Starting phenix.real_space_refine on Wed Feb 4 06:56:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9quq_53380/02_2026/9quq_53380.cif Found real_map, /net/cci-nas-00/data/ceres_data/9quq_53380/02_2026/9quq_53380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9quq_53380/02_2026/9quq_53380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9quq_53380/02_2026/9quq_53380.map" model { file = "/net/cci-nas-00/data/ceres_data/9quq_53380/02_2026/9quq_53380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9quq_53380/02_2026/9quq_53380.cif" } resolution = 3.28 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= 0.002 sd= 0.029 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 37 5.16 5 C 5956 2.51 5 N 1572 2.21 5 O 1613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9178 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1703 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1721 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 5, 'TRANS': 213} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1721 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 5, 'TRANS': 213} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1721 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 5, 'TRANS': 213} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1703 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 189 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 189 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 2.65, per 1000 atoms: 0.29 Number of scatterers: 9178 At special positions: 0 Unit cell: (86.9, 102.3, 117.7, 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 37 16.00 O 1613 8.00 N 1572 7.00 C 5956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.95 Conformation dependent library (CDL) restraints added in 409.4 milliseconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 91.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'H' and resid 7 through 35 removed outlier: 3.731A pdb=" N ASP H 35 " --> pdb=" O TRP H 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 13 Processing helix chain 'A' and resid 14 through 57 removed outlier: 3.728A pdb=" N ARG A 40 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TRP A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 70 Processing helix chain 'A' and resid 71 through 76 removed outlier: 5.599A pdb=" N ASP A 74 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 76 " --> pdb=" O ARG A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 95 removed outlier: 3.511A pdb=" N ARG A 95 " --> pdb=" O VAL A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 124 Processing helix chain 'A' and resid 126 through 159 removed outlier: 3.722A pdb=" N LEU A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.533A pdb=" N VAL A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 221 removed outlier: 3.593A pdb=" N THR A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Proline residue: A 187 - end of helix removed outlier: 3.845A pdb=" N GLN A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 13 Processing helix chain 'B' and resid 14 through 57 removed outlier: 4.027A pdb=" N ARG B 40 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE B 41 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B 42 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 70 removed outlier: 3.550A pdb=" N LEU B 65 " --> pdb=" O GLU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 78 through 97 Processing helix chain 'B' and resid 100 through 124 Processing helix chain 'B' and resid 127 through 158 removed outlier: 4.217A pdb=" N GLY B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR B 132 " --> pdb=" O PRO B 128 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL B 133 " --> pdb=" O PHE B 129 " (cutoff:3.500A) Proline residue: B 138 - end of helix Processing helix chain 'B' and resid 163 through 222 removed outlier: 4.136A pdb=" N VAL B 167 " --> pdb=" O THR B 163 " (cutoff:3.500A) Proline residue: B 169 - end of helix removed outlier: 3.555A pdb=" N ALA B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Proline residue: B 187 - end of helix removed outlier: 3.513A pdb=" N ARG B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN B 197 " --> pdb=" O ASN B 193 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG B 198 " --> pdb=" O ARG B 194 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 199 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN B 200 " --> pdb=" O ASN B 196 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B 222 " --> pdb=" O HIS B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 13 Processing helix chain 'C' and resid 14 through 57 removed outlier: 3.673A pdb=" N ARG C 40 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TRP C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 70 Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 78 through 97 removed outlier: 4.254A pdb=" N ILE C 82 " --> pdb=" O GLY C 78 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY C 86 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS C 88 " --> pdb=" O TYR C 84 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU C 89 " --> pdb=" O SER C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 124 removed outlier: 3.605A pdb=" N VAL C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 105 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 159 removed outlier: 3.686A pdb=" N LEU C 130 " --> pdb=" O HIS C 126 " (cutoff:3.500A) Proline residue: C 138 - end of helix removed outlier: 3.736A pdb=" N GLY C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 223 removed outlier: 3.785A pdb=" N ILE C 171 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Proline residue: C 187 - end of helix removed outlier: 4.419A pdb=" N THR C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 13 Processing helix chain 'D' and resid 14 through 57 removed outlier: 3.597A pdb=" N ARG D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.670A pdb=" N LYS D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 77 removed outlier: 3.679A pdb=" N LEU D 76 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N THR D 77 " --> pdb=" O ASP D 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 73 through 77' Processing helix chain 'D' and resid 78 through 97 removed outlier: 3.719A pdb=" N ILE D 82 " --> pdb=" O GLY D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 124 removed outlier: 3.778A pdb=" N GLU D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 157 removed outlier: 3.957A pdb=" N GLY D 131 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR