 5.75 - 7.66: 12 7.66 - 9.58: 2 Bond angle restraints: 11935 Sorted by residual: angle pdb=" N ASN E 194 " pdb=" CA ASN E 194 " pdb=" C ASN E 194 " ideal model delta sigma weight residual 108.60 115.15 -6.55 1.46e+00 4.69e-01 2.01e+01 angle pdb=" N SER E 193 " pdb=" CA SER E 193 " pdb=" C SER E 193 " ideal model delta sigma weight residual 111.36 115.78 -4.42 1.09e+00 8.42e-01 1.64e+01 angle pdb=" CA CYS R 79 " pdb=" C CYS R 79 " pdb=" N PRO R 80 " ideal model delta sigma weight residual 120.81 117.35 3.46 8.60e-01 1.35e+00 1.62e+01 angle pdb=" N MET E 192 " pdb=" CA MET E 192 " pdb=" C MET E 192 " ideal model delta sigma weight residual 113.28 107.55 5.73 1.57e+00 4.06e-01 1.33e+01 angle pdb=" N ARG E 191 " pdb=" CA ARG E 191 " pdb=" C ARG E 191 " ideal model delta sigma weight residual 113.72 108.47 5.25 1.52e+00 4.33e-01 1.19e+01 ... (remaining 11930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.80: 4825 23.80 - 47.61: 302 47.61 - 71.41: 23 71.41 - 95.21: 5 95.21 - 119.02: 1 Dihedral angle restraints: 5156 sinusoidal: 1935 harmonic: 3221 Sorted by residual: dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 157.95 -64.95 1 1.00e+01 1.00e-02 5.53e+01 dihedral pdb=" C8 2YB R 401 " pdb=" C6 2YB R 401 " pdb=" C7 2YB R 401 " pdb=" O5 2YB R 401 " ideal model delta sinusoidal sigma weight residual 180.08 61.06 119.02 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" C GLN B 17 " pdb=" N GLN B 17 " pdb=" CA GLN B 17 " pdb=" CB GLN B 17 " ideal model delta harmonic sigma weight residual -122.60 -132.37 9.77 0 2.50e+00 1.60e-01 1.53e+01 ... (remaining 5153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1212 0.074 - 0.149: 126 0.149 - 0.223: 5 0.223 - 0.297: 0 0.297 - 0.372: 1 Chirality restraints: 1344 Sorted by residual: chirality pdb=" CA GLN B 17 " pdb=" N GLN B 17 " pdb=" C GLN B 17 " pdb=" CB GLN B 17 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CA ASN R 272 " pdb=" N ASN R 272 " pdb=" C ASN R 272 " pdb=" CB ASN R 272 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" CB ILE R 263 " pdb=" CA ILE R 263 " pdb=" CG1 ILE R 263 " pdb=" CG2 ILE R 263 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.54e-01 ... (remaining 1341 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.050 5.00e-02 4.00e+02 7.69e-02 9.47e+00 pdb=" N PRO C 49 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 88 " 0.045 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO R 89 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO R 89 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO R 89 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET C 38 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.49e+00 pdb=" C MET C 38 " -0.041 2.00e-02 2.50e+03 pdb=" O MET C 38 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA C 39 " 0.014 2.00e-02 2.50e+03 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 232 2.70 - 3.25: 8474 3.25 - 3.80: 13612 3.80 - 4.35: 17100 4.35 - 4.90: 29678 Nonbonded interactions: 69096 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.152 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.166 3.040 nonbonded pdb=" OD1 ASP B 27 " pdb=" NZ LYS C 29 " model vdw 2.187 3.120 nonbonded pdb=" OG SER E 161 " pdb=" O LYS E 163 " model vdw 2.212 3.040 nonbonded pdb=" OG1 THR B 165 " pdb=" O PHE B 180 " model vdw 2.235 3.040 ... (remaining 69091 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.560 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.450 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 0.113 8786 Z= 0.192 Angle : 0.614 9.576 11939 Z= 0.320 Chirality : 0.045 0.372 1344 Planarity : 0.005 0.077 1526 Dihedral : 14.084 119.016 3082 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.11 % Allowed : 0.22 % Favored : 99.66 % Cbeta Deviations : 0.10 % 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: 0.74 (0.26), residues: 1106 helix: 1.71 (0.27), residues: 369 sheet: 0.44 (0.32), residues: 302 loop : -0.47 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 24 TYR 0.027 0.001 TYR B 59 PHE 0.016 0.001 PHE A 66 TRP 0.015 0.001 TRP B 211 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.19 ( 8784) covalent geometry : angle 0.61349 / 0.32 (11935) SS BOND : bond 0.00425 / 0.21 ( 2) SS BOND : angle 0.80189 / 0.46 ( 4) hydrogen