Starting phenix.real_space_refine on Thu Jul 2 16:08:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7f03_31395/07_2026/7f03_31395.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f03_31395/07_2026/7f03_31395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7f03_31395/07_2026/7f03_31395.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7f03_31395/07_2026/7f03_31395.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f03_31395/07_2026/7f03_31395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f03_31395/07_2026/7f03_31395.map" model { file = "/net/cci-nas-00/data/ceres_data/7f03_31395/07_2026/7f03_31395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f03_31395/07_2026/7f03_31395.cif" } resolution = 3.29 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= 0.003 sd= 0.051 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: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 2 5.21 5 S 46 5.16 5 C 5798 2.51 5 N 1517 2.21 5 O 1521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8891 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1586 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "B" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1663 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1848 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 11, 'TRANS': 219} Chain: "D" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "E" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1586 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "F" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1663 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.94, per 1000 atoms: 0.22 Number of scatterers: 8891 At special positions: 0 Unit cell: (100.672, 94.848, 117.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 46 16.00 P 7 15.00 Mg 2 11.99 O 1521 8.00 N 1517 7.00 C 5798 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: 0.69 Conformation dependent library (CDL) restraints added in 225.9 milliseconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2084 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 5 sheets defined 67.0% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 39 through 48 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 90 through 98 removed outlier: 3.505A pdb=" N ASN A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR A 98 " --> pdb=" O ASN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.635A pdb=" N GLU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 130 through 138 Processing helix chain 'A' and resid 138 through 143 removed outlier: 3.865A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 176 removed outlier: 3.884A pdb=" N GLN A 175 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY A 176 " --> pdb=" O HIS A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 22 through 34 Processing helix chain 'B' and resid 35 through 40 Processing helix chain 'B' and resid 42 through 76 removed outlier: 3.584A pdb=" N LEU B 46 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG B 48 " --> pdb=" O GLN B 44 " (cutoff:3.500A) Proline residue: B 51 - end of helix removed outlier: 3.631A pdb=" N GLU B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASP B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP B 76 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 111 removed outlier: 4.052A pdb=" N LEU B 106 " --> pdb=" O MET B 102 " (cutoff:3.500A) Proline residue: B 107 - end of helix Processing helix chain 'B' and resid 111 through 119 removed outlier: 3.857A pdb=" N MET B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 136 Processing helix chain 'B' and resid 136 through 144 removed outlier: 3.785A pdb=" N GLY B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 154 Processing helix chain 'B' and resid 158 through 165 removed outlier: 3.726A pdb=" N LEU B 164 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 165 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 185 Processing helix chain 'B' and resid 189 through 205 removed outlier: 3.932A pdb=" N ILE B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 220 removed outlier: 3.686A pdb=" N GLN B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 40 Proline residue: C 23 - end of helix Processing helix chain 'C' and resid 50 through 55 Processing helix chain 'C' and resid 56 through 84 Proline residue: C 62 - end of helix removed outlier: 3.637A pdb=" N MET C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 120 removed outlier: 3.557A pdb=" N ASN C 90 " --> pdb=" O MET C 86 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) Proline residue: C 98 - end of helix Proline residue: C 117 - end of helix Processing helix chain 'C' and resid 126 through 147 removed outlier: 3.728A pdb=" N LEU C 133 