D 132 " --> pdb=" O PRO D 128 " (cutoff:3.500A) Proline residue: D 138 - end of helix removed outlier: 3.634A pdb=" N GLY D 157 " --> pdb=" O PHE D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 222 removed outlier: 3.896A pdb=" N VAL D 167 " --> pdb=" O THR D 163 " (cutoff:3.500A) Proline residue: D 169 - end of helix removed outlier: 3.697A pdb=" N ALA D 172 " --> pdb=" O ALA D 168 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Proline residue: D 187 - end of helix removed outlier: 4.052A pdb=" N ASN D 193 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE D 222 " --> pdb=" O HIS D 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 14 through 57 removed outlier: 3.722A pdb=" N THR E 39 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE E 41 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP E 57 " --> pdb=" O GLU E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 72 removed outlier: 3.844A pdb=" N LYS E 72 " --> pdb=" O GLU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 77 removed outlier: 4.195A pdb=" N LEU E 76 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR E 77 " --> pdb=" O ASP E 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 73 through 77' Processing helix chain 'E' and resid 78 through 95 removed outlier: 3.754A pdb=" N ILE E 82 " --> pdb=" O GLY E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 124 removed outlier: 3.750A pdb=" N VAL E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 159 removed outlier: 3.947A pdb=" N GLY E 131 " --> pdb=" O ILE E 127 " (cutoff:3.500A) Proline residue: E 138 - end of helix removed outlier: 3.682A pdb=" N GLY E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 220 Proline residue: E 169 - end of helix removed outlier: 3.546A pdb=" N ALA E 172 " --> pdb=" O ALA E 168 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA E 177 " --> pdb=" O GLU E 173 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Proline residue: E 187 - end of helix removed outlier: 3.751A pdb=" N ASN E 193 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS E 201 " --> pdb=" O GLN E 197 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU E 202 " --> pdb=" O ARG E 198 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 33 removed outlier: 4.211A pdb=" N VAL F 24 " --> pdb=" O PRO F 20 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE F 31 " --> pdb=" O VAL F 27 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET F 33 " --> pdb=" O LEU F 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 35 775 hydrogen bonds defined for protein. 2322 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: 1.49 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1891 1.33 - 1.45: 2060 1.45 - 1.57: 5329 1.57 - 1.69: 0 1.69 - 1.80: 74 Bond restraints: 9354 Sorted by residual: bond pdb=" N ILE G 18 " pdb=" CA ILE G 18 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.19e-02 7.06e+03 8.41e+00 bond pdb=" N GLU G 15 " pdb=" CA GLU G 15 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.02e+00 bond pdb=" N ASN G 17 " pdb=" CA ASN G 17 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.21e+00 bond pdb=" N VAL G 19 " pdb=" CA VAL G 19 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.23e-02 6.61e+03 5.41e+00 bond pdb=" N ILE G 16 " pdb=" CA ILE G 16 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.23e-02 6.61e+03 4.61e+00 ... (remaining 9349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 12488 1.54 - 3.08: 119 3.08 - 4.63: 33 4.63 - 6.17: 15 6.17 - 7.71: 2 Bond angle restraints: 12657 Sorted by residual: angle pdb=" C ASN G 17 " pdb=" N ILE G 18 " pdb=" CA ILE G 18 " ideal model delta sigma weight residual 122.66 118.12 4.54 9.70e-01 1.06e+00 2.19e+01 angle pdb=" C VAL G 19 " pdb=" N PRO G 20 " pdb=" CA PRO G 20 " ideal model delta sigma weight residual 119.05 123.66 -4.61 1.11e+00 8.12e-01 1.73e+01 angle pdb=" C SER G 14 " pdb=" N GLU G 15 " pdb=" CA GLU G 15 " ideal model delta sigma weight residual 121.54 128.76 -7.22 1.91e+00 2.74e-01 1.43e+01 angle pdb=" N VAL G 19 " pdb=" CA VAL G 19 " pdb=" C VAL G 19 " ideal model delta sigma weight residual 108.88 116.59 -7.71 2.16e+00 2.14e-01 1.27e+01 angle pdb=" CA VAL G 19 " pdb=" C VAL G 19 " pdb=" N PRO G 20 " ideal model delta sigma weight residual 118.88 124.00 -5.12 1.54e+00 4.22e-01 1.11e+01 ... (remaining 12652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 5200 17.89 - 35.79: 290 35.79 - 53.68: 49 53.68 - 71.58: 25 71.58 - 89.47: 15 Dihedral angle restraints: 5579 sinusoidal: 2192 harmonic: 3387 Sorted by residual: dihedral pdb=" C VAL G 19 " pdb=" N VAL G 19 " pdb=" CA VAL G 19 " pdb=" CB VAL G 19 " ideal model delta harmonic sigma weight residual -122.00 -130.40 8.40 0 2.50e+00 1.60e-01 1.13e+01 dihedral pdb=" CB GLU B 106 " pdb=" CG GLU B 106 " pdb=" CD GLU B 106 " pdb=" OE1 GLU B 106 " ideal model delta sinusoidal sigma weight residual 0.00 -89.47 89.47 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG B 92 " pdb=" CD ARG B 92 " pdb=" NE ARG B 92 " pdb=" CZ ARG B 92 " ideal model delta sinusoidal sigma weight residual 180.00 -135.31 -44.69 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 5576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1232 0.050 - 0.100: 203 0.100 - 0.150: 31 0.150 - 0.200: 1 0.200 - 0.249: 2 Chirality restraints: 1469 Sorted by residual: chirality pdb=" CA ILE G 16 " pdb=" N ILE G 16 " pdb=" C ILE G 16 " pdb=" CB ILE G 16 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA VAL G 19 " pdb=" N VAL G 19 " pdb=" C VAL G 19 " pdb=" CB VAL G 19 " both_signs ideal model delta sigma weight residual False 2.44 2.22 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA GLU G 15 " pdb=" N GLU G 15 " pdb=" C GLU G 15 " pdb=" CB GLU G 15 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.26e-01 ... (remaining 1466 not shown) Planarity restraints: 1601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 19 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.33e+00 pdb=" C VAL G 19 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL G 19 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO G 20 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 17 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" C ASN G 17 " -0.028 2.00e-02 2.50e+03 pdb=" O ASN G 17 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE G 18 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 19 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.11e+00 pdb=" N PRO G 20 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO G 20 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 