Starting phenix.real_space_refine on Sat Dec 28 22:04:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f03_31395/12_2024/7f03_31395.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f03_31395/12_2024/7f03_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_31395/12_2024/7f03_31395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f03_31395/12_2024/7f03_31395.map" model { file = "/net/cci-nas-00/data/ceres_data/7f03_31395/12_2024/7f03_31395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f03_31395/12_2024/7f03_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.83, per 1000 atoms: 0.66 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: 2.66 Conformation dependent library (CDL) restraints added in 1.2 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: 0.88 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: 2.80 Time building geometry restraints manager: 2.94 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.060 Find NCS groups from input model: 0.290 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:3.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.510 ------------------------------------------------------------------------------- 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 : 0.914 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: 0.2545 time to fit residues: 70.0643 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 : 1.012 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 : 0.943 Fit side-chains REVERT: B 68 ARG cc_start: 0.8471 (ttm170) cc_final: 0.8234 (ttm-80) REVERT: B 71 ARG cc_start: 0.8132 (ttp80) cc_final: 0.7878 (ttp80) outliers start: 16 outliers final: 10 residues processed: 194 average time/residue: 0.2341 time to fit residues: 60.8663 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 : 1.100 ------------------------------------------------------------------------------- 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 56 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 100 optimal weight: 0.0770 overall best weight: 1.3942 ------------------------------------------------------------------------------- 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 C 49 GLN F 17 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9102 Z= 0.264 Angle : 0.645 8.511 12424 Z= 0.316 Chirality : 0.044 0.230 1463 Planarity : 0.005 0.044 1523 Dihedral : 8.627 77.230 1311 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.05 % Allowed : 13.41 % Favored : 83.53 % 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: 0.17 (0.26), residues: 1118 helix: 1.05 (0.21), residues: 700 sheet: -1.01 (0.83), residues: 34 loop : -1.53 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 55 HIS 0.008 0.001 HIS A 73 PHE 0.014 0.002 PHE A 97 TYR 0.008 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: 28 poor density : 162 time to evaluate : 0.994 Fit side-chains REVERT: B 68 ARG cc_start: 0.8544 (ttm170) cc_final: 0.8276 (ttm-80) REVERT: B 71 ARG cc_start: 0.8142 (ttp80) cc_final: 0.7925 (ttp80) REVERT: C 48 TYR cc_start: 0.6476 (p90) cc_final: 0.5950 (p90) outliers start: 28 outliers final: 18 residues processed: 182 average time/residue: 0.2354 time to fit residues: 57.6960 Evaluate side-chains 178 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 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 76 optimal weight: 0.0050 chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 0.0050 chunk 102 optimal weight: 0.4980 chunk 108 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.4808 ------------------------------------------------------------------------------- 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 E 172 HIS F 17 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1999 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= 0.170 Angle : 0.592 7.777 12424 Z= 0.289 Chirality : 0.042 0.209 1463 Planarity : 0.005 0.043 1523 Dihedral : 8.117 76.040 1311 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.73 % Allowed : 15.27 % Favored : 82.01 % 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: 0.49 (0.27), residues: 1118 helix: 1.37 (0.21), residues: 693 sheet: -0.63 (0.83), residues: 34 loop : -1.52 (0.31), residues: 391 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 C 41 TYR 0.021 0.001 TYR C 48 ARG 0.005 0.000 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 191 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 1.025 Fit side-chains REVERT: B 68 ARG cc_start: 0.8540 (ttm170) cc_final: 0.8308 (ttm-80) REVERT: B 71 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7905 (ttp80) outliers start: 25 outliers final: 16 residues processed: 182 average time/residue: 0.2340 time to fit residues: 57.5093 Evaluate side-chains 174 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 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 228 MET Chi-restraints excluded: chain D residue 8 TRP Chi-restraints excluded: chain E residue 9 CYS 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 61 optimal weight: 1.9990 chunk 1 optimal weight: 0.0870 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- 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 F 17 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2078 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= 0.210 Angle : 0.603 6.811 12424 Z= 0.295 