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C 135 " --> pdb=" O SER C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 185 Proline residue: C 171 - end of helix removed outlier: 3.887A pdb=" N THR C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 199 through 229 Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'D' and resid 17 through 53 Proline residue: D 31 - end of helix removed outlier: 3.696A pdb=" N ALA D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN D 53 " --> pdb=" O GLY D 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 48 Processing helix chain 'E' and resid 90 through 97 Processing helix chain 'E' and resid 106 through 115 Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 130 through 138 removed outlier: 3.728A pdb=" N ALA E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 142 Processing helix chain 'E' and resid 158 through 177 removed outlier: 3.607A pdb=" N ALA E 170 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN E 171 " --> pdb=" O GLN E 167 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N THR E 173 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN E 175 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY E 176 " --> pdb=" O HIS E 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 17 Processing helix chain 'F' and resid 21 through 39 removed outlier: 4.203A pdb=" N LEU F 25 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE F 35 " --> pdb=" O VAL F 31 " (cutoff:3.500A) Proline residue: F 36 - end of helix Processing helix chain 'F' and resid 42 through 66 removed outlier: 3.651A pdb=" N LEU F 46 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG F 48 " --> pdb=" O GLN F 44 " (cutoff:3.500A) Proline residue: F 51 - end of helix Processing helix chain 'F' and resid 67 through 69 No H-bonds generated for 'chain 'F' and resid 67 through 69' Processing helix chain 'F' and resid 70 through 75 removed outlier: 3.906A pdb=" N LEU F 74 " --> pdb=" O PHE F 70 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 70 through 75' Processing helix chain 'F' and resid 88 through 111 removed outlier: 3.527A pdb=" N VAL F 103 " --> pdb=" O ALA F 99 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU F 106 " --> pdb=" O MET F 102 " (cutoff:3.500A) Proline residue: F 107 - end of helix Processing helix chain 'F' and resid 111 through 119 removed outlier: 3.698A pdb=" N MET F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 152 Proline residue: F 138 - end of helix Proline residue: F 146 - end of helix Processing helix chain 'F' and resid 160 through 164 removed outlier: 3.529A pdb=" N LEU F 164 " --> pdb=" O LEU F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 169 through 185 removed outlier: 3.779A pdb=" N MET F 185 " --> pdb=" O ASP F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 220 removed outlier: 3.880A pdb=" N ILE F 195 " --> pdb=" O GLY F 191 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR F 205 " --> pdb=" O ALA F 201 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU F 206 " --> pdb=" O GLY F 202 " (cutoff:3.500A) Proline residue: F 208 - end of helix removed outlier: 3.770A pdb=" N GLN F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 23 removed outlier: 5.177A pdb=" N THR A 15 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG A 11 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 17 " --> pdb=" O CYS A 9 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LEU A 7 " --> pdb=" O GLY A 19 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER A 21 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARG A 5 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR A 23 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLU A 3 " --> pdb=" O THR A 23 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 57 " --> pdb=" O ARG A 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.280A pdb=" N LEU A 77 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASP A 151 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE A 79 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 179 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TRP A 29 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ILE A 197 " --> pdb=" O TRP A 29 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLN A 31 " --> pdb=" O ILE A 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 14 through 20 removed outlier: 7.248A pdb=" N CYS E 9 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER E 18 " --> pdb=" O LEU E 7 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU E 7 " --> pdb=" O SER E 18 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU E 20 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG E 5 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 14 