20 " 0.019 5.00e-02 4.00e+02 ... (remaining 1598 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1647 2.77 - 3.30: 9172 3.30 - 3.84: 14785 3.84 - 4.37: 14564 4.37 - 4.90: 27571 Nonbonded interactions: 67739 Sorted by model distance: nonbonded pdb=" NH2 ARG D 38 " pdb=" OG1 THR D 125 " model vdw 2.239 3.120 nonbonded pdb=" NH2 ARG E 38 " pdb=" O LEU E 123 " model vdw 2.296 3.120 nonbonded pdb=" OG SER B 109 " pdb=" NH1 ARG B 113 " model vdw 2.375 3.120 nonbonded pdb=" O GLN C 81 " pdb=" OG SER C 85 " model vdw 2.404 3.040 nonbonded pdb=" O LYS B 55 " pdb=" OG SER B 58 " model vdw 2.454 3.040 ... (remaining 67734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 5 through 220 or (resid 221 and (name N or name CA or name \ C or name CB )))) selection = (chain 'C' and (resid 5 through 220 or (resid 221 and (name N or name CA or name \ C or name CB )))) selection = (chain 'D' and (resid 5 through 220 or (resid 221 and (name N or name CA or name \ C or name CB )))) selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.650 Find NCS groups from input model: 0.270 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 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 : 0.003 0.035 9354 Z= 0.155 Angle : 0.463 7.709 12657 Z= 0.263 Chirality : 0.037 0.249 1469 Planarity : 0.003 0.036 1601 Dihedral : 13.457 89.473 3379 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.47 % Favored : 98.44 % Rotamer: Outliers : 0.32 % Allowed : 0.42 % Favored : 99.26 % 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: 4.59 (0.24), residues: 1154 helix: 3.44 (0.15), residues: 997 sheet: None (None), residues: 0 loop : -0.08 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 95 TYR 0.012 0.001 TYR D 192 PHE 0.010 0.001 PHE B 90 TRP 0.008 0.001 TRP C 57 HIS 0.003 0.000 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9354) covalent geometry : angle 0.46328 (12657) hydrogen bonds : bond 0.11904 ( 775) hydrogen bonds : angle 3.54227 ( 2322) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 328 time to evaluate : 0.355 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR C 223 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 48 GLU cc_start: 0.7909 (tp30) cc_final: 0.7397 (tp30) REVERT: A 109 SER cc_start: 0.8638 (m) cc_final: 0.8253 (p) REVERT: A 147 TRP cc_start: 0.8270 (t-100) cc_final: 0.8028 (t60) REVERT: A 183 PHE cc_start: 0.8231 (t80) cc_final: 0.7813 (t80) REVERT: A 198 ARG cc_start: 0.8472 (mtt180) cc_final: 0.8237 (mtt-85) REVERT: A 201 LYS cc_start: 0.8681 (tptt) cc_final: 0.8311 (tptt) REVERT: A 207 ASP cc_start: 0.8441 (t0) cc_final: 0.8188 (t0) REVERT: A 219 ARG cc_start: 0.7847 (ttp-110) cc_final: 0.7624 (ttm110) REVERT: B 88 LYS cc_start: 0.7209 (tptt) cc_final: 0.6880 (tptt) REVERT: B 95 ARG cc_start: 0.6643 (mmt90) cc_final: 0.6319 (mpt180) REVERT: B 109 SER cc_start: 0.8109 (t) cc_final: 0.7812 (t) REVERT: B 112 MET cc_start: 0.6923 (mmt) cc_final: 0.6672 (mmt) REVERT: B 121 GLU cc_start: 0.7833 (pt0) cc_final: 0.7500 (pt0) REVERT: B 166 MET cc_start: 0.7159 (tpt) cc_final: 0.6798 (tpt) REVERT: B 173 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7245 (mt-10) REVERT: B 198 ARG cc_start: 0.8288 (mtp85) cc_final: 0.8059 (mmm160) REVERT: B 211 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7848 (mt-10) REVERT: B 213 PHE cc_start: 0.8688 (t80) cc_final: 0.8439 (t80) REVERT: C 21 MET cc_start: 0.7152 (mtp) cc_final: 0.6835 (mtp) REVERT: C 27 PHE cc_start: 0.8297 (m-80) cc_final: 0.7961 (m-10) REVERT: C 121 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7182 (mt-10) REVERT: C 130 LEU cc_start: 0.7945 (mt) cc_final: 0.7694 (mt) REVERT: C 203 GLU cc_start: 0.7972 (tt0) cc_final: 0.7767 (tt0) REVERT: C 211 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7194 (mt-10) REVERT: C 212 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7412 (mt-10) REVERT: D 50 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7526 (tm-30) REVERT: D 67 GLN cc_start: 0.7652 (pt0) cc_final: 0.7405 (pt0) REVERT: D 81 GLN cc_start: 0.8630 (tp40) cc_final: 0.8111 (tp40) REVERT: D 116 MET cc_start: 0.8788 (ttp) cc_final: 0.8570 (ttm) REVERT: D 151 HIS cc_start: 0.7709 (t-170) cc_final: 0.7501 (t-170) REVERT: D 164 LEU cc_start: 0.7069 (pp) cc_final: 0.6784 (pp) REVERT: D 173 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7468 (mt-10) REVERT: D 201 LYS cc_start: 0.8393 (ttpt) cc_final: 0.8172 (ttpt) REVERT: D 214 THR cc_start: 0.8383 (p) cc_final: 0.8085 (p) REVERT: E 62 LEU cc_start: 0.8435 (mp) cc_final: 0.8167 (mt) REVERT: E 81 GLN cc_start: 0.8320 (tp-100) cc_final: 0.8022 (tp40) REVERT: E 109 SER cc_start: 0.8450 (t) cc_final: 0.8211 (t) REVERT: E 135 SER cc_start: 0.8896 (t) cc_final: 0.8191 (m) REVERT: E 166 MET cc_start: 0.7649 (ttt) cc_final: 0.7405 (ttt) REVERT: E 198 ARG cc_start: 0.7738 (ttm-80) cc_final: 0.7227 (mtp180) REVERT: E 210 MET cc_start: 0.7606 (mmm) cc_final: 0.7194 (mmm) REVERT: E 212 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7418 (mt-10) REVERT: F 18 ILE cc_start: 0.8573 (mt) cc_final: 0.8160 (mm) REVERT: F 29 LEU cc_start: 0.8687 (mt) cc_final: 0.8460 (mt) REVERT: F 31 ILE cc_start: 0.8560 (mt) cc_final: 0.8329 (mt) outliers start: 3 outliers final: 0 residues processed: 329 average time/residue: 0.1089 time to fit residues: 48.6160 Evaluate side-chains 297 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.0770 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 151 HIS B 75 ASN C 193 ASN D 37 GLN D 43 ASN E 165 GLN F 17 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.164900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.137728 restraints weight = 14758.005| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.54 r_work: 0.3618 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9354 Z= 0.143 Angle : 0.497 7.194 12657 Z= 0.261 Chirality : 0.036 0.122 1469 Planarity : 0.003 0.048 1601 Dihedral : 3.207 16.104 1253 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.56 % Favored : 98.35 % Rotamer: Outliers : 2.31 % Allowed : 12.39 % Favored : 85.29 % 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 are not related in a simple way. whole: 4.65 (0.24), residues: 1154 helix: 3.50 (0.15), residues: 999 sheet: None (None), residues: 0 loop : -0.26 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 40 TYR 0.011 0.001 TYR B 192 PHE 0.022 0.001 PHE C 183 TRP 0.007 0.001 TRP D 147 HIS 0.005 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9354) covalent geometry : angle 0.49712 (12657) hydrogen bonds : bond 0.06301 ( 775) hydrogen bonds : angle 3.16582 ( 