bonds : bond 0.14767 / 10.32 ( 428) hydrogen bonds : angle 6.08790 / 4.37 ( 1206) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 11 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7554 (tm-30) REVERT: E 73 ASP cc_start: 0.7513 (t0) cc_final: 0.7283 (t0) REVERT: E 82 GLN cc_start: 0.8001 (tp40) cc_final: 0.7754 (mm110) REVERT: R 135 LEU cc_start: 0.9295 (mt) cc_final: 0.8892 (pp) REVERT: R 241 ASN cc_start: 0.9094 (m110) cc_final: 0.8617 (m-40) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.0711 time to fit residues: 15.6656 Evaluate side-chains 132 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 GLN C 24 ASN E 167 HIS R 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.105755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.083069 restraints weight = 16852.788| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.65 r_work: 0.2941 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8786 Z= 0.178 Angle : 0.587 10.855 11939 Z= 0.307 Chirality : 0.045 0.234 1344 Planarity : 0.004 0.062 1526 Dihedral : 5.282 84.883 1226 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.13 % Allowed : 8.61 % Favored : 89.26 % 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: 0.91 (0.26), residues: 1106 helix: 1.96 (0.26), residues: 376 sheet: 0.41 (0.31), residues: 294 loop : -0.40 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 24 TYR 0.022 0.001 TYR B 59 PHE 0.018 0.002 PHE R 9 TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS E 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 ( 8784) covalent geometry : angle 0.58673 / 0.31 (11935) SS BOND : bond 0.00460 / 0.23 ( 2) SS BOND : angle 1.11537 / 0.57 ( 4) hydrogen bonds : bond 0.04233 / 2.91 ( 428) hydrogen bonds : angle 4.81553 / 3.46 ( 1206) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.9032 (m-30) cc_final: 0.8791 (m-30) REVERT: A 235 TYR cc_start: 0.9343 (m-80) cc_final: 0.9000 (m-80) REVERT: B 20 ASP cc_start: 0.8412 (m-30) cc_final: 0.8038 (m-30) REVERT: C 11 GLN cc_start: 0.8119 (tm-30) cc_final: 0.7742 (tm-30) REVERT: C 42 GLU cc_start: 0.8366 (mp0) cc_final: 0.7840 (mp0) REVERT: E 73 ASP cc_start: 0.8059 (t0) cc_final: 0.7577 (t0) REVERT: E 82 GLN cc_start: 0.8315 (tp40) cc_final: 0.8027 (mm110) REVERT: E 246 GLU cc_start: 0.6579 (mp0) cc_final: 0.6379 (mp0) REVERT: R 241 ASN cc_start: 0.9261 (m110) cc_final: 0.8858 (m110) outliers start: 19 outliers final: 12 residues processed: 151 average time/residue: 0.0659 time to fit residues: 14.0223 Evaluate side-chains 145 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 216 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 186 GLN R 23 ASN R 47 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.106229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.083457 restraints weight = 16785.845| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.66 r_work: 0.2948 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8786 Z= 0.139 Angle : 0.559 10.263 11939 Z= 0.287 Chirality : 0.044 0.267 1344 Planarity : 0.004 0.057 1526 Dihedral : 5.221 81.039 1226 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.46 % Allowed : 13.53 % Favored : 84.00 % 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: 0.99 (0.26), residues: 1106 helix: 2.06 (0.27), residues: 376 sheet: 0.37 (0.31), residues: 297 loop : -0.33 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 24 TYR 0.011 0.001 TYR B 59 PHE 0.018 0.001 PHE R 9 TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS E 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 8784) covalent geometry : angle 0.55913 / 0.29 (11935) SS BOND : bond 0.00593 / 0.29 ( 2) SS BOND : angle 0.92206 / 0.47 ( 4) hydrogen bonds : bond 0.03761 / 2.60 ( 428) hydrogen bonds : angle 4.58822 / 3.29 ( 1206) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.9021 (m-30) cc_final: 0.8758 (m-30) REVERT: A 235 TYR cc_start: 0.9325 (m-80) cc_final: 0.8886 (m-80) REVERT: B 19 ARG cc_start: 0.8446 (mmt90) cc_final: 0.8162 (mmt90) REVERT: B 20 ASP cc_start: 0.8375 (m-30) cc_final: 0.8007 (m-30) REVERT: B 57 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8968 (pttt) REVERT: B 127 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8871 (mttt) REVERT: B 258 ASP cc_start: 0.7327 (t0) cc_final: 0.6978 (t0) REVERT: C 9 