Starting phenix.real_space_refine on Sat Aug 23 00:10:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ejk_28185/08_2025/8ejk_28185.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejk_28185/08_2025/8ejk_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_28185/08_2025/8ejk_28185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejk_28185/08_2025/8ejk_28185.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ejk_28185/08_2025/8ejk_28185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejk_28185/08_2025/8ejk_28185.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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-2.0-5787/lib/python3.9/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: 1.95, per 1000 atoms: 0.23 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: 0.55 Conformation dependent library (CDL) restraints added in 254.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.17 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: 0.85 Time building geometry restraints manager: 0.78 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: 4835 23.80 - 47.61: 304 47.61 - 71.41: 23 71.41 - 95.21: 6 95.21 - 119.02: 1 Dihedral angle restraints: 5169 sinusoidal: 1948 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 5166 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: 0.510 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.940 Find NCS groups from input model: 0.030 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 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 : 14.172 119.016 3095 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 aren 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 covalent geometry : bond 0.00388 ( 8784) covalent geometry : angle 0.61349 (11935) SS BOND : bond 0.00425 ( 2) SS BOND : angle 0.80189 ( 4) hydrogen bonds : bond 0.14767 ( 428) hydrogen bonds : angle 6.08790 ( 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 : 0.196 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: 0.0670 time to fit residues: 14.8613 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 : 0.192 ------------------------------------------------------------------------------- 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: 0.0870 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: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN E 167 HIS E 186 GLN R 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.106126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.083062 restraints weight = 16884.422| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.71 r_work: 0.2942 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8786 Z= 0.167 Angle : 0.580 10.843 11939 Z= 0.302 Chirality : 0.045 0.236 1344 Planarity : 0.004 0.061 1526 Dihedral : 5.847 86.725 1239 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.13 % Allowed : 8.72 % Favored : 89.15 % 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 aren not related in a simple way. whole: 0.94 (0.26), residues: 1106 helix: 1.99 (0.26), residues: 376 sheet: 0.42 (0.31), residues: 294 loop : -0.39 (0.32), 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 0.001 PHE R 9 TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS E 232 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8784) covalent geometry : angle 0.58002 (11935) SS BOND : bond 0.01001 ( 2) SS BOND : angle 1.12198 ( 4) hydrogen bonds : bond 0.04126 ( 428) hydrogen bonds : angle 4.77231 ( 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 160 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8793 (m-30) cc_final: 0.8538 (m-30) REVERT: A 235 TYR cc_start: 0.9272 (m-80) cc_final: 0.8940 (m-80) REVERT: B 20 ASP cc_start: 0.8296 (m-30) cc_final: 0.7912 (m-30) REVERT: B 45 MET cc_start: 0.8992 (mmm) cc_final: 0.8787 (mtp) REVERT: C 11 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7697 (tm-30) REVERT: C 42 GLU cc_start: 0.8189 (mp0) cc_final: 0.7656 (mp0) REVERT: E 73 ASP cc_start: 0.7886 (t0) cc_final: 0.7459 (t0) REVERT: E 82 GLN cc_start: 0.8216 (tp40) cc_final: 0.7926 (mm110) REVERT: R 241 ASN cc_start: 0.9190 (m110) cc_final: 0.8776 (m110) outliers start: 19 outliers final: 13 residues processed: 153 average time/residue: 0.0664 time to fit residues: 14.4628 Evaluate side-chains 146 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 67 LEU 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: 0.2980 chunk 42 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 chunk 64 optimal weight: 5.9990 chunk 66 optimal weight: 0.2980 chunk 32 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN R 23 ASN R 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.109101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.086365 restraints weight = 16754.850| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.72 r_work: 0.3000 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 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 : 0.002 0.030 8786 Z= 0.100 Angle : 0.535 10.664 11939 Z= 0.271 Chirality : 0.043 0.275 1344 Planarity : 0.004 0.055 1526 Dihedral : 5.669 89.345 1239 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.13 % Allowed : 13.09 % Favored : 84.79 % 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 aren not