2322) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 289 time to evaluate : 0.273 Fit side-chains TARDY: cannot create tardy model for: "THR C 223 " (corrupted residue). Skipping it. REVERT: A 47 ARG cc_start: 0.7945 (mmt90) cc_final: 0.7730 (mmt90) REVERT: A 48 GLU cc_start: 0.8175 (tp30) cc_final: 0.7651 (tp30) REVERT: A 89 GLU cc_start: 0.7963 (tp30) cc_final: 0.7643 (tp30) REVERT: A 109 SER cc_start: 0.8669 (m) cc_final: 0.8306 (p) REVERT: A 147 TRP cc_start: 0.8452 (t-100) cc_final: 0.8202 (t-100) REVERT: A 183 PHE cc_start: 0.8244 (t80) cc_final: 0.7860 (t80) REVERT: A 201 LYS cc_start: 0.8855 (tptt) cc_final: 0.8502 (tptt) REVERT: A 207 ASP cc_start: 0.8314 (t0) cc_final: 0.8098 (t0) REVERT: B 88 LYS cc_start: 0.7267 (tptt) cc_final: 0.6969 (tptt) REVERT: B 95 ARG cc_start: 0.6362 (mmt90) cc_final: 0.6084 (mpt180) REVERT: B 166 MET cc_start: 0.7380 (tpt) cc_final: 0.6942 (tpt) REVERT: B 211 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7923 (mt-10) REVERT: B 213 PHE cc_start: 0.8746 (t80) cc_final: 0.8479 (t80) REVERT: C 21 MET cc_start: 0.7227 (mtp) cc_final: 0.6964 (mtp) REVERT: C 80 GLU cc_start: 0.7618 (tt0) cc_final: 0.7197 (tt0) REVERT: C 121 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7323 (mt-10) REVERT: C 143 PHE cc_start: 0.8392 (t80) cc_final: 0.8156 (t80) REVERT: C 193 ASN cc_start: 0.8523 (m-40) cc_final: 0.8135 (m-40) REVERT: C 211 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7102 (mt-10) REVERT: C 212 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7433 (mt-10) REVERT: D 81 GLN cc_start: 0.8556 (tp40) cc_final: 0.8071 (tp40) REVERT: D 164 LEU cc_start: 0.7027 (pp) cc_final: 0.6794 (pp) REVERT: D 173 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7634 (mt-10) REVERT: D 201 LYS cc_start: 0.8529 (ttpt) cc_final: 0.8304 (ttpt) REVERT: D 214 THR cc_start: 0.8337 (p) cc_final: 0.8018 (p) REVERT: E 81 GLN cc_start: 0.8322 (tp-100) cc_final: 0.8113 (tp40) REVERT: E 109 SER cc_start: 0.8319 (t) cc_final: 0.8102 (t) REVERT: E 135 SER cc_start: 0.8915 (t) cc_final: 0.8157 (m) REVERT: E 166 MET cc_start: 0.7817 (ttt) cc_final: 0.7557 (ttt) REVERT: E 194 ARG cc_start: 0.7597 (ttp80) cc_final: 0.7296 (ttp80) REVERT: E 198 ARG cc_start: 0.7888 (ttm-80) cc_final: 0.7431 (mtp180) REVERT: E 210 MET cc_start: 0.7477 (mmm) cc_final: 0.7189 (mmm) REVERT: F 31 ILE cc_start: 0.8745 (mt) cc_final: 0.8423 (mt) outliers start: 22 outliers final: 15 residues processed: 293 average time/residue: 0.1065 time to fit residues: 42.0835 Evaluate side-chains 298 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 283 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 55 LYS Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 30 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 91 optimal weight: 0.0570 chunk 80 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 110 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN D 151 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.165687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.138306 restraints weight = 14900.407| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.52 r_work: 0.3628 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9354 Z= 0.132 Angle : 0.490 13.842 12657 Z= 0.253 Chirality : 0.035 0.136 1469 Planarity : 0.003 0.042 1601 Dihedral : 3.168 15.767 1253 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.56 % Favored : 98.35 % Rotamer: Outliers : 2.52 % Allowed : 14.50 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.59 (0.24), residues: 1154 helix: 3.44 (0.15), residues: 1002 sheet: None (None), residues: 0 loop : -0.23 (0.51), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 92 TYR 0.012 0.001 TYR C 66 PHE 0.022 0.001 PHE C 183 TRP 0.007 0.001 TRP D 147 HIS 0.012 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9354) covalent geometry : angle 0.49047 (12657) hydrogen bonds : bond 0.05910 ( 775) hydrogen bonds : angle 3.08027 ( 2322) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 284 time to evaluate : 0.339 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR C 223 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8355 (mm) cc_final: 0.8150 (mp) REVERT: A 47 ARG cc_start: 0.7916 (mmt90) cc_final: 0.7710 (mmt90) REVERT: A 48 GLU cc_start: 0.8127 (tp30) cc_final: 0.7605 (tp30) REVERT: A 109 SER cc_start: 0.8654 (m) cc_final: 0.8247 (p) REVERT: A 147 TRP cc_start: 0.8473 (t-100) cc_final: 0.8202 (t-100) REVERT: A 183 PHE cc_start: 0.8220 (t80) cc_final: 0.7830 (t80) REVERT: A 193 ASN cc_start: 0.8361 (m-40) cc_final: 0.7979 (m-40) REVERT: A 201 LYS cc_start: 0.8856 (tptt) cc_final: 0.8505 (tptt) REVERT: A 207 ASP cc_start: 0.8315 (t0) cc_final: 0.8091 (t0) REVERT: B 88 LYS cc_start: 0.7437 (tptt) cc_final: 0.7202 (tptt) REVERT: B 95 ARG cc_start: 0.6345 (mmt90) cc_final: 0.6079 (mpt180) REVERT: B 166 MET cc_start: 0.7315 (tpt) cc_final: 0.6903 (tpt) REVERT: B 213 PHE cc_start: 0.8711 (t80) cc_final: 0.8448 (t80) REVERT: C 21 MET cc_start: 0.7087 (mtp) cc_final: 0.6869 (mtp) REVERT: C 80 GLU cc_start: 0.7542 (tt0) cc_final: 0.7220 (tt0) REVERT: C 121 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7362 (mt-10) REVERT: C 193 ASN cc_start: 0.8501 (m-40) cc_final: 0.8120 (m-40) REVERT: C 211 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7104 (mt-10) REVERT: C 212 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7458 (mt-10) REVERT: D 67 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7314 (pt0) REVERT: D 81 GLN cc_start: 0.8533 (tp40) cc_final: 0.8061 (tp40) REVERT: D 164 LEU cc_start: 0.7107 (pp) cc_final: 0.6862 (pp) REVERT: D 173 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7681 (mt-10) REVERT: D 201 LYS cc_start: 0.8535 (ttpt) cc_final: 0.8331 (ttpt) REVERT: D 207 ASP cc_start: 0.8013 (m-30) cc_final: 0.7801 (m-30) REVERT: D 214 THR cc_start: 0.8296 (p) cc_final: 0.7972 (p) REVERT: E 81 GLN cc_start: 0.8311 (tp-100) cc_final: 0.8095 (tp40) REVERT: E 109 SER cc_start: 0.8308 (t) cc_final: 0.8066 (t) REVERT: E 135 SER cc_start: 0.8968 (t) cc_final: 0.8198 (m) REVERT: E 166 MET cc_start: 0.7846 (ttt) cc_final: 0.7565 (ttt) REVERT: E 210 MET cc_start: 0.7424 (mmm) cc_final: 0.7138 (mmm) REVERT: F 31 ILE cc_start: 0.8708 (mt) cc_final: 0.8428 (mt) outliers start: 24 outliers final: 16 residues processed: 288 average time/residue: 0.1065 time to fit residues: 41.3430 Evaluate side-chains 299 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 282 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 55 LYS Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 211 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 