through 20 removed outlier: 7.248A pdb=" N CYS E 9 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER E 18 " --> pdb=" O LEU E 7 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU E 7 " --> pdb=" O SER E 18 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU E 20 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG E 5 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU E 7 " --> pdb=" O ALA E 55 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA E 55 " --> pdb=" O LEU E 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 77 through 79 removed outlier: 5.985A pdb=" N LEU E 77 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASP E 151 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE E 79 " --> pdb=" O ASP E 151 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL E 30 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP E 29 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE E 197 " --> pdb=" O TRP E 29 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLN E 31 " --> pdb=" O ILE E 197 " (cutoff:3.500A) 492 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1353 1.31 - 1.43: 2352 1.43 - 1.56: 5297 1.56 - 1.68: 13 1.68 - 1.81: 87 Bond restraints: 9102 Sorted by residual: bond pdb=" N3B ANP A 302 " pdb=" PG ANP A 302 " ideal model delta sigma weight residual 1.795 1.629 0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" N3B ANP E 302 " pdb=" PG ANP E 302 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.75e+01 bond pdb=" O3A ANP E 302 " pdb=" PB ANP E 302 " ideal model delta sigma weight residual 1.700 1.603 0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" O3A ANP A 302 " pdb=" PB ANP A 302 " ideal model delta sigma weight residual 1.700 1.603 0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C11 3PE D 101 " pdb=" O13 3PE D 101 " ideal model delta sigma weight residual 1.408 1.485 -0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 9097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 12135 2.21 - 4.41: 228 4.41 - 6.62: 54 6.62 - 8.82: 4 8.82 - 11.03: 3 Bond angle restraints: 12424 Sorted by residual: angle pdb=" N ALA E 105 " pdb=" CA ALA E 105 " pdb=" C ALA E 105 " ideal model delta sigma weight residual 114.75 108.13 6.62 1.26e+00 6.30e-01 2.76e+01 angle pdb=" C12 3PE D 101 " pdb=" C11 3PE D 101 " pdb=" O13 3PE D 101 " ideal model delta sigma weight residual 108.28 119.31 -11.03 3.00e+00 1.11e-01 1.35e+01 angle pdb=" N3B ANP E 302 " pdb=" PG ANP E 302 " pdb=" O2G ANP E 302 " ideal model delta sigma weight residual 101.05 110.71 -9.66 3.00e+00 1.11e-01 1.04e+01 angle pdb=" N3B ANP A 302 " pdb=" PG ANP A 302 " pdb=" O2G ANP A 302 " ideal model delta sigma weight residual 101.05 110.56 -9.51 3.00e+00 1.11e-01 1.00e+01 angle pdb=" N GLU F 80 " pdb=" CA GLU F 80 " pdb=" C GLU F 80 " ideal model delta sigma weight residual 113.72 109.16 4.56 1.52e+00 4.33e-01 8.99e+00 ... (remaining 12419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 4764 17.47 - 34.93: 442 34.93 - 52.40: 84 52.40 - 69.87: 12 69.87 - 87.33: 5 Dihedral angle restraints: 5307 sinusoidal: 2083 harmonic: 3224 Sorted by residual: dihedral pdb=" CA PRO C 12 " pdb=" C PRO C 12 " pdb=" N ARG C 13 " pdb=" CA ARG C 13 " ideal model delta harmonic sigma weight residual 180.00 155.09 24.91 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA LEU A 127 " pdb=" C LEU A 127 " pdb=" N SER A 128 " pdb=" CA SER A 128 " ideal model delta harmonic sigma weight residual -180.00 -156.05 -23.95 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA ILE C 10 " pdb=" C ILE C 10 " pdb=" N PRO C 11 " pdb=" CA PRO C 11 " ideal model delta harmonic sigma weight residual 180.00 159.61 20.39 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 5304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1347 0.078 - 0.156: 112 0.156 - 0.233: 1 0.233 - 0.311: 1 0.311 - 0.389: 2 Chirality restraints: 1463 Sorted by residual: chirality pdb=" C3' ANP A 302 " pdb=" C2' ANP A 302 " pdb=" C4' ANP A 302 " pdb=" O3' ANP A 302 " both_signs ideal model delta sigma weight residual False -2.36 -2.75 0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" C3' ANP E 302 " pdb=" C2' ANP E 302 " pdb=" C4' ANP E 302 " pdb=" O3' ANP E 302 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" C2' ANP E 302 " pdb=" C1' ANP E 302 " pdb=" C3' ANP E 302 " pdb=" O2' ANP E 302 " both_signs ideal model delta sigma weight residual False -2.72 -2.47 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1460 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN F 23 " -0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO F 24 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO F 24 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 24 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 