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7805 (tp) REVERT: C 11 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7755 (tm-30) REVERT: C 42 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: E 73 ASP cc_start: 0.8085 (t0) cc_final: 0.7788 (t0) REVERT: E 82 GLN cc_start: 0.8185 (tp-100) cc_final: 0.7886 (mm110) REVERT: E 246 GLU cc_start: 0.6545 (mp0) cc_final: 0.6287 (mp0) REVERT: R 259 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9125 (ttpt) outliers start: 22 outliers final: 10 residues processed: 154 average time/residue: 0.0730 time to fit residues: 15.7668 Evaluate side-chains 145 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 259 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 103 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.106582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.083539 restraints weight = 16956.448| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.74 r_work: 0.2946 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8786 Z= 0.128 Angle : 0.537 9.529 11939 Z= 0.278 Chirality : 0.043 0.223 1344 Planarity : 0.004 0.055 1526 Dihedral : 5.110 74.981 1226 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.02 % Allowed : 15.66 % Favored : 81.32 % 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: 0.99 (0.26), residues: 1106 helix: 2.11 (0.27), residues: 373 sheet: 0.34 (0.31), residues: 298 loop : -0.34 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 24 TYR 0.016 0.001 TYR A 107 PHE 0.017 0.001 PHE R 9 TRP 0.013 0.001 TRP B 211 HIS 0.002 0.001 HIS E 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 8784) covalent geometry : angle 0.53696 / 0.28 (11935) SS BOND : bond 0.00498 / 0.24 ( 2) SS BOND : angle 0.91383 / 0.44 ( 4) hydrogen bonds : bond 0.03556 / 2.47 ( 428) hydrogen bonds : angle 4.49588 / 3.23 ( 1206) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8770 (m-30) cc_final: 0.8484 (m-30) REVERT: A 235 TYR cc_start: 0.9239 (m-80) cc_final: 0.8742 (m-80) REVERT: B 19 ARG cc_start: 0.8344 (mmt90) cc_final: 0.8061 (mmt90) REVERT: B 20 ASP cc_start: 0.8302 (m-30) cc_final: 0.7942 (m-30) REVERT: B 258 ASP cc_start: 0.7116 (t0) cc_final: 0.6870 (t0) REVERT: B 291 ASP cc_start: 0.8454 (m-30) cc_final: 0.7711 (m-30) REVERT: C 9 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7768 (tp) REVERT: C 42 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: E 73 ASP cc_start: 0.7898 (t0) cc_final: 0.7503 (t0) REVERT: E 82 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7795 (mm110) REVERT: E 246 GLU cc_start: 0.6595 (mp0) cc_final: 0.6353 (mp0) REVERT: R 259 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.9059 (ttpt) outliers start: 27 outliers final: 13 residues processed: 156 average time/residue: 0.0659 time to fit residues: 14.6025 Evaluate side-chains 150 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 259 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 5 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 72 optimal weight: 0.2980 chunk 96 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.106497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.083489 restraints weight = 16734.408| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.68 r_work: 0.2949 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8786 Z= 0.148 Angle : 0.555 10.683 11939 Z= 0.288 Chirality : 0.044 0.331 1344 Planarity : 0.004 0.051 1526 Dihedral : 5.154 73.139 1226 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.24 % Allowed : 16.33 % Favored : 80.43 % 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: 1.00 (0.26), residues: 1106 helix: 2.09 (0.27), residues: 376 sheet: 0.36 (0.31), residues: 296 loop : -0.34 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 160 TYR 0.017 0.001 TYR A 107 PHE 0.018 0.001 PHE R 9 TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS E 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 8784) covalent geometry : angle 0.55438 / 0.29 (11935) SS BOND : bond 0.00569 / 0.28 ( 2) SS BOND : angle 0.95275 / 0.45 ( 4) hydrogen bonds : bond 0.03657 / 2.56 ( 428) hydrogen bonds : angle 4.52646 / 3.25 ( 1206) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.9030 (m-30) cc_final: 0.8726 (m-30) REVERT: B 19 ARG cc_start: 0.8445 (mmt90) cc_final: 0.8139 (mmt90) REVERT: B 20 ASP cc_start: 0.8410 (m-30) cc_final: 0.8055 (m-30) REVERT: B 258 ASP cc_start: 0.7262 (t0) cc_final: 0.6995 (t0) REVERT: B 291 ASP cc_start: 0.8636 (m-30) cc_final: 0.7877 (m-30) REVERT: C 9 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7683 (tp) REVERT: C 42 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7778 (mp0) REVERT: E 246 GLU cc_start: 0.6604 (mp0) cc_final: 0.6333 (mp0) REVERT: R 59 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8621 (mt) REVERT: R 241 ASN cc_start: 0.9155 (m110) cc_final: 0.8770 (m110) REVERT: R 259 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.9009 (ttpt) outliers start: 29 outliers final: 19 residues processed: 152 average time/residue: 0.0725 time to fit residues: 15.6704 Evaluate side-chains 152 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 47 ASN Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 259 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 27 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 0.3980 chunk 97 optimal weight: 0.0770 chunk 57 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.107800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.084846 restraints weight = 16764.060| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.71 r_work: 0.2972 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8786 Z= 0.114 Angle : 0.542 10.623 11939 Z= 0.278 Chirality : 0.044 0.363 1344 Planarity : 0.004 0.056 1526 Dihedral : 5.068 69.514 1226 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.35 % Allowed : 17.34 % Favored : 80.31 % 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: 1.05 (0.27), residues: 1106 helix: 2.20 (0.27), residues: 373 sheet: 0.33 (0.31), residues: 298 loop : -0.30 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 160 TYR 0.018 0.001 TYR A 107 PHE 0.019 0.001 PHE R 9 TRP 0.012 0.001 TRP B 211 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 8784) covalent geometry : angle 0.54147 / 0.28 (11935) SS BOND : bond 0.00502 / 0.24 ( 2) SS BOND : angle 0.95394 / 0.43 ( 4) hydrogen bonds : bond 0.03375 / 2.36 ( 428) hydrogen bonds : angle 4.43733 / 3.18 ( 1206) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8735 (m-30) cc_final: 0.8438 (m-30) REVERT: A 90 GLN cc_start: 0.9024 (pt0) cc_final: 0.8713 (pt0) REVERT: A 235 TYR cc_start: 0.9242 (m-80) cc_final: 0.8783 (m-80) REVERT: B 19 ARG cc_start: 0.8355 (mmt90) cc_final: 0.8108 (mmt90) REVERT: B 20 ASP cc_start: 0.8285 (m-30) cc_final: 0.7937 (m-30) REVERT: B 258 ASP cc_start: 0.7070 (t0) cc_final: 0.6843 (t0) REVERT: B 291 ASP cc_start: 0.8452 (m-30) cc_final: 0.7759 (m-30) REVERT: C 42 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: R 59 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8554 (mt) REVERT: R 259 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.9091 (ttpt) outliers start: 21 outliers final: 12 residues processed: 159 average time/residue: 0.0677 time to fit residues: 15.2836 Evaluate side-chains 148 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain R residue 47 ASN Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 259 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 26 optimal weight: 0.0270 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.108380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.085253 restraints weight = 16984.137| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.75 r_work: 0.2974 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8786 Z= 0.111 Angle : 0.566 14.645 11939 Z= 0.282 Chirality : 0.044 0.394 1344 Planarity : 0.004 0.056 1526 Dihedral : 4.971 66.077 1226 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.02 % Allowed : 18.12 % Favored : 78.86 % 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: 1.12 (0.27), residues: 1106 helix: 2.22 (0.27), residues: 373 sheet: 0.49 (0.32), residues: 284 loop : -0.31 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 200 TYR 0.017 0.001 TYR A 107 PHE 0.021 0.001 PHE R 9 TRP 0.012 0.001 TRP B 211 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 8784) covalent geometry : angle 0.56534 / 0.28 (11935) SS BOND : bond 0.00501 / 0.24 ( 2) SS BOND : angle 0.97466 / 0.43 ( 4) hydrogen bonds : bond 0.03283 / 2.31 ( 428) hydrogen bonds : angle 4.41747 / 3.16 ( 