Starting phenix.real_space_refine on Wed Sep 17 14:53:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f03_31395/09_2025/7f03_31395.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f03_31395/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7f03_31395/09_2025/7f03_31395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f03_31395/09_2025/7f03_31395.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f03_31395/09_2025/7f03_31395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f03_31395/09_2025/7f03_31395.map" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 2 5.21 5 S 46 5.16 5 C 5798 2.51 5 N 1517 2.21 5 O 1521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8891 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1586 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "B" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1663 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1848 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 11, 'TRANS': 219} Chain: "D" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "E" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1586 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "F" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1663 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.33, per 1000 atoms: 0.26 Number of scatterers: 8891 At special positions: 0 Unit cell: (100.672, 94.848, 117.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 46 16.00 P 7 15.00 Mg 2 11.99 O 1521 8.00 N 1517 7.00 C 5798 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 341.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.30 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: 1.33 Time building geometry restraints manager: 1.15 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: 2.160 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.720 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.740 ------------------------------------------------------------------------------- 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= 0.235 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 : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.11 % Allowed : 0.33 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.26), residues: 1118 helix: 0.60 (0.22), residues: 666 sheet: -0.39 (1.16), residues: 22 loop : -1.51 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 52 TYR 0.014 0.001 TYR F 124 PHE 0.018 0.001 PHE B 3 TRP 0.015 0.001 TRP F 55 HIS 0.006 0.001 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 9102) covalent geometry : angle 0.74943 (12424) hydrogen bonds : bond 0.19663 ( 489) hydrogen bonds : angle 7.00678 ( 1404) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 0.365 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: 0.1146 time to fit residues: 31.3870 Evaluate side-chains 166 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.0020 chunk 49 optimal weight: 0.0870 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.0070 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN C 49 GLN C 181 ASN F 17 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.116762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.102836 restraints weight = 14560.953| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.99 r_work: 0.3267 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1397 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= 0.119 Angle : 0.626 8.191 12424 Z= 0.307 Chirality : 0.042 0.146 1463 Planarity : 0.005 0.056 1523 Dihedral : 9.668 80.834 1311 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.42 % Allowed : 10.25 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.26), residues: 1118 helix: 0.97 (0.21), residues: 697 sheet: -0.56 (1.07), residues: 22 loop : -1.56 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 100 TYR 0.012 0.001 TYR C 48 PHE 0.021 0.001 PHE A 97 TRP 0.014 0.001 TRP F 55 HIS 0.006 0.001 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9102) covalent geometry : angle 0.62552 (12424) hydrogen bonds : bond 0.03815 ( 489) hydrogen bonds : angle 4.54222 ( 1404) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.241 Fit side-chains REVERT: B 68 ARG cc_start: 0.8710 (ttm170) cc_final: 0.8449 (ttm-80) REVERT: B 71 ARG cc_start: 0.8568 (ttp80) cc_final: 0.8312 (ttp80) REVERT: C 49 GLN cc_start: 0.7704 (mt0) cc_final: 0.7454 (mt0) REVERT: F 10 GLU cc_start: 0.8756 (tp30) cc_final: 0.8529 (tp30) outliers start: 13 outliers final: 8 residues processed: 196 average time/residue: 0.1090 time to fit residues: 28.9133 Evaluate side-chains 167 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 159 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain D residue 8 TRP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 102 optimal weight: 0.0070 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- 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 C 7 GLN E 172 HIS F 17 HIS F 127 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.115032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.100884 restraints weight = 14690.999| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.01 r_work: 0.3231 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1690 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= 0.133 Angle : 0.613 7.644 12424 Z= 0.300 Chirality : 0.042 0.206 1463 Planarity : 0.005 0.043 1523 Dihedral : 8.498 75.475 1311 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.73 % Allowed : 12.87 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.26), residues: 1118 helix: 1.18 (0.21), residues: 698 sheet: -0.90 (0.79), residues: 34 loop : -1.51 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 100 TYR 0.006 0.001 TYR C 48 PHE 0.013 0.001 PHE A 97 TRP 0.015 0.001 TRP F 55 HIS 0.006 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9102) covalent geometry : angle 0.61257 (12424) hydrogen bonds : bond 0.03463 ( 489) hydrogen bonds : angle 4.33165 ( 1404) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.343 Fit side-chains REVERT: B 68 ARG cc_start: 0.8765 (ttm170) cc_final: 0.8559 (ttm-80) REVERT: B 71 ARG cc_start: 0.8570 (ttp80) cc_final: 0.8254 (ttp80) REVERT: C 48 TYR cc_start: 0.7123 (p90) cc_final: 0.6903 (p90) REVERT: C 49 GLN cc_start: 0.7687 (mt0) cc_final: 0.7480 (mt0) outliers start: 25 outliers final: 18 residues processed: 184 average time/residue: 0.1117 time to fit residues: 27.6399 Evaluate side-chains 181 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 56 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain D residue 8 TRP Chi-restraints excluded: chain D residue 47 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 79 optimal weight: 3.9990 chunk 42 optimal weight