195 " 0.029 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO C 196 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 196 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 196 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 44 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO C 45 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 45 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 45 " -0.025 5.00e-02 4.00e+02 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 45 2.49 - 3.09: 6304 3.09 - 3.69: 13309 3.69 - 4.30: 19395 4.30 - 4.90: 32866 Nonbonded interactions: 71919 Sorted by model distance: nonbonded pdb="MG MG A 301 " pdb=" O3G ANP A 302 " model vdw 1.885 2.170 nonbonded pdb=" OG1 THR A 41 " pdb="MG MG A 301 " model vdw 1.939 2.170 nonbonded pdb=" OG1 THR E 41 " pdb="MG MG E 301 " model vdw 1.988 2.170 nonbonded pdb="MG MG A 301 " pdb=" O HOH A 402 " model vdw 2.000 2.170 nonbonded pdb="MG MG E 301 " pdb=" O HOH E 401 " model vdw 2.005 2.170 ... (remaining 71914 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 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.910 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 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 : 0.005 0.166 9102 Z= 0.235 Angle : 0.749 11.028 12424 Z= 0.375 Chirality : 0.045 0.389 1463 Planarity : 0.005 0.045 1523 Dihedral : 13.829 87.332 3223 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.11 % Allowed : 0.33 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.26), residues: 1118 helix: 0.60 (0.22), residues: 666 sheet: -0.39 (1.16), residues: 22 loop : -1.51 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 52 TYR 0.014 0.001 TYR F 124 PHE 0.018 0.001 PHE B 3 TRP 0.015 0.001 TRP F 55 HIS 0.006 0.001 HIS E 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.23 ( 9102) covalent geometry : angle 0.74943 / 0.38 (12424) hydrogen bonds : bond 0.19663 / 12.91 ( 489) hydrogen bonds : angle 7.00678 / 4.81 ( 1404) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 0.297 Fit side-chains REVERT: B 68 ARG cc_start: 0.8505 (ttm170) cc_final: 0.8158 (mtm-85) REVERT: B 71 ARG cc_start: 0.8038 (ttp80) cc_final: 0.7838 (ttp80) REVERT: C 181 ASN cc_start: 0.8600 (t160) cc_final: 0.8238 (t0) REVERT: C 233 PRO cc_start: 0.8412 (Cg_endo) cc_final: 0.8166 (Cg_exo) REVERT: F 10 GLU cc_start: 0.8049 (tp30) cc_final: 0.7804 (tp30) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.0924 time to fit residues: 25.6432 Evaluate side-chains 166 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.0020 chunk 49 optimal weight: 0.0870 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.0070 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN C 49 GLN C 181 ASN F 17 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.116637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.102675 restraints weight = 14553.646| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.00 r_work: 0.3266 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9102 Z= 0.120 Angle : 0.621 8.057 12424 Z= 0.307 Chirality : 0.042 0.149 1463 Planarity : 0.005 0.056 1523 Dihedral : 6.531 59.783 1243 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.53 % Allowed : 10.14 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.26), residues: 1118 helix: 0.98 (0.21), residues: 697 sheet: -0.54 (1.07), residues: 22 loop : -1.56 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 100 TYR 0.012 0.001 TYR C 48 PHE 0.020 0.001 PHE A 97 TRP 0.014 0.001 TRP F 55 HIS 0.007 0.001 HIS E 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 9102) covalent geometry : angle 0.62089 / 0.31 (12424) hydrogen bonds : bond 0.03807 / 2.54 ( 489) hydrogen bonds : angle 4.54532 / 3.11 ( 1404) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.346 Fit side-chains REVERT: B 68 ARG cc_start: 0.8726 (ttm170) cc_final: 0.8466 (ttm-80) REVERT: B 71 ARG cc_start: 0.8560 (ttp80) cc_final: 0.8307 (ttp80) REVERT: C 49 GLN cc_start: 0.7707 (mt0) cc_final: 0.7464 (mt0) REVERT: F 10 GLU cc_start: 0.8761 (tp30) cc_final: 0.8528 (tp30) outliers start: 14 outliers final: 8 residues processed: 195 average time/residue: 0.1000 time to fit residues: 26.7120 Evaluate side-chains 168 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain D residue 8 TRP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 57 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 ASN ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN B 81 GLN C 7 GLN E 172 HIS F 17 HIS F 127 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.113484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.099252 restraints weight = 14734.277| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.01 r_work: 0.3209 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9102 