11 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 122 ASN A 151 HIS B 75 ASN D 151 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.164225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.136702 restraints weight = 14981.067| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.54 r_work: 0.3610 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9354 Z= 0.149 Angle : 0.519 14.661 12657 Z= 0.267 Chirality : 0.036 0.147 1469 Planarity : 0.003 0.046 1601 Dihedral : 3.216 16.295 1253 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.56 % Favored : 98.35 % Rotamer: Outliers : 2.84 % Allowed : 15.86 % Favored : 81.30 % 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: 4.49 (0.24), residues: 1154 helix: 3.37 (0.15), residues: 1003 sheet: None (None), residues: 0 loop : -0.28 (0.51), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 64 TYR 0.023 0.001 TYR C 66 PHE 0.021 0.001 PHE C 183 TRP 0.007 0.001 TRP D 147 HIS 0.011 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9354) covalent geometry : angle 0.51870 (12657) hydrogen bonds : bond 0.06260 ( 775) hydrogen bonds : angle 3.15289 ( 2322) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 287 time to evaluate : 0.349 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR C 223 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7915 (mmt90) cc_final: 0.7708 (mmt90) REVERT: A 48 GLU cc_start: 0.8176 (tp30) cc_final: 0.7640 (tp30) REVERT: A 89 GLU cc_start: 0.7988 (tp30) cc_final: 0.7716 (tp30) REVERT: A 109 SER cc_start: 0.8675 (m) cc_final: 0.8272 (p) REVERT: A 147 TRP cc_start: 0.8459 (t-100) cc_final: 0.8209 (t-100) REVERT: A 183 PHE cc_start: 0.8229 (t80) cc_final: 0.7837 (t80) REVERT: A 193 ASN cc_start: 0.8395 (m-40) cc_final: 0.8011 (m-40) REVERT: A 201 LYS cc_start: 0.8837 (tptt) cc_final: 0.8505 (tptt) REVERT: A 207 ASP cc_start: 0.8355 (t0) cc_final: 0.8142 (t0) REVERT: B 88 LYS cc_start: 0.7563 (tptt) cc_final: 0.7311 (tptt) REVERT: B 95 ARG cc_start: 0.6383 (mmt90) cc_final: 0.6108 (mpt180) REVERT: B 166 MET cc_start: 0.7302 (tpt) cc_final: 0.6895 (tpt) REVERT: B 173 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7814 (mt-10) REVERT: B 213 PHE cc_start: 0.8731 (t80) cc_final: 0.8525 (t80) REVERT: C 21 MET cc_start: 0.7114 (mtp) cc_final: 0.6900 (mtp) REVERT: C 121 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7354 (mt-10) REVERT: C 193 ASN cc_start: 0.8545 (m-40) cc_final: 0.8160 (m-40) REVERT: C 211 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7197 (mt-10) REVERT: C 212 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7348 (mt-10) REVERT: D 18 LYS cc_start: 0.7726 (mtpp) cc_final: 0.7376 (mtpp) REVERT: D 67 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7206 (pt0) REVERT: D 164 LEU cc_start: 0.7110 (pp) cc_final: 0.6889 (pp) REVERT: D 173 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7702 (mt-10) REVERT: D 201 LYS cc_start: 0.8564 (ttpt) cc_final: 0.8349 (ttpt) REVERT: D 207 ASP cc_start: 0.8030 (m-30) cc_final: 0.7783 (m-30) REVERT: D 214 THR cc_start: 0.8302 (p) cc_final: 0.7986 (p) REVERT: E 81 GLN cc_start: 0.8317 (tp-100) cc_final: 0.8105 (tp40) REVERT: E 109 SER cc_start: 0.8344 (t) cc_final: 0.8120 (t) REVERT: E 118 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7758 (ttm170) REVERT: E 166 MET cc_start: 0.7841 (ttt) cc_final: 0.7546 (ttt) REVERT: E 203 GLU cc_start: 0.8099 (tt0) cc_final: 0.7869 (tp30) REVERT: E 210 MET cc_start: 0.7402 (mmm) cc_final: 0.7156 (mmm) REVERT: F 31 ILE cc_start: 0.8825 (mt) cc_final: 0.8472 (mp) outliers start: 27 outliers final: 15 residues processed: 292 average time/residue: 0.1073 time to fit residues: 42.0702 Evaluate side-chains 299 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 282 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 55 LYS Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 26 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 39 optimal weight: 0.0870 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 122 ASN A 151 HIS E 43 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.165784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.138261 restraints weight = 14864.639| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.51 r_work: 0.3630 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9354 Z= 0.134 Angle : 0.508 14.272 12657 Z= 0.260 Chirality : 0.035 0.143 1469 Planarity : 0.003 0.054 1601 Dihedral : 3.223 15.958 1253 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.56 % Favored : 98.35 % Rotamer: Outliers : 2.52 % Allowed : 17.12 % Favored : 80.36 % 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: 4.56 (0.24), residues: 1154 helix: 3.43 (0.15), residues: 1003 sheet: None (None), residues: 0 loop : -0.37 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 64 TYR 0.016 0.001 TYR C 66 PHE 0.010 0.001 PHE C 183 TRP 0.008 0.001 TRP B 57 HIS 0.003 0.000 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9354) covalent geometry : angle 0.50798 (12657) hydrogen bonds : bond 0.05868 ( 775) hydrogen bonds : angle 3.06482 ( 2322) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 283 time to evaluate : 0.241 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR C 223 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8376 (mm) cc_final: 0.8173 (mp) REVERT: A 48 GLU cc_start: 0.8161 (tp30) cc_final: 0.7645 (tp30) REVERT: A 64 ARG cc_start: 0.6537 (ptt90) cc_final: 0.6198 (ptp90) REVERT: A 109 SER cc_start: 0.8673 (m) cc_final: 0.8268 (p) REVERT: A 147 TRP cc_start: 0.8426 (t-100) cc_final: 0.8179 (t-100) REVERT: A 183 PHE cc_start: 0.8212 (t80) cc_final: 0.7831 (t80) REVERT: A 201 LYS cc_start: 0.8853 (tptt) cc_final: 0.8534 (tptt) REVERT: A 207 ASP cc_start: 0.8344 (t0) cc_final: 0.8139 (t0) REVERT: B 88 LYS cc_start: 0.7568 (tptt) cc_final: 0.7307 (tptt) REVERT: B 112 MET cc_start: 0.6400 (OUTLIER) cc_final: 0.5572 (mmp) REVERT: B 113 ARG cc_start: 0.7278 (ttm-80) cc_final: 0.6940 (mtm-85) REVERT: B 166 MET cc_start: 0.7230 (tpt) cc_final: 0.6853 (tpt) REVERT: C 121 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7340 (mt-10) REVERT: C 193 ASN cc_start: 0.8538 (m-40) cc_final: 0.8156 (m-40) REVERT: C 211 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7183 (mt-10) REVERT: C 212 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7323 (mt-10) REVERT: D 18 LYS cc_start: 0.7660 (mtpp) cc_final: 0.7325 (mtpp) REVERT: D 67 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7256 (pt0) REVERT: D 164 LEU cc_start: 0.7091 (pp) cc_final: 0.6861 (pp) REVERT: D 207 ASP cc_start: 0.8039 (m-30) cc_final: 0.7750 (m-30) REVERT: D 214 THR cc_start: 0.8222 (p) cc_final: 0.7900 (p) REVERT: E 81 GLN cc_start: 0.8287 (tp-100) cc_final: 0.8086 (tp40) REVERT: E 109 SER cc_start: 0.8297 (t) cc_final: 0.8081 (t) REVERT: E 118 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7740 (ttm170) REVERT: E 166 MET cc_start: 0.7850 (ttt) cc_final: 0.7562 (ttt) REVERT: E 194 ARG cc_start: 0.7455 (ttp80) cc_final: 0.7116 (ttp80) REVERT: E 203 GLU cc_start: 0.8110 (tt0) cc_final: 0.7867 (tp30) REVERT: E 210 MET cc_start: 0.7354 (mmm) cc_final: 0.7094 (mmm) outliers start: 24 outliers final: 17 residues processed: 288 average time/residue: 0.0925 time to fit residues: 36.0578 Evaluate side-chains 299 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 279 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 55 LYS Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 211 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 55 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 0.0670 chunk 3 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 122 ASN A 151 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.165743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.138216 restraints weight = 14853.842| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.56 r_work: 0.3623 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9354 Z= 0.136 Angle : 0.517 15.185 12657 Z= 0.262 Chirality : 0.035 0.146 1469 Planarity : 0.003 0.047 1601 Dihedral : 3.209 16.043 1253 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.65 % Favored : 98.27 % Rotamer: Outliers : 2.84 % Allowed : 17.54 % Favored : 79.62 % 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: 4.55 (0.24), residues: 1154 helix: 3.42 (0.15), residues: 1003 sheet: None (None), residues: 0 loop : -0.29 (0.51), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 64 TYR 0.013 0.001 TYR B 192 PHE 0.015 0.001 PHE C 143 TRP 0.008 0.001 TRP B 57 HIS 0.005 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9354) covalent geometry : angle 0.51681 (12657) hydrogen bonds : bond 0.05902 ( 775) hydrogen bonds : angle 3.05918 ( 2322) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 283 time to evaluate : 0.345 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR C 223 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8561 (mmp-170) cc_final: 0.8304 (mmm160) REVERT: A 48 GLU cc_start: 0.8196 (tp30) cc_final: 0.7667 (tp30) REVERT: A 109 SER cc_start: 0.8682 (m) cc_final: 0.8267 (p) REVERT: A 147 TRP cc_start: 0.8426 (t-100) cc_final: 0.8173 (t-100) REVERT: A 183 PHE cc_start: 0.8202 (t80) cc_final: 0.7811 (t80) REVERT: A 207 ASP cc_start: 0.8375 (t0) cc_final: 0.8171 (t0) REVERT: B 88 LYS cc_start: 0.7561 (tptt) cc_final: 0.7309 (tptt) REVERT: B 112 MET cc_start: 0.6363 (mmt) cc_final: 0.5557 (mmp) REVERT: B 113 ARG cc_start: 0.7304 (ttm-80) cc_final: 0.6911 (mtm-85) REVERT: B 166 MET cc_start: 0.7288 (tpt) cc_final: 0.6888 (tpt) REVERT: C 121 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7319 (mt-10) REVERT: C 193 ASN cc_start: 0.8530 (m-40) cc_final: 0.8141 (m-40) REVERT: C 211 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7105 (mt-10) REVERT: C 212 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7333 (mt-10) REVERT: D 18 LYS cc_start: 0.7656 (mtpp) cc_final: 0.7314 (mtpp) REVERT: D 67 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7224 (pt0) REVERT: D 207 ASP cc_start: 0.8064 (m-30) cc_final: 0.7761 (m-30) REVERT: D 214 THR cc_start: 0.8269 (p) cc_final: 0.7938 (p) REVERT: E 81 GLN cc_start: 0.8301 (tp-100) cc_final: 0.8094 (tp40) REVERT: E 109 SER cc_start: 0.8297 (t) cc_final: 0.8083 (t) REVERT: E 166 MET cc_start: 0.7855 (ttt) cc_final: 0.7564 (ttt) REVERT: E 198 ARG cc_start: 0.7947 (mtp180) cc_final: 0.7581 (mtp180) REVERT: E 210 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.7077 (mmm) REVERT: F 31 ILE cc_start: 0.8765 (mt) cc_final: 0.8405 (mt) outliers start: 27 outliers final: 17 residues processed: 290 average time/residue: 0.0972 time to fit residues: 38.4034 Evaluate side-chains 299 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 280 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 55 LYS Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain F residue 30 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 0.2980 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 151 HIS D 151 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.165779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.138421 restraints weight = 14847.699| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.55 r_work: 0.3627 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9354 Z= 0.137 Angle : 0.528 15.138 12657 Z= 0.268 Chirality : 0.036 0.173 1469 Planarity : 0.003 0.056 1601 Dihedral : 3.201 16.019 1253 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.65 % Favored : 98.27 % Rotamer: Outliers : 3.36 % Allowed : 16.70 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.56 (0.24), residues: 1154 helix: 3.39 (0.15), residues: 1010 sheet: None (None), residues: 0 loop : -0.21 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 64 TYR 0.012 0.001 TYR B 192 PHE 0.009 0.001 PHE E 183 TRP 0.008 0.001 TRP B 57 HIS 0.009 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9354) covalent geometry : angle 0.52820 (12657) hydrogen bonds : bond 0.05844 ( 775) hydrogen bonds : angle 3.05106 ( 2322) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 285 time to evaluate : 0.260 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR C 223 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8398 (mm) cc_final: 0.8119 (mp) REVERT: A 38 ARG cc_start: 0.8569 (mmp-170) cc_final: 0.8310 (mmm160) REVERT: A 48 GLU cc_start: 0.8180 (tp30) cc_final: 0.7656 (tp30) REVERT: A 89 GLU cc_start: 0.8030 (tp30) cc_final: 0.7611 (tp30) REVERT: A 93 LEU cc_start: 0.7734 (mt) cc_final: 0.7360 (mt) REVERT: A 109 SER cc_start: 0.8682 (m) cc_final: 0.8266 (p) REVERT: A 147 TRP cc_start: 0.8431 (t-100) cc_final: 0.8152 (t-100) REVERT: A 183 PHE cc_start: 0.8202 (t80) cc_final: 0.7807 (t80) REVERT: A 207 ASP cc_start: 0.8357 (t0) cc_final: 0.8150 (t0) REVERT: B 88 LYS cc_start: 0.7568 (tptt) cc_final: 0.7319 (tptt) REVERT: B 112 MET cc_start: 0.6329 (OUTLIER) cc_final: 0.5523 (mmp) REVERT: B 113 ARG cc_start: 0.7315 (ttm-80) cc_final: 0.7026 (mtm-85) REVERT: B 166 MET cc_start: 0.7284 (tpt) cc_final: 0.6897 (tpt) REVERT: B 212 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7986 (mt-10) REVERT: C 121 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7321 (mt-10) REVERT: C 193 ASN cc_start: 0.8518 (m-40) cc_final: 0.8131 (m-40) REVERT: C 211 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7174 (mt-10) REVERT: C 212 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7322 (mt-10) REVERT: D 18 LYS cc_start: 0.7641 (mtpp) cc_final: 0.7294 (mtpp) REVERT: D 67 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7207 (pt0) REVERT: D 207 ASP cc_start: 0.8078 (m-30) cc_final: 0.7755 (m-30) REVERT: D 214 THR cc_start: 0.8133 (p) cc_final: 0.7830 (p) REVERT: E 81 GLN cc_start: 0.8285 (tp-100) cc_final: 0.8080 (tp40) REVERT: E 109 SER cc_start: 0.8291 (t) cc_final: 0.8081 (t) REVERT: E 118 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7724 (ttm170) REVERT: E 166 MET cc_start: 0.7844 (ttt) cc_final: 0.7539 (ttt) REVERT: E 194 ARG cc_start: 0.7471 (ttp80) cc_final: 0.7207 (ttp80) REVERT: E 198 ARG cc_start: 0.7758 (mtp180) cc_final: 0.7553 (mtp180) REVERT: E 210 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.7080 (mmm) outliers start: 32 outliers final: 23 residues processed: 289 average time/residue: 0.0983 time to fit residues: 38.1213 Evaluate side-chains 311 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 284 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 55 LYS Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 30 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 94 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 151 HIS D 151 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.165104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.137740 restraints weight = 14871.808| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.55 r_work: 0.3608 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9354 Z= 0.146 Angle : 0.533 16.250 12657 Z= 0.271 Chirality : 0.036 0.161 1469 Planarity : 0.003 0.044 1601 Dihedral : 3.199 16.291 1253 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.65 % Favored : 98.27 % Rotamer: Outliers : 3.36 % Allowed : 17.44 % Favored : 79.20 % 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: 4.50 (0.24), residues: 1154 helix: 3.35 (0.15), residues: 1010 sheet: None (None), residues: 0 loop : -0.20 (0.53), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 92 TYR 0.014 0.001 TYR B 192 PHE 0.017 0.001 PHE C 143 TRP 0.008 0.001 TRP B 57 HIS 0.009 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9354) covalent geometry : angle 0.53316 (12657) hydrogen bonds : bond 0.06072 ( 775) hydrogen bonds : angle 3.09225 ( 2322) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 287 time to evaluate : 0.315 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR C 223 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8533 (mmp-170) cc_final: 0.8286 (mmm160) REVERT: A 48 GLU cc_start: 0.8202 (tp30) cc_final: 0.7676 (tp30) REVERT: A 109 SER cc_start: 0.8683 (m) cc_final: 0.8265 (p) REVERT: A 147 TRP cc_start: 0.8467 (t-100) cc_final: 0.8145 (t60) REVERT: A 183 PHE cc_start: 0.8215 (t80) cc_final: 0.7798 (t80) REVERT: B 88 LYS cc_start: 0.7558 (tptt) cc_final: 0.7304 (tptt) REVERT: B 112 MET cc_start: 0.6343 (OUTLIER) cc_final: 0.5580 (mmp) REVERT: B 113 ARG cc_start: 0.7299 (ttm-80) cc_final: 0.7008 (mtm-85) REVERT: B 166 MET cc_start: 0.7197 (tpt) cc_final: 0.6836 (tpt) REVERT: B 212 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8034 (mt-10) REVERT: C 121 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7395 (mt-10) REVERT: C 193 ASN cc_start: 0.8533 (m-40) cc_final: 0.8130 (m-40) REVERT: C 211 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7187 (mt-10) REVERT: C 212 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7322 (mt-10) REVERT: D 18 LYS cc_start: 0.7649 (mtpp) cc_final: 0.7294 (mtpp) REVERT: D 67 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7190 (pt0) REVERT: D 207 ASP cc_start: 0.8098 (m-30) cc_final: 0.7797 (m-30) REVERT: D 214 THR cc_start: 0.8202 (p) cc_final: 0.7934 (p) REVERT: E 81 GLN cc_start: 0.8325 (tp-100) cc_final: 0.8082 (tp40) REVERT: E 109 SER cc_start: 0.8293 (t) cc_final: 0.8072 (t) REVERT: E 166 MET cc_start: 0.7861 (ttt) cc_final: 0.7564 (ttt) REVERT: E 210 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.7110 (mmm) outliers start: 32 outliers final: 23 residues processed: 290 average time/residue: 0.0882 time to fit residues: 34.6788 Evaluate side-chains 312 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 286 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 55 LYS Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 30 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 53 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 101 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 87 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 122 ASN A 151 HIS D 151 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.164943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.137509 restraints weight = 14782.417| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.54 r_work: 0.3616 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9354 Z= 0.147 Angle : 0.559 16.428 12657 Z= 0.283 Chirality : 0.036 0.155 1469 Planarity : 0.003 0.044 1601 Dihedral : 3.212 16.167 1253 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.65 % Favored : 98.27 % Rotamer: Outliers : 3.36 % Allowed : 18.38 % Favored : 78.26 % 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: 4.48 (0.24), residues: 1154 helix: 3.33 (0.16), residues: 1010 sheet: None (None), residues: 0 loop : -0.21 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 92 TYR 0.013 0.001 TYR B 192 PHE 0.011 0.001 PHE B 153 TRP 0.009 0.001 TRP B 57 HIS 0.009 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9354) covalent geometry : angle 0.55910 (12657) hydrogen bonds : bond 0.06048 ( 775) hydrogen bonds : angle 3.10457 ( 2322) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 287 time to evaluate : 0.257 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR C 223 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8392 (mm) cc_final: 0.8155 (mp) REVERT: A 38 ARG cc_start: 0.8571 (mmp-170) cc_final: 0.8300 (mmm160) REVERT: A 48 GLU cc_start: 0.8195 (tp30) cc_final: 0.7736 (tp30) REVERT: A 89 GLU cc_start: 0.8071 (tp30) cc_final: 0.7456 (tp30) REVERT: A 93 LEU cc_start: 0.7841 (mt) cc_final: 0.7352 (mt) REVERT: A 109 SER cc_start: 0.8664 (m) cc_final: 0.8268 (p) REVERT: A 147 TRP cc_start: 0.8450 (t-100) cc_final: 0.8114 (t60) REVERT: A 183 PHE cc_start: 0.8236 (t80) cc_final: 0.7831 (t80) REVERT: B 88 LYS cc_start: 0.7557 (tptt) cc_final: 0.7303 (tptt) REVERT: B 112 MET cc_start: 0.6337 (OUTLIER) cc_final: 0.5583 (mmt) REVERT: B 113 ARG cc_start: 0.7346 (ttm-80) cc_final: 0.7043 (mtm-85) REVERT: B 166 MET cc_start: 0.7241 (tpt) cc_final: 0.6871 (tpt) REVERT: C 121 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7323 (mt-10) REVERT: C 193 ASN cc_start: 0.8544 (m-40) cc_final: 0.8147 (m-40) REVERT: C 211 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7162 (mt-10) REVERT: C 212 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7307 (mt-10) REVERT: D 18 LYS cc_start: 0.7706 (mtpp) cc_final: 0.7320 (mtpp) REVERT: D 67 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7189 (pt0) REVERT: D 207 ASP cc_start: 0.8033 (m-30) cc_final: 0.7737 (m-30) REVERT: D 214 THR cc_start: 0.8280 (p) cc_final: 0.7947 (p) REVERT: E 81 GLN cc_start: 0.8307 (tp-100) cc_final: 0.8079 (tp40) REVERT: E 109 SER cc_start: 0.8300 (t) cc_final: 0.8094 (t) REVERT: E 166 MET cc_start: 0.7870 (ttt) cc_final: 0.7568 (ttt) REVERT: E 194 ARG cc_start: 0.7408 (ttp80) cc_final: 0.7065 (ttp80) REVERT: E 203 GLU cc_start: 0.8110 (tp30) cc_final: 0.7856 (tp30) REVERT: E 210 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.7109 (mmm) outliers start: 32 outliers final: 25 residues processed: 289 average time/residue: 0.0937 time to fit residues: 36.8457 Evaluate side-chains 314 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 286 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 55 LYS Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 30 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 7.9990 chunk 102 optimal weight: 0.0870 chunk 55 optimal weight: 0.0670 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 50.0000 chunk 9 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 overall best weight: 0.6296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 151 HIS D 151 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.165471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.137916 restraints weight = 14785.749| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.53 r_work: 0.3621 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9354 Z= 0.143 Angle : 0.556 16.217 12657 Z= 0.281 Chirality : 0.036 0.160 1469 Planarity : 0.003 0.045 1601 Dihedral : 3.207 16.040 1253 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.73 % Favored : 98.18 % Rotamer: Outliers : 2.73 % Allowed : 19.33 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.52 (0.24), residues: 1154 helix: 3.36 (0.16), residues: 1010 sheet: None (None), residues: 0 loop : -0.20 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 92 TYR 0.012 0.001 TYR B 192 PHE 0.017 0.001 PHE C 143 TRP 0.009 0.001 TRP B 57 HIS 0.010 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9354) covalent geometry : angle 0.55637 (12657) hydrogen bonds : bond 0.05921 ( 775) hydrogen bonds : angle 3.07675 ( 2322) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 286 time to evaluate : 0.316 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR C 223 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8414 (mm) cc_final: 0.8145 (mp) REVERT: A 38 ARG cc_start: 0.8562 (mmp-170) cc_final: 0.8297 (mmm160) REVERT: A 48 GLU cc_start: 0.8175 (tp30) cc_final: 0.7721 (tp30) REVERT: A 68 GLU cc_start: 0.7808 (tt0) cc_final: 0.7583 (tt0) REVERT: A 89 GLU cc_start: 0.8021 (tp30) cc_final: 0.7410 (tp30) REVERT: A 93 LEU cc_start: 0.7782 (mt) cc_final: 0.7296 (mt) REVERT: A 109 SER cc_start: 0.8645 (m) cc_final: 0.8261 (p) REVERT: A 147 TRP cc_start: 0.8438 (t-100) cc_final: 0.8119 (t60) REVERT: A 183 PHE cc_start: 0.8194 (t80) cc_final: 0.7777 (t80) REVERT: B 88 LYS cc_start: 0.7558 (tptt) cc_final: 0.7301 (tptt) REVERT: B 112 MET cc_start: 0.6352 (OUTLIER) cc_final: 0.5609 (mmt) REVERT: B 113 ARG cc_start: 0.7333 (ttm-80) cc_final: 0.7024 (mtm-85) REVERT: B 166 MET cc_start: 0.7197 (tpt) cc_final: 0.6828 (tpt) REVERT: C 121 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7325 (mt-10) REVERT: C 193 ASN cc_start: 0.8540 (m-40) cc_final: 0.8145 (m-40) REVERT: C 211 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7153 (mt-10) REVERT: C 212 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7317 (mt-10) REVERT: D 18 LYS cc_start: 0.7630 (mtpp) cc_final: 0.7276 (mtpp) REVERT: D 67 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7183 (pt0) REVERT: D 122 ASN cc_start: 0.8681 (t0) cc_final: 0.8469 (t0) REVERT: D 207 ASP cc_start: 0.8022 (m-30) cc_final: 0.7715 (m-30) REVERT: D 214 THR cc_start: 0.8225 (p) cc_final: 0.7893 (p) REVERT: E 81 GLN cc_start: 0.8300 (tp-100) cc_final: 0.8063 (tp40) REVERT: E 109 SER cc_start: 0.8291 (t) cc_final: 0.8087 (t) REVERT: E 166 MET cc_start: 0.7887 (ttt) cc_final: 0.7587 (ttt) REVERT: E 194 ARG cc_start: 0.7410 (ttp80) cc_final: 0.7086 (ttp80) REVERT: E 203 GLU cc_start: 0.8081 (tp30) cc_final: 0.7797 (tp30) REVERT: E 210 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.7070 (mmm) outliers start: 26 outliers final: 20 residues processed: 288 average time/residue: 0.0894 time to fit residues: 34.6349 Evaluate side-chains 307 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 284 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain D residue 40 ARG Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 55 LYS Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain F residue 30 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 77 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 81 optimal weight: 0.1980 chunk 102 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 151 HIS D 151 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.166083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.138572 restraints weight = 14642.709| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.52 r_work: 0.3624 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9354 Z= 0.139 Angle : 0.554 16.298 12657 Z= 0.279 Chirality : 0.036 0.185 1469 Planarity : 0.003 0.044 1601 Dihedral : 3.198 15.808 1253 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.65 % Favored : 98.27 % Rotamer: Outliers : 2.63 % Allowed : 19.75 % 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: 4.60 (0.24), residues: 1154 helix: 3.42 (0.15), residues: 1006 sheet: None (None), residues: 0 loop : -0.16 (0.51), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 92 TYR 0.012 0.001 TYR B 192 PHE 0.011 0.001 PHE B 153 TRP 0.009 0.001 TRP B 57 HIS 0.010 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9354) covalent geometry : angle 0.55406 (12657) hydrogen bonds : bond 0.05747 ( 775) hydrogen bonds : angle 3.05829 ( 2322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1986.14 seconds wall clock time: 34 minutes 47.39 seconds (2087.39 seconds total)