1206) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8738 (m-30) cc_final: 0.8433 (m-30) REVERT: A 235 TYR cc_start: 0.9238 (m-80) cc_final: 0.8834 (m-80) REVERT: B 19 ARG cc_start: 0.8337 (mmt90) cc_final: 0.8101 (mmt90) REVERT: B 20 ASP cc_start: 0.8295 (m-30) cc_final: 0.7940 (m-30) REVERT: C 42 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7643 (mp0) REVERT: R 59 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8523 (mt) REVERT: R 259 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.9083 (ttpt) outliers start: 27 outliers final: 16 residues processed: 159 average time/residue: 0.0695 time to fit residues: 15.9612 Evaluate side-chains 156 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 47 ASN Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 259 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 73 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 19 optimal weight: 0.0270 chunk 51 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.106404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.083450 restraints weight = 16740.001| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.65 r_work: 0.2948 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8786 Z= 0.165 Angle : 0.599 14.536 11939 Z= 0.304 Chirality : 0.045 0.411 1344 Planarity : 0.004 0.057 1526 Dihedral : 5.086 65.072 1226 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.80 % Allowed : 18.90 % Favored : 78.30 % 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: 1.05 (0.26), residues: 1106 helix: 2.18 (0.27), residues: 376 sheet: 0.44 (0.31), residues: 284 loop : -0.38 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 200 TYR 0.021 0.002 TYR R 202 PHE 0.021 0.001 PHE R 9 TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS E 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 8784) covalent geometry : angle 0.59852 / 0.30 (11935) SS BOND : bond 0.00639 / 0.31 ( 2) SS BOND : angle 1.08855 / 0.49 ( 4) hydrogen bonds : bond 0.03574 / 2.51 ( 428) hydrogen bonds : angle 4.52933 / 3.25 ( 1206) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.9021 (m-30) cc_final: 0.8715 (m-30) REVERT: A 235 TYR cc_start: 0.9306 (m-80) cc_final: 0.8843 (m-80) REVERT: B 19 ARG cc_start: 0.8419 (mmt90) cc_final: 0.8166 (mmt90) REVERT: B 20 ASP cc_start: 0.8408 (m-30) cc_final: 0.8054 (m-30) REVERT: C 42 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: E 246 GLU cc_start: 0.6457 (mp0) cc_final: 0.6244 (mp0) REVERT: R 59 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8578 (mt) REVERT: R 241 ASN cc_start: 0.9096 (m110) cc_final: 0.8823 (m110) REVERT: R 259 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.9020 (ttpt) outliers start: 25 outliers final: 19 residues processed: 153 average time/residue: 0.0764 time to fit residues: 16.4872 Evaluate side-chains 155 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 47 ASN Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 131 TRP Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 259 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.0670 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 91 optimal weight: 0.4980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 GLN E 186 GLN R 47 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.108620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.085785 restraints weight = 16700.935| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.71 r_work: 0.2990 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8786 Z= 0.109 Angle : 0.578 15.316 11939 Z= 0.289 Chirality : 0.044 0.433 1344 Planarity : 0.004 0.052 1526 Dihedral : 4.948 60.629 1226 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.80 % Allowed : 19.13 % Favored : 78.08 % 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: 1.07 (0.27), residues: 1106 helix: 2.20 (0.27), residues: 373 sheet: 0.44 (0.31), residues: 287 loop : -0.35 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 200 TYR 0.017 0.001 TYR A 107 PHE 0.022 0.001 PHE R 9 TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 8784) covalent geometry : angle 0.57786 / 0.29 (11935) SS BOND : bond 0.00474 / 0.23 ( 2) SS BOND : angle 1.03599 / 0.45 ( 4) hydrogen bonds : bond 0.03265 / 2.31 ( 428) hydrogen bonds : angle 4.45911 / 3.19 ( 