Z= 0.156 Angle : 0.631 8.110 12424 Z= 0.310 Chirality : 0.043 0.208 1463 Planarity : 0.005 0.044 1523 Dihedral : 6.125 58.168 1243 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.94 % Allowed : 12.76 % Favored : 84.30 % 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: 0.25 (0.26), residues: 1118 helix: 1.12 (0.21), residues: 700 sheet: -0.94 (0.81), residues: 34 loop : -1.50 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 52 TYR 0.005 0.001 TYR C 48 PHE 0.012 0.001 PHE A 97 TRP 0.016 0.001 TRP F 55 HIS 0.007 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 9102) covalent geometry : angle 0.63096 / 0.31 (12424) hydrogen bonds : bond 0.03634 / 2.42 ( 489) hydrogen bonds : angle 4.38326 / 2.99 ( 1404) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.352 Fit side-chains REVERT: A 78 TRP cc_start: 0.8845 (t60) cc_final: 0.8609 (t60) REVERT: B 68 ARG cc_start: 0.8857 (ttm170) cc_final: 0.8630 (ttm-80) REVERT: B 71 ARG cc_start: 0.8575 (ttp80) cc_final: 0.8305 (ttp80) outliers start: 27 outliers final: 21 residues processed: 181 average time/residue: 0.1086 time to fit residues: 26.6578 Evaluate side-chains 182 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain D residue 8 TRP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 79 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 72 optimal weight: 0.2980 chunk 88 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.109131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.094674 restraints weight = 15312.715| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.04 r_work: 0.3137 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9102 Z= 0.173 Angle : 0.639 8.287 12424 Z= 0.312 Chirality : 0.043 0.201 1463 Planarity : 0.005 0.043 1523 Dihedral : 5.973 54.855 1243 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.49 % Allowed : 15.38 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.27), residues: 1118 helix: 1.22 (0.21), residues: 696 sheet: -0.71 (0.87), residues: 34 loop : -1.53 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 52 TYR 0.008 0.001 TYR C 48 PHE 0.013 0.001 PHE B 3 TRP 0.017 0.001 TRP F 55 HIS 0.009 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 ( 9102) covalent geometry : angle 0.63945 / 0.31 (12424) hydrogen bonds : bond 0.03549 / 2.38 ( 489) hydrogen bonds : angle 4.26525 / 2.92 ( 1404) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 0.339 Fit side-chains REVERT: B 71 ARG cc_start: 0.8467 (ttp80) cc_final: 0.8150 (ttp80) REVERT: E 163 ASP cc_start: 0.8825 (t0) cc_final: 0.8595 (t0) outliers start: 32 outliers final: 23 residues processed: 188 average time/residue: 0.1094 time to fit residues: 27.7776 Evaluate side-chains 185 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain D residue 8 TRP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 38 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN C 7 GLN F 17 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.108890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.094399 restraints weight = 15174.380| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.02 r_work: 0.3136 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9102 Z= 0.164 Angle : 0.633 7.203 12424 Z= 0.310 Chirality : 0.043 0.162 1463 Planarity : 0.005 0.042 1523 Dihedral : 5.860 52.271 1243 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.49 % Allowed : 16.58 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.27), residues: 1118 helix: 1.36 (0.21), residues: 687 sheet: -0.45 (0.91), residues: 34 loop : -1.60 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 52 TYR 0.007 0.001 TYR C 139 PHE 0.013 0.001 PHE B 3 TRP 0.018 0.001 TRP F 55 HIS 0.007 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 ( 9102) covalent geometry : angle 0.63287 / 0.31 (12424) hydrogen bonds : bond 0.03438 / 2.30 ( 489) hydrogen bonds : angle 4.24225 / 2.90 ( 1404) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.350 Fit side-chains REVERT: B 71 ARG cc_start: 0.8440 (ttp80) cc_final: 0.8137 (ttp80) outliers start: 32 outliers final: 26 residues processed: 186 average time/residue: 0.1053 time to fit residues: 26.6146 Evaluate side-chains 188 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain D residue 8 TRP Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN E 66 HIS F 17 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.109998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.095567 restraints weight = 15048.748| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.01 r_work: 0.3154 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9102 Z= 0.136 Angle : 0.608 6.704 12424 Z= 0.299 Chirality : 0.042 0.165 1463 Planarity : 0.005 0.041 1523 Dihedral : 5.702 49.627 1243 