Starting phenix.real_space_refine on Thu Mar 13 20:44:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f03_31395/03_2025/7f03_31395.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f03_31395/03_2025/7f03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7f03_31395/03_2025/7f03_31395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f03_31395/03_2025/7f03_31395.map" model { file = "/net/cci-nas-00/data/ceres_data/7f03_31395/03_2025/7f03_31395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f03_31395/03_2025/7f03_31395.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.36, per 1000 atoms: 0.72 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: 2.68 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.00 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: 2.43 Time building geometry restraints manager: 3.11 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 - 17.99: 4805 17.99 - 35.99: 444 35.99 - 53.98: 88 53.98 - 71.97: 20 71.97 - 89.96: 18 Dihedral angle restraints: 5375 sinusoidal: 2151 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 5372 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: 15.820 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.380 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.166 9102 Z= 0.278 Angle : 0.749 11.028 12424 Z= 0.375 Chirality : 0.045 0.389 1463 Planarity : 0.005 0.045 1523 Dihedral : 15.391 89.964 3291 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.01 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.001 TRP F 55 HIS 0.006 0.001 HIS E 73 PHE 0.018 0.001 PHE B 3 TYR 0.014 0.001 TYR F 124 ARG 0.008 0.000 ARG E 52 *********************** 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 : 1.176 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: 0.2488 time to fit residues: 68.3647 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 : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 57 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 0.0870 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 = 0.3553 r_free = 0.3553 target = 0.115673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.101789 restraints weight = 14381.173| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.97 r_work: 0.3258 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9102 Z= 0.188 Angle : 0.632 8.140 12424 Z= 0.311 Chirality : 0.043 0.147 1463 Planarity : 0.005 0.058 1523 Dihedral : 9.646 80.484 1311 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.74 % Allowed : 10.03 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.26), residues: 1118 helix: 0.95 (0.21), residues: 697 sheet: -0.56 (1.09), residues: 22 loop : -1.56 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 55 HIS 0.007 0.001 HIS E 73 PHE 0.021 0.001 PHE A 97 TYR 0.011 0.001 TYR C 48 ARG 0.007 0.000 ARG E 100 *********************** 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: 16 poor density : 185 time to evaluate : 1.119 Fit side-chains REVERT: B 68 ARG cc_start: 0.8758 (ttm170) cc_final: 0.8512 (ttm-80) REVERT: B 71 ARG cc_start: 0.8582 (ttp80) cc_final: 0.8321 (ttp80) REVERT: C 49 GLN cc_start: 0.7729 (mt0) cc_final: 0.7502 (mt0) REVERT: F 10 GLU cc_start: 0.8771 (tp30) cc_final: 0.8553 (tp30) outliers start: 16 outliers final: 10 residues processed: 194 average time/residue: 0.2734 time to fit residues: 71.1410 Evaluate side-chains 169 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 159 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 C residue 228 MET Chi-restraints excluded: chain D residue 8 TRP Chi-restraints excluded: chain E residue 30 VAL 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 107 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 chunk 79 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3558 r_free = 0.3558 target = 0.115872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.101756 restraints weight = 14680.369| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.00 r_work: 0.3258 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9102 Z= 0.180 Angle : 0.601 7.302 12424 Z= 0.294 Chirality : 0.042 0.218 1463 Planarity : 0.005 0.044 1523 Dihedral : 8.345 74.989 1311 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.84 % Allowed : 13.30 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.26), residues: 1118 helix: 1.25 (0.21), residues: 692 sheet: -0.87 (0.81), residues: 34 loop : -1.57 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 55 HIS 0.006 0.001 HIS E 73 PHE 0.015 0.001 PHE A 97 TYR 0.006 0.001 TYR C 48 ARG 0.005 0.000 ARG E 52 *********************** 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: 26 poor density : 164 time to evaluate : 0.983 Fit side-chains REVERT: B 68 ARG