related in a simple way. whole: 1.11 (0.26), residues: 1106 helix: 2.18 (0.27), residues: 373 sheet: 0.61 (0.32), residues: 281 loop : -0.39 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 24 TYR 0.010 0.001 TYR R 250 PHE 0.020 0.001 PHE R 9 TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS R 137 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 8784) covalent geometry : angle 0.53525 (11935) SS BOND : bond 0.00529 ( 2) SS BOND : angle 0.88676 ( 4) hydrogen bonds : bond 0.03395 ( 428) hydrogen bonds : angle 4.41828 ( 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 168 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8716 (m-30) cc_final: 0.8471 (m-30) REVERT: A 235 TYR cc_start: 0.9234 (m-80) cc_final: 0.8764 (m-80) REVERT: B 19 ARG cc_start: 0.8333 (mmt90) cc_final: 0.8119 (mmt90) REVERT: B 20 ASP cc_start: 0.8206 (m-30) cc_final: 0.7844 (m-30) REVERT: B 57 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8753 (pttt) REVERT: B 127 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8801 (mttt) REVERT: C 9 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7775 (tp) REVERT: C 11 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7740 (tm-30) REVERT: C 42 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: E 82 GLN cc_start: 0.8032 (tp-100) cc_final: 0.7769 (mm110) REVERT: E 246 GLU cc_start: 0.6627 (mp0) cc_final: 0.6384 (mp0) REVERT: R 136 CYS cc_start: 0.8916 (m) cc_final: 0.8698 (p) REVERT: R 259 LYS cc_start: 0.9388 (OUTLIER) cc_final: 0.9067 (ttpt) outliers start: 19 outliers final: 7 residues processed: 156 average time/residue: 0.0652 time to fit residues: 14.3615 Evaluate side-chains 147 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 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 R residue 55 LEU Chi-restraints excluded: chain R residue 97 LEU 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: 2.9990 chunk 1 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.106731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.083773 restraints weight = 17030.402| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.74 r_work: 0.2953 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1657 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= 0.134 Angle : 0.537 9.113 11939 Z= 0.279 Chirality : 0.043 0.236 1344 Planarity : 0.004 0.053 1526 Dihedral : 5.694 89.533 1239 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.68 % Allowed : 15.44 % Favored : 81.88 % 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 aren not related in a simple way. whole: 1.09 (0.26), residues: 1106 helix: 2.19 (0.27), residues: 376 sheet: 0.59 (0.32), residues: 281 loop : -0.42 (0.31), residues: 449 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 0.018 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 covalent geometry : bond 0.00307 ( 8784) covalent geometry : angle 0.53728 (11935) SS BOND : bond 0.00509 ( 2) SS BOND : angle 0.89162 ( 4) hydrogen bonds : bond 0.03506 ( 428) hydrogen bonds : angle 4.43285 ( 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 172 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8787 (m-30) cc_final: 0.8508 (m-30) REVERT: A 235 TYR cc_start: 0.9228 (m-80) cc_final: 0.8661 (m-80) REVERT: B 19 ARG cc_start: 0.8342 (mmt90) cc_final: 0.8078 (mmt90) REVERT: B 20 ASP cc_start: 0.8278 (m-30) cc_final: 0.7913 (m-30) REVERT: B 127 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8815 (mttt) REVERT: C 9 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7771 (tp) REVERT: C 11 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7896 (tm-30) REVERT: C 42 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: E 76 LYS cc_start: 0.9113 (mtmm) cc_final: 0.8895 (mtmm) REVERT: E 82 GLN cc_start: 0.8030 (tp-100) cc_final: 0.7777 (mm110) REVERT: E 246 GLU cc_start: 0.6399 (mp0) cc_final: 0.6091 (mp0) REVERT: R 241 ASN cc_start: 0.9046 (m110) cc_final: 0.8664 (m110) REVERT: R 259 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9052 (ttpt) outliers start: 24 outliers final: 10 residues processed: 158 average time/residue: 0.0671 time to fit residues: 15.0030 Evaluate side-chains 152 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 197 ILE 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: 9.9990 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN R 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.107293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.084175 restraints weight = 16737.182| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.71 r_work: 0.2958 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1754 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= 0.135 Angle : 0.549 12.261 11939 Z= 0.282 Chirality : 0.044 0.368 1344 Planarity : 0.004 0.051 1526 Dihedral : 5.720 89.468 1239 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.91 % Allowed : 15.88 % Favored : 81.21 % 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 aren not related in a simple way. whole: 1.09 (0.26), residues: 1106 helix: 2.19 (0.27), residues: 376 sheet: 0.51 (0.32), residues: 284 loop : -0.37 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 160 TYR 0.016 0.001 TYR A 107 PHE 0.019 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 covalent