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.49 % Allowed : 16.90 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.27), residues: 1118 helix: 1.48 (0.21), residues: 687 sheet: -0.30 (0.92), residues: 34 loop : -1.56 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 100 TYR 0.005 0.001 TYR C 71 PHE 0.013 0.001 PHE B 3 TRP 0.017 0.001 TRP F 55 HIS 0.005 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 9102) covalent geometry : angle 0.60846 / 0.30 (12424) hydrogen bonds : bond 0.03219 / 2.15 ( 489) hydrogen bonds : angle 4.12170 / 2.81 ( 1404) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.345 Fit side-chains REVERT: B 71 ARG cc_start: 0.8415 (ttp80) cc_final: 0.8021 (ttp80) outliers start: 32 outliers final: 25 residues processed: 186 average time/residue: 0.1039 time to fit residues: 26.2634 Evaluate side-chains 189 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain D residue 8 TRP Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 93 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN F 17 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.107996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.093186 restraints weight = 15240.667| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.05 r_work: 0.3100 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9102 Z= 0.212 Angle : 0.670 6.578 12424 Z= 0.330 Chirality : 0.044 0.307 1463 Planarity : 0.005 0.040 1523 Dihedral : 5.884 49.959 1243 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.98 % Favored : 92.93 % Rotamer: Outliers : 3.60 % Allowed : 18.10 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.26), residues: 1118 helix: 1.32 (0.21), residues: 690 sheet: -0.53 (0.93), residues: 34 loop : -1.58 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 55 TYR 0.008 0.001 TYR C 71 PHE 0.014 0.002 PHE D 20 TRP 0.017 0.001 TRP F 55 HIS 0.008 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 ( 9102) covalent geometry : angle 0.66975 / 0.33 (12424) hydrogen bonds : bond 0.03758 / 2.50 ( 489) hydrogen bonds : angle 4.26486 / 2.92 ( 1404) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.350 Fit side-chains REVERT: B 2 MET cc_start: 0.7840 (ttt) cc_final: 0.7300 (ttm) REVERT: B 71 ARG cc_start: 0.8362 (ttp80) cc_final: 0.8033 (ttp80) REVERT: B 87 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8473 (pt) REVERT: C 48 TYR cc_start: 0.7274 (p90) cc_final: 0.6492 (p90) REVERT: F 10 GLU cc_start: 0.8754 (tp30) cc_final: 0.8327 (tp30) outliers start: 33 outliers final: 26 residues processed: 188 average time/residue: 0.1034 time to fit residues: 26.5102 Evaluate side-chains 188 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain D residue 8 TRP Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN F 17 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.110373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.095833 restraints weight = 14987.179| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.03 r_work: 0.3146 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9102 Z= 0.136 Angle : 0.627 9.851 12424 Z= 0.308 Chirality : 0.042 0.246 1463 Planarity : 0.005 0.041 1523 Dihedral : 5.714 48.158 1243 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.49 % Allowed : 18.76 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.27), residues: 1118 helix: 1.52 (0.21), residues: 687 sheet: -0.24 (0.94), residues: 34 loop : -1.52 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 52 TYR 0.022 0.001 TYR C 54 PHE 0.013 0.001 PHE B 3 TRP 0.017 0.001 TRP F 55 HIS 0.005 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 9102) covalent geometry : angle 0.62739 / 0.31 (12424) hydrogen bonds : bond 0.03238 / 2.16 ( 489) hydrogen bonds : angle 4.10890 / 2.81 ( 1404) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.344 Fit side-chains REVERT: B 2 MET cc_start: 0.7801 (ttt) cc_final: 0.7274 (ttm) REVERT: B 71 ARG cc_start: 0.8361 (ttp80) cc_final: 0.8041 (ttp80) REVERT: B 87 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8496 (pt) REVERT: C 48 TYR cc_start: 0.7094 (p90) cc_final: 0.6610 (p90) REVERT: C 49 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8159 (mm-40) outliers start: 32 outliers final: 28 residues processed: 186 average time/residue: 0.1088 time to fit residues: 27.4121 Evaluate side-chains 192 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain D residue 8 TRP Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 35 optimal weight: 0.0030 chunk 37 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 107 optimal weight: 0.0070 chunk 94 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 overall best weight: 0.5208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN F 17 