1206) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8716 (m-30) cc_final: 0.8406 (m-30) REVERT: A 235 TYR cc_start: 0.9219 (m-80) cc_final: 0.8756 (m-80) REVERT: B 19 ARG cc_start: 0.8336 (mmt90) cc_final: 0.8092 (mmt90) REVERT: B 20 ASP cc_start: 0.8268 (m-30) cc_final: 0.7920 (m-30) REVERT: C 42 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: E 140 MET cc_start: 0.8981 (mmm) cc_final: 0.8724 (mmm) REVERT: R 59 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8498 (mt) REVERT: R 259 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.9021 (ttpt) outliers start: 25 outliers final: 18 residues processed: 160 average time/residue: 0.0692 time to fit residues: 15.8967 Evaluate side-chains 157 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 183 GLN Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 47 ASN Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 259 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 15 optimal weight: 0.0870 chunk 4 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.109182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.086278 restraints weight = 16767.490| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.72 r_work: 0.2993 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8786 Z= 0.109 Angle : 0.581 16.771 11939 Z= 0.289 Chirality : 0.044 0.381 1344 Planarity : 0.004 0.054 1526 Dihedral : 4.877 58.415 1226 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.46 % Allowed : 19.57 % Favored : 77.96 % 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: 1.06 (0.27), residues: 1106 helix: 2.20 (0.27), residues: 373 sheet: 0.41 (0.31), residues: 284 loop : -0.33 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 200 TYR 0.017 0.001 TYR A 107 PHE 0.026 0.001 PHE R 9 TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 8784) covalent geometry : angle 0.58037 / 0.29 (11935) SS BOND : bond 0.00466 / 0.23 ( 2) SS BOND : angle 1.04829 / 0.46 ( 4) hydrogen bonds : bond 0.03226 / 2.28 ( 428) hydrogen bonds : angle 4.42684 / 3.17 ( 1206) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8716 (m-30) cc_final: 0.8409 (m-30) REVERT: A 235 TYR cc_start: 0.9218 (m-80) cc_final: 0.8742 (m-80) REVERT: B 19 ARG cc_start: 0.8341 (mmt90) cc_final: 0.8100 (mmt90) REVERT: B 20 ASP cc_start: 0.8275 (m-30) cc_final: 0.7927 (m-30) REVERT: B 45 MET cc_start: 0.8726 (mmm) cc_final: 0.8424 (mtp) REVERT: C 32 LYS cc_start: 0.8688 (tttp) cc_final: 0.8404 (tptm) REVERT: C 42 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: R 59 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8501 (mt) REVERT: R 241 ASN cc_start: 0.8815 (m110) cc_final: 0.8593 (m-40) REVERT: R 259 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.9030 (ttpt) outliers start: 22 outliers final: 18 residues processed: 154 average time/residue: 0.0691 time to fit residues: 15.3870 Evaluate side-chains 158 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 47 ASN Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 131 TRP Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 259 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.107392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.084466 restraints weight = 16720.446| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.67 r_work: 0.2965 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8786 Z= 0.147 Angle : 0.599 15.631 11939 Z= 0.301 Chirality : 0.044 0.423 1344 Planarity : 0.004 0.055 1526 Dihedral : 4.971 57.881 1226 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.80 % Allowed : 19.57 % Favored : 77.63 % 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: 1.03 (0.27), residues: 1106 helix: 2.18 (0.27), residues: 376 sheet: 0.37 (0.31), residues: 284 loop : -0.36 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 200 TYR 0.017 0.001 TYR A 107 PHE 0.024 0.001 PHE R 9 TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS E 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 8784) covalent geometry : angle 0.59831 / 0.30 (11935) SS BOND : bond 0.00572 / 0.28 ( 2) SS BOND : angle 1.10531 / 0.49 ( 4) hydrogen bonds : bond 0.03466 / 2.45 ( 428) hydrogen bonds : angle 4.49862 / 3.22 ( 1206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1726.51 seconds wall clock time: 30 minutes 14.65 seconds (1814.65 seconds total)