geometry : bond 0.00313 ( 8784) covalent geometry : angle 0.54887 (11935) SS BOND : bond 0.00535 ( 2) SS BOND : angle 0.92344 ( 4) hydrogen bonds : bond 0.03497 ( 428) hydrogen bonds : angle 4.42788 ( 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 171 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8770 (m-30) cc_final: 0.8465 (m-30) REVERT: A 235 TYR cc_start: 0.9230 (m-80) cc_final: 0.8747 (m-80) REVERT: B 19 ARG cc_start: 0.8363 (mmt90) cc_final: 0.8078 (mmt90) REVERT: B 20 ASP cc_start: 0.8267 (m-30) cc_final: 0.7920 (m-30) REVERT: B 291 ASP cc_start: 0.8453 (m-30) cc_final: 0.7677 (m-30) REVERT: C 9 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7632 (tp) REVERT: C 11 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7889 (tm-30) REVERT: C 15 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8020 (mp) REVERT: C 42 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: R 59 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8552 (mt) REVERT: R 241 ASN cc_start: 0.9037 (m110) cc_final: 0.8722 (m110) REVERT: R 259 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.9104 (ttpt) outliers start: 26 outliers final: 16 residues processed: 158 average time/residue: 0.0676 time to fit residues: 15.0677 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 : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 197 ILE 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: 7.9990 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 101 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.105282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.082206 restraints weight = 16842.822| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.65 r_work: 0.2926 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 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 : 0.004 0.038 8786 Z= 0.183 Angle : 0.580 8.909 11939 Z= 0.303 Chirality : 0.045 0.323 1344 Planarity : 0.004 0.060 1526 Dihedral : 5.882 89.624 1239 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.91 % Allowed : 17.11 % Favored : 79.98 % 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 aren not related in a simple way. whole: 0.98 (0.26), residues: 1106 helix: 2.11 (0.27), residues: 376 sheet: 0.39 (0.31), residues: 289 loop : -0.41 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.017 0.002 TYR A 107 PHE 0.019 0.002 PHE R 9 TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS E 232 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 8784) covalent geometry : angle 0.58024 (11935) SS BOND : bond 0.00688 ( 2) SS BOND : angle 0.98446 ( 4) hydrogen bonds : bond 0.03832 ( 428) hydrogen bonds : angle 4.56721 ( 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: 26 poor density : 142 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.9032 (m-30) cc_final: 0.8733 (m-30) REVERT: B 19 ARG cc_start: 0.8356 (mmt90) cc_final: 0.8094 (mmt90) REVERT: B 20 ASP cc_start: 0.8462 (m-30) cc_final: 0.8108 (m-30) REVERT: C 11 GLN cc_start: 0.8286 (tm-30) cc_final: 0.7926 (tm-30) REVERT: C 15 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8032 (mp) REVERT: C 42 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: E 246 GLU cc_start: 0.6472 (mp0) cc_final: 0.6261 (mp0) REVERT: R 59 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8608 (mt) REVERT: R 241 ASN cc_start: 0.9178 (m110) cc_final: 0.8850 (m110) REVERT: R 259 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9012 (ttpt) outliers start: 26 outliers final: 14 residues processed: 155 average time/residue: 0.0616 time to fit residues: 13.5237 Evaluate side-chains 151 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 15 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 30 SER 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 164 VAL Chi-restraints excluded: chain R residue 197 ILE 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: 2.9990 chunk 67 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 0.0770 chunk 27 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 0.0970 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.107469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.084579 restraints weight = 16991.604| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.65 r_work: 0.2974 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8786 Z= 0.119 Angle : 0.567 14.762 11939 Z= 0.285 Chirality : 0.044 0.432 1344 Planarity : 0.004 0.061 1526 Dihedral : 5.636 85.393 1239 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.02 % Allowed : 18.46 % Favored : 78.52 % 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 aren not related in a simple way. whole: 1.03 (0.26), residues: 1106 helix: 2.15 (0.27), residues: 373 sheet: 0.44 (0.31), residues: 287 loop : -0.38 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 24 TYR 0.015 0.001 TYR A 107 PHE 0.020 0.001 PHE R 9 TRP 0.011 0.001 TRP B 211 HIS 0.002 0.001 HIS E 232 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8784) covalent geometry : angle 0.56631 (11935) SS BOND : bond 0.00542 ( 2) SS BOND : angle 1.00643 ( 4) hydrogen bonds : bond 0.03424 ( 428) hydrogen bonds : angle 4.45166 ( 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 172 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8982 (m-30) cc_final: 