cc_start: 0.8832 (ttm170) cc_final: 0.8610 (ttm-80) REVERT: B 71 ARG cc_start: 0.8601 (ttp80) cc_final: 0.8288 (ttp80) outliers start: 26 outliers final: 19 residues processed: 182 average time/residue: 0.2694 time to fit residues: 66.0275 Evaluate side-chains 180 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 0.0980 chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3444 r_free = 0.3444 target = 0.107867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.093173 restraints weight = 15147.862| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.04 r_work: 0.3101 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 9102 Z= 0.370 Angle : 0.689 8.706 12424 Z= 0.340 Chirality : 0.045 0.209 1463 Planarity : 0.005 0.042 1523 Dihedral : 8.536 78.836 1311 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.53 % Favored : 93.38 % Rotamer: Outliers : 3.49 % Allowed : 15.16 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.27), residues: 1118 helix: 1.03 (0.21), residues: 700 sheet: -0.86 (0.86), residues: 34 loop : -1.59 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 55 HIS 0.011 0.001 HIS A 73 PHE 0.016 0.002 PHE D 20 TYR 0.008 0.001 TYR C 71 ARG 0.006 0.001 ARG E 52 *********************** 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 194 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 1.137 Fit side-chains REVERT: B 71 ARG cc_start: 0.8463 (ttp80) cc_final: 0.8190 (ttp80) outliers start: 32 outliers final: 22 residues processed: 182 average time/residue: 0.3094 time to fit residues: 75.5782 Evaluate side-chains 181 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 1.419 ------------------------------------------------------------------------------- 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 94 ASN 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 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 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 Chi-restraints excluded: chain F residue 139 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3480 r_free = 0.3480 target = 0.110319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.095681 restraints weight = 14969.483| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.04 r_work: 0.3152 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9102 Z= 0.206 Angle : 0.612 8.251 12424 Z= 0.302 Chirality : 0.042 0.171 1463 Planarity : 0.005 0.042 1523 Dihedral : 8.300 78.530 1311 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.73 % Allowed : 16.90 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.27), residues: 1118 helix: 1.33 (0.21), residues: 693 sheet: -0.48 (0.91), residues: 34 loop : -1.53 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 55 HIS 0.006 0.001 HIS A 73 PHE 0.013 0.001 PHE B 3 TYR 0.008 0.001 TYR C 139 ARG 0.005 0.000 ARG E 52 *********************** 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 195 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 1.242 Fit side-chains REVERT: B 71 ARG cc_start: 0.8440 (ttp80) cc_final: 0.8059 (ttp80) REVERT: F 156 ARG cc_start: 0.7380 (tpp80) cc_final: 0.7164 (tpp80) outliers start: 25 outliers final: 20 residues processed: 184 average time/residue: 0.2671 time to fit residues: 65.7551 Evaluate side-chains 185 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 1.421 ------------------------------------------------------------------------------- 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 93 GLU Chi-restraints excluded: chain A residue 94 ASN 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 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 47 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3493 r_free = 0.3493 target = 0.111125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.096451 restraints weight = 14835.199| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.03 r_work: 0.3156 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9102 Z= 0.204 Angle : 0.606 6.829 12424 Z= 0.297 Chirality : 0.042 0.165 1463 Planarity : 0.004 0.041 1523 Dihedral : 8.093 73.357 1311 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.60 % Allowed : 17.45 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.27), residues: 1118 helix: 1.53 (0.21), residues: 687 sheet: -0.36 (0.91), residues: 34 loop : -1.57 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 55 HIS 0.006 0.001 HIS A 73 PHE 0.012 0.001 PHE B 3 TYR 0.006 0.001 TYR C 71 ARG 0.005 0.000 ARG E 52 *********************** 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 205 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 1.098 Fit side-chains REVERT: B 71 ARG cc_start: 0.8409 (ttp80) cc_final: 0.8018 (ttp80) REVERT: D 14 MET cc_start: 0.6942 (pmm) cc_final: 