Chirality : 0.042 0.155 1463 Planarity : 0.004 0.041 1523 Dihedral : 8.038 72.490 1311 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.73 % Allowed : 17.45 % Favored : 79.83 % 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: 0.55 (0.27), residues: 1118 helix: 1.40 (0.21), residues: 694 sheet: -0.43 (0.90), residues: 34 loop : -1.49 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 55 HIS 0.005 0.001 HIS A 73 PHE 0.013 0.001 PHE B 3 TYR 0.008 0.001 TYR C 48 ARG 0.004 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 189 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.991 Fit side-chains REVERT: B 71 ARG cc_start: 0.8128 (ttp80) cc_final: 0.7822 (ttp80) REVERT: D 14 MET cc_start: 0.6590 (pmm) cc_final: 0.6148 (ptm) outliers start: 25 outliers final: 21 residues processed: 179 average time/residue: 0.2340 time to fit residues: 56.4462 Evaluate side-chains 180 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 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 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 8 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 108 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 147 HIS F 17 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9102 Z= 0.365 Angle : 0.688 7.198 12424 Z= 0.339 Chirality : 0.045 0.159 1463 Planarity : 0.005 0.041 1523 Dihedral : 8.367 73.700 1311 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.71 % Favored : 93.20 % Rotamer: Outliers : 4.14 % Allowed : 17.12 % 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: 0.32 (0.26), residues: 1118 helix: 1.29 (0.21), residues: 688 sheet: -0.56 (0.91), residues: 34 loop : -1.66 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 55 HIS 0.009 0.001 HIS A 73 PHE 0.016 0.002 PHE D 20 TYR 0.012 0.001 TYR C 48 ARG 0.004 0.001 ARG C 55 *********************** 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 202 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 164 time to evaluate : 0.944 Fit side-chains REVERT: B 2 MET cc_start: 0.7439 (ttt) cc_final: 0.7070 (ttm) REVERT: B 71 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7855 (ttp80) REVERT: D 14 MET cc_start: 0.6535 (pmm) cc_final: 0.6265 (ptm) REVERT: F 10 GLU cc_start: 0.8119 (tp30) cc_final: 0.7876 (tp30) outliers start: 38 outliers final: 27 residues processed: 189 average time/residue: 0.2536 time to fit residues: 64.4542 Evaluate side-chains 185 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 A residue 149 ILE Chi-restraints excluded: chain B residue 49 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 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 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 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 12 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2282 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= 0.190 Angle : 0.606 6.954 12424 Z= 0.299 Chirality : 0.042 0.321 1463 Planarity : 0.004 0.041 1523 Dihedral : 8.000 70.094 1311 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.38 % Allowed : 18.21 % Favored : 78.41 % 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: 0.64 (0.27), residues: 1118 helix: 1.54 (0.21), residues: 686 sheet: -0.25 (0.93), residues: 34 loop : -1.56 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 55 HIS 0.005 0.001 HIS A 73 PHE 0.013 0.001 PHE B 3 TYR 0.009 0.001 TYR C 48 ARG 0.003 0.000 ARG B 68 *********************** 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: 31 poor density : 167 time to evaluate : 0.927 Fit side-chains REVERT: B 71 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7728 (ttp80) REVERT: B 87 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8574 (pt) REVERT: C 71 TYR cc_start: 0.8781 (t80) cc_final: 0.8578 (t80) REVERT: D 14 MET cc_start: 0.6405 (pmm) cc_final: 0.6164 (ptm) REVERT: E 95 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8897 (mt) outliers start: 31 outliers final: 26 residues processed: 184 average time/residue: 0.2387 time to fit residues: 59.2048 Evaluate side-chains 188 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 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 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 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 90 THR Chi-restraints excluded: chain E residue 93 GLU 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 Chi-restraints excluded: chain F residue 173 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 F 127 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2378 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= 0.221 Angle : 0.615 7.095 12424 Z= 0.304 Chirality : 0.042 0.236 1463 Planarity : 0.004 0.040 1523 Dihedral : 7.846 68.064 1311 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.38 % Allowed : 18.65 % 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: 0.69 (0.27), residues: 1118 helix: 1.58 (0.21), residues: 687 sheet: -0.23 (0.93), residues: 34 loop : -1.54 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 55 HIS 0.005 0.001 HIS A 73 PHE 0.013 0.001 PHE B 3 TYR 0.014 0.001 TYR C 54 ARG 0.004 0.000 ARG F 156 *********************** 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 195 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 1.107 Fit side-chains REVERT: B 2 MET cc_start: 0.7323 (ttt) cc_final: 0.6963 (ttm) REVERT: B 71 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7746 (ttp80) REVERT: B 87 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8560 (pt) REVERT: C 71 TYR cc_start: 0.8810 (t80) cc_final: 0.8595 (t80) REVERT: D 14 MET cc_start: 0.6398 (pmm) cc_final: 0.6144 (ptm) REVERT: E 95 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8891 (mt) outliers start: 31 outliers final: 25 residues processed: 182 average time/residue: 0.2377 time to fit residues: 58.3344 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 : 1.023 ------------------------------------------------------------------------------- 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 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 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 84 LEU Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 173 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 103 optimal weight: 0.0980 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2466 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= 0.182 Angle : 0.606 10.527 12424 Z= 0.297 Chirality : 0.041 0.217 1463 Planarity : 0.004 0.040 1523 Dihedral : 7.623 65.238 1311 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.38 % Allowed : 19.08 % 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: 0.84 (0.27), residues: 1118 helix: 1.71 (0.21), residues: 686 sheet: -0.02 (0.93), residues: 34 loop : -1.50 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 66 HIS 0.005 0.001 HIS A 73 PHE 0.014 0.001 PHE B 3 TYR 0.019 0.001 TYR C 54 ARG 0.003 0.000 ARG F 156 *********************** 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 203 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.920 Fit side-chains REVERT: B 2 MET cc_start: 0.7244 (ttt) cc_final: 0.6892 (ttm) REVERT: B 71 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7737 (ttp80) REVERT: B 87 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8526 (pt) REVERT: E 95 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8888 (mt) outliers start: 31 outliers final: 24 residues processed: 187 average time/residue: 0.2344 time to fit residues: 59.1658 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 : 1.096 ------------------------------------------------------------------------------- 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 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 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 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 64 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 0.0670 chunk 111 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2529 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= 0.223 Angle : 0.620 9.507 12424 Z= 0.304 Chirality : 0.042 0.218 1463 Planarity : 0.004 0.040 1523 Dihedral : 7.593 64.487 1311 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.83 % 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: 0.81 (0.27), residues: 1118 helix: 1.69 (0.21), residues: 686 sheet: -0.07 (0.95), residues: 34 loop : -1.51 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 66 HIS 0.005 0.001 HIS A 73 PHE 0.013 0.001 PHE B 3 TYR 0.017 0.001 TYR C 54 ARG 0.002 0.000 ARG E 100 ********************** 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 196 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 1.011 Fit side-chains REVERT: B 2 MET cc_start: 0.7298 (ttt) cc_final: 0.6948 (ttm) REVERT: B 71 ARG cc_start: 0.8082 (ttp80) cc_final: 0.7752 (ttp80) REVERT: B 87 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8544 (pt) REVERT: E 95 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8901 (mt) outliers start: 28 outliers final: 26 residues processed: 184 average time/residue: 0.2277 time to fit residues: 56.2365 Evaluate side-chains 193 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 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 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 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 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 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 27 optimal weight: 0.0060 chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 37 optimal weight: 0.1980 chunk 91 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 0.0010 overall best weight: 1.2406 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.110272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.095654 restraints weight = 14906.342| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.05 r_work: 0.3155 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9102 Z= 0.253 Angle : 0.634 9.535 12424 Z= 0.311 Chirality : 0.043 0.222 1463 Planarity : 0.004 0.040 1523 Dihedral : 7.608 64.171 1311 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.26 % Favored : 93.65 % Rotamer: Outliers : 3.16 % Allowed : 19.96 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.78 (0.27), residues: 1118 helix: 1.66 (0.21), residues: 686 sheet: -0.11 (0.95), residues: 34 loop : -1.52 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 55 HIS 0.005 0.001 HIS A 73 PHE 0.013 0.001 PHE B 3 TYR 0.017 0.001 TYR C 54 ARG 0.003 0.000 ARG C 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2218.83 seconds wall clock time: 40 minutes 54.95 seconds (2454.95 seconds total)