0.8686 (m-30) REVERT: A 55 ILE cc_start: 0.7424 (OUTLIER) cc_final: 0.7183 (tt) REVERT: A 75 MET cc_start: 0.8961 (ttt) cc_final: 0.8748 (ttt) REVERT: A 90 GLN cc_start: 0.9130 (pt0) cc_final: 0.8813 (pt0) REVERT: A 235 TYR cc_start: 0.9334 (m-80) cc_final: 0.8832 (m-80) REVERT: B 19 ARG cc_start: 0.8404 (mmt90) cc_final: 0.8155 (mmt90) REVERT: B 20 ASP cc_start: 0.8376 (m-30) cc_final: 0.8031 (m-30) REVERT: B 30 LEU cc_start: 0.8759 (tt) cc_final: 0.8551 (tt) REVERT: C 11 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7921 (tm-30) REVERT: C 15 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8296 (mp) REVERT: C 19 LEU cc_start: 0.6190 (mm) cc_final: 0.5983 (mm) REVERT: C 42 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: E 73 ASP cc_start: 0.7723 (t0) cc_final: 0.7371 (t70) REVERT: R 59 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8599 (mt) REVERT: R 241 ASN cc_start: 0.9071 (m110) cc_final: 0.8811 (m110) REVERT: R 259 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.9013 (ttpt) outliers start: 27 outliers final: 18 residues processed: 164 average time/residue: 0.0633 time to fit residues: 14.8090 Evaluate side-chains 158 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 127 LYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET 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 E residue 91 THR Chi-restraints excluded: chain R residue 36 LEU 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 131 TRP Chi-restraints excluded: chain R residue 162 THR Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 206 LEU 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: 9.9990 chunk 76 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN R 23 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.106929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.084040 restraints weight = 16712.243| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.65 r_work: 0.2959 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8786 Z= 0.137 Angle : 0.573 15.324 11939 Z= 0.291 Chirality : 0.044 0.379 1344 Planarity : 0.004 0.058 1526 Dihedral : 5.644 85.600 1239 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.58 % Allowed : 18.34 % 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 aren not related in a simple way. whole: 0.99 (0.26), residues: 1106 helix: 2.18 (0.27), residues: 375 sheet: 0.38 (0.31), residues: 289 loop : -0.44 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 200 TYR 0.018 0.001 TYR A 107 PHE 0.021 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 covalent geometry : bond 0.00318 ( 8784) covalent geometry : angle 0.57286 (11935) SS BOND : bond 0.00541 ( 2) SS BOND : angle 1.08901 ( 4) hydrogen bonds : bond 0.03513 ( 428) hydrogen bonds : angle 4.52007 ( 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 170 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8999 (m-30) cc_final: 0.8683 (m-30) REVERT: A 75 MET cc_start: 0.8938 (ttt) cc_final: 0.8730 (ttt) REVERT: A 235 TYR cc_start: 0.9318 (m-80) cc_final: 0.8787 (m-80) REVERT: B 19 ARG cc_start: 0.8368 (mmt90) cc_final: 0.8114 (mmt90) REVERT: B 20 ASP cc_start: 0.8402 (m-30) cc_final: 0.8059 (m-30) REVERT: B 30 LEU cc_start: 0.8740 (tt) cc_final: 0.8539 (tt) REVERT: C 11 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7923 (tm-30) REVERT: C 15 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8035 (mp) REVERT: C 42 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: E 246 GLU cc_start: 0.6578 (mp0) cc_final: 0.6376 (mp0) REVERT: R 59 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8671 (mt) REVERT: R 241 ASN cc_start: 0.9095 (m110) cc_final: 0.8880 (m110) REVERT: R 259 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9053 (ttpt) outliers start: 32 outliers final: 20 residues processed: 159 average time/residue: 0.0722 time to fit residues: 16.6231 Evaluate side-chains 160 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 143 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain R residue 36 LEU 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 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 162 THR Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 197 ILE 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: 10.0000 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 0.0170 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.108432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.085578 restraints weight = 16717.796| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.72 r_work: 0.2986 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8786 Z= 0.113 Angle : 0.575 16.222 11939 Z= 0.289 Chirality : 0.044 0.391 1344 Planarity : 0.004 0.057 1526 Dihedral : 5.474 82.642 1239 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.02 % Allowed : 19.02 % 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 aren not related in a simple way. whole: 1.03 (0.27), residues: 1106 helix: 2.28 (0.27), residues: 371 sheet: 0.36 (0.31), residues: 292 loop : -0.43 (0.32), residues: 443 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 0.023 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 covalent geometry : bond 0.00255 ( 8784) covalent geometry : angle 0.57431 (11935) SS BOND : bond 