0.6578 (ptm) outliers start: 33 outliers final: 24 residues processed: 193 average time/residue: 0.2510 time to fit residues: 65.2852 Evaluate side-chains 191 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 104 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 173 LEU 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 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 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 57 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 28 optimal weight: 0.0000 chunk 105 optimal weight: 6.9990 chunk 108 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.111766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.097159 restraints weight = 15042.487| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.03 r_work: 0.3177 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2330 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= 0.183 Angle : 0.598 6.728 12424 Z= 0.294 Chirality : 0.042 0.325 1463 Planarity : 0.004 0.041 1523 Dihedral : 7.904 71.912 1311 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.27 % Allowed : 17.99 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.27), residues: 1118 helix: 1.63 (0.21), residues: 686 sheet: -0.21 (0.91), residues: 34 loop : -1.51 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 55 HIS 0.004 0.001 HIS A 73 PHE 0.013 0.001 PHE B 3 TYR 0.008 0.001 TYR C 139 ARG 0.006 0.000 ARG E 52 *********************** 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 201 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 1.105 Fit side-chains REVERT: B 71 ARG cc_start: 0.8333 (ttp80) cc_final: 0.8004 (ttp80) REVERT: B 87 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8470 (pt) REVERT: C 48 TYR cc_start: 0.7124 (p90) cc_final: 0.6298 (p90) REVERT: C 71 TYR cc_start: 0.8906 (t80) cc_final: 0.8680 (t80) REVERT: D 14 MET cc_start: 0.6890 (pmm) cc_final: 0.6589 (ptm) REVERT: E 95 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9017 (mt) REVERT: F 127 GLN cc_start: 0.7745 (mt0) cc_final: 0.7540 (mt0) outliers start: 30 outliers final: 24 residues processed: 188 average time/residue: 0.2320 time to fit residues: 58.3291 Evaluate side-chains 190 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 134 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 173 LEU 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 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 69 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 43 optimal weight: 0.0470 chunk 76 optimal weight: 0.0570 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3507 r_free = 0.3507 target = 0.112145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.097469 restraints weight = 15111.865| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.08 r_work: 0.3182 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2432 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= 0.186 Angle : 0.602 6.279 12424 Z= 0.295 Chirality : 0.042 0.244 1463 Planarity : 0.004 0.040 1523 Dihedral : 7.730 70.985 1311 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.05 % Allowed : 18.97 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.27), residues: 1118 helix: 1.68 (0.21), residues: 686 sheet: -0.21 (0.89), residues: 34 loop : -1.48 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 55 HIS 0.005 0.001 HIS E 73 PHE 0.013 0.001 PHE B 3 TYR 0.019 0.001 TYR C 54 ARG 0.006 0.000 ARG E 52 *********************** 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 198 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 1.357 Fit side-chains REVERT: B 71 ARG cc_start: 0.8349 (ttp80) cc_final: 0.8027 (ttp80) REVERT: B 75 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8121 (mm-40) REVERT: B 87 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8466 (pt) REVERT: C 48 TYR cc_start: 0.7108 (p90) cc_final: 0.6597 (p90) REVERT: C 49 GLN cc_start: 0.8319 (mm-40) cc_final: 0.8112 (mm-40) REVERT: D 14 MET cc_start: 0.6907 (pmm) cc_final: 0.6600 (ptm) REVERT: E 95 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8989 (mt) outliers start: 28 outliers final: 24 residues processed: 186 average time/residue: 0.2494 time to fit residues: 61.8167 Evaluate side-chains 191 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 104 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 173 LEU 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 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 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 95 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 5 optimal weight: 0.0070 chunk 51 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3514 r_free = 0.3514 target = 0.112625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.098060 