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.111901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.097411 restraints weight = 14947.812| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.02 r_work: 0.3183 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9102 Z= 0.118 Angle : 0.609 9.399 12424 Z= 0.299 Chirality : 0.041 0.227 1463 Planarity : 0.004 0.040 1523 Dihedral : 5.508 45.955 1243 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.84 % Allowed : 19.52 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.27), residues: 1118 helix: 1.68 (0.21), residues: 687 sheet: -0.03 (0.94), residues: 34 loop : -1.48 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 52 TYR 0.017 0.001 TYR C 54 PHE 0.014 0.001 PHE B 3 TRP 0.014 0.001 TRP F 55 HIS 0.003 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 9102) covalent geometry : angle 0.60891 / 0.30 (12424) hydrogen bonds : bond 0.02963 / 1.98 ( 489) hydrogen bonds : angle 4.02377 / 2.74 ( 1404) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.338 Fit side-chains REVERT: B 71 ARG cc_start: 0.8321 (ttp80) cc_final: 0.7975 (ttp80) REVERT: B 87 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8491 (pt) REVERT: C 48 TYR cc_start: 0.7041 (p90) cc_final: 0.6601 (p90) REVERT: E 95 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9021 (mt) outliers start: 26 outliers final: 20 residues processed: 188 average time/residue: 0.1046 time to fit residues: 26.7871 Evaluate side-chains 188 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 178 GLU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain D residue 8 TRP Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN F 17 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.110322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.095597 restraints weight = 15041.095| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.08 r_work: 0.3150 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9102 Z= 0.147 Angle : 0.632 9.275 12424 Z= 0.311 Chirality : 0.042 0.215 1463 Planarity : 0.005 0.040 1523 Dihedral : 5.573 46.904 1243 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.83 % Rotamer: Outliers : 2.84 % Allowed : 19.96 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.27), residues: 1118 helix: 1.68 (0.21), residues: 688 sheet: -0.03 (0.96), residues: 34 loop : -1.49 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 52 TYR 0.017 0.001 TYR C 54 PHE 0.013 0.001 PHE B 3 TRP 0.014 0.001 TRP F 55 HIS 0.005 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 9102) covalent geometry : angle 0.63244 / 0.31 (12424) hydrogen bonds : bond 0.03210 / 2.14 ( 489) hydrogen bonds : angle 4.06958 / 2.78 ( 1404) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.394 Fit side-chains REVERT: A 182 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.9078 (p) REVERT: B 2 MET cc_start: 0.7763 (ttt) cc_final: 0.7240 (ttm) REVERT: B 71 ARG cc_start: 0.8336 (ttp80) cc_final: 0.8056 (ttp80) REVERT: B 87 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8427 (pt) REVERT: C 48 TYR cc_start: 0.7346 (p90) cc_final: 0.7106 (p90) REVERT: C 49 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8270 (mm-40) REVERT: E 95 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8967 (mt) outliers start: 26 outliers final: 22 residues processed: 180 average time/residue: 0.1093 time to fit residues: 26.5984 Evaluate side-chains 191 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain D residue 8 TRP Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 31 optimal weight: 0.0570 chunk 84 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 105 optimal weight: 0.4980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.110934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.096329 restraints weight = 14820.131| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.06 r_work: 0.3162 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.188 9102 Z= 0.198 Angle : 0.744 31.141 12424 Z= 0.394 Chirality : 0.044 0.408 1463 Planarity : 0.006 0.136 1523 Dihedral : 5.574 46.772 1243 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.99 % Favored : 93.92 % Rotamer: Outliers : 2.94 % Allowed : 19.63 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.27), residues: 1118 helix: 1.74 (0.21), residues: 688 sheet: -0.02 (0.95), residues: 34 loop : -1.48 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 52 TYR 0.016 0.001 TYR C 54 PHE 0.014 0.001 PHE B 28 TRP 0.016 0.001 TRP F 55 HIS 0.006 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 ( 9102) covalent geometry : angle 0.74446 / 0.39 (12424) hydrogen bonds : bond 0.03175 / 2.12 ( 489) hydrogen bonds : angle 4.05006 / 2.76 ( 1404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2298.57 seconds wall clock time: 40 minutes 7.87 seconds (2407.87 seconds total)