0.00502 ( 2) SS BOND : angle 1.07222 ( 4) hydrogen bonds : bond 0.03294 ( 428) hydrogen bonds : angle 4.44175 ( 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 171 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8718 (m-30) cc_final: 0.8410 (m-30) REVERT: A 75 MET cc_start: 0.8717 (ttt) cc_final: 0.8455 (ttt) REVERT: A 235 TYR cc_start: 0.9249 (m-80) cc_final: 0.8742 (m-80) REVERT: B 19 ARG cc_start: 0.8356 (mmt90) cc_final: 0.8116 (mmt90) REVERT: B 20 ASP cc_start: 0.8256 (m-30) cc_final: 0.7913 (m-30) REVERT: C 11 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7888 (tm-30) REVERT: C 15 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8123 (mp) REVERT: C 42 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: R 59 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8593 (mt) REVERT: R 241 ASN cc_start: 0.8964 (m110) cc_final: 0.8736 (m110) outliers start: 27 outliers final: 20 residues processed: 162 average time/residue: 0.0680 time to fit residues: 15.8428 Evaluate side-chains 160 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 262 MET Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain R residue 36 LEU 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 123 SER Chi-restraints excluded: chain R residue 131 TRP 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 197 ILE Chi-restraints excluded: chain R residue 206 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 4.9990 chunk 74 optimal weight: 0.0980 chunk 90 optimal weight: 3.9990 chunk 106 optimal weight: 0.0030 chunk 21 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN E 183 GLN E 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.109611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.086891 restraints weight = 16758.595| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.71 r_work: 0.3005 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 8786 Z= 0.105 Angle : 0.581 16.488 11939 Z= 0.287 Chirality : 0.043 0.387 1344 Planarity : 0.004 0.057 1526 Dihedral : 5.317 80.397 1239 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.57 % Allowed : 19.13 % 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 aren not related in a simple way. whole: 1.09 (0.27), residues: 1106 helix: 2.32 (0.27), residues: 371 sheet: 0.46 (0.32), residues: 282 loop : -0.42 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 200 TYR 0.016 0.001 TYR A 107 PHE 0.024 0.001 PHE R 9 TRP 0.011 0.001 TRP B 211 HIS 0.002 0.000 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8784) covalent geometry : angle 0.58117 (11935) SS BOND : bond 0.00449 ( 2) SS BOND : angle 1.02962 ( 4) hydrogen bonds : bond 0.03201 ( 428) hydrogen bonds : angle 4.36519 ( 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 168 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8689 (m-30) cc_final: 0.8405 (m-30) REVERT: A 75 MET cc_start: 0.8702 (ttt) cc_final: 0.8372 (ttt) REVERT: A 235 TYR cc_start: 0.9223 (m-80) cc_final: 0.8700 (m-80) REVERT: B 19 ARG cc_start: 0.8346 (mmt90) cc_final: 0.8130 (mmt90) REVERT: B 20 ASP cc_start: 0.8214 (m-30) cc_final: 0.7875 (m-30) REVERT: C 11 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7857 (tm-30) REVERT: C 42 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: R 59 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8508 (mt) REVERT: R 241 ASN cc_start: 0.8867 (m110) cc_final: 0.8655 (m110) outliers start: 23 outliers final: 17 residues processed: 161 average time/residue: 0.0712 time to fit residues: 16.3030 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 : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 18 ILE 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 48 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 131 TRP 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 197 ILE Chi-restraints excluded: chain R residue 206 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 91 optimal weight: 0.0370 chunk 79 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN E 39 GLN E 142 GLN E 179 GLN ** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.109707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.086981 restraints weight = 16651.656| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.70 r_work: 0.3012 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 8786 Z= 0.125 Angle : 0.908 59.198 11939 Z= 0.504 Chirality : 0.044 0.394 1344 Planarity : 0.004 0.057 1526 Dihedral : 5.321 80.388 1239 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.91 % Allowed : 19.80 % Favored : 77.29 % 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 aren not related in a simple way. whole: 1.10 (0.27), residues: 1106 helix: 2.34 (0.27), residues: 371 sheet: 0.47 (0.32), residues: 282 loop : -0.43 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 200 TYR 0.017 0.001 TYR R 202 PHE 0.023 0.001 PHE R 9 TRP 0.011 0.001 TRP B 211 HIS 0.002 0.000 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8784) covalent geometry : angle 0.90773 (11935) SS BOND : bond 0.00353 ( 2) SS BOND : angle 1.56848 ( 4) hydrogen bonds : bond 0.03207 ( 428) hydrogen bonds : angle 4.36652 ( 1206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1649.07 seconds wall clock time: 29 minutes 0.95 seconds (1740.95 seconds total)