restraints weight = 14939.266| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.06 r_work: 0.3191 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2487 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= 0.185 Angle : 0.612 9.791 12424 Z= 0.297 Chirality : 0.041 0.223 1463 Planarity : 0.004 0.040 1523 Dihedral : 7.589 70.681 1311 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.16 % Allowed : 19.30 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.27), residues: 1118 helix: 1.73 (0.21), residues: 687 sheet: -1.45 (0.69), residues: 52 loop : -1.33 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 55 HIS 0.004 0.001 HIS A 73 PHE 0.013 0.001 PHE B 3 TYR 0.016 0.001 TYR C 54 ARG 0.006 0.000 ARG E 52 *********************** 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 202 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.957 Fit side-chains REVERT: B 71 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7940 (ttp80) REVERT: B 87 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8407 (pt) REVERT: C 48 TYR cc_start: 0.7231 (p90) cc_final: 0.6947 (p90) REVERT: D 14 MET cc_start: 0.6837 (pmm) cc_final: 0.6619 (ptm) REVERT: E 95 LEU cc_start: 0.9167 (tp) cc_final: 0.8956 (mt) outliers start: 29 outliers final: 24 residues processed: 189 average time/residue: 0.2454 time to fit residues: 62.1301 Evaluate side-chains 190 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 104 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 173 LEU 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 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 30 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.0020 chunk 73 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3472 r_free = 0.3472 target = 0.109676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.094943 restraints weight = 15075.634| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.07 r_work: 0.3141 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2482 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= 0.268 Angle : 0.651 9.419 12424 Z= 0.317 Chirality : 0.043 0.220 1463 Planarity : 0.005 0.040 1523 Dihedral : 7.715 72.035 1311 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.26 % Favored : 93.65 % Rotamer: Outliers : 3.05 % Allowed : 19.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.27), residues: 1118 helix: 1.62 (0.21), residues: 687 sheet: -1.61 (0.71), residues: 52 loop : -1.36 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 55 HIS 0.007 0.001 HIS A 73 PHE 0.013 0.001 PHE B 28 TYR 0.017 0.001 TYR C 54 ARG 0.007 0.000 ARG E 52 ********************** 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: 28 poor density : 164 time to evaluate : 0.993 Fit side-chains REVERT: A 182 THR cc_start: 0.9374 (OUTLIER) cc_final: 0.9086 (p) REVERT: B 71 ARG cc_start: 0.8321 (ttp80) cc_final: 0.8057 (ttp80) REVERT: B 87 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8470 (pt) REVERT: E 95 LEU cc_start: 0.9179 (tp) cc_final: 0.8950 (mt) REVERT: F 10 GLU cc_start: 0.8756 (tp30) cc_final: 0.8359 (tp30) outliers start: 28 outliers final: 24 residues processed: 181 average time/residue: 0.2294 time to fit residues: 55.9505 Evaluate side-chains 189 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 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 112 SER Chi-restraints excluded: chain C residue 121 THR 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 181 LEU 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 Chi-restraints excluded: chain F residue 173 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 65 optimal weight: 0.0770 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3505 r_free = 0.3505 target = 0.111950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.097126 restraints weight = 15150.291| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.10 r_work: 0.3173 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2535 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= 0.192 Angle : 0.627 9.480 12424 Z= 0.306 Chirality : 0.042 0.207 1463 Planarity : 0.004 0.040 1523 Dihedral : 7.568 71.799 1311 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.90 % Favored : 94.01 % Rotamer: Outliers : 3.16 % Allowed : 19.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.27), residues: 1118 helix: 1.73 (0.21), residues: 687 sheet: -1.48 (0.70), residues: 52 loop : -1.31 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 55 HIS 0.005 0.001 HIS A 73 PHE 0.014 0.001 PHE B 3 TYR 0.015 0.001 TYR C 54 ARG 0.006 0.000 ARG E 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5060.07 seconds wall clock time: 90 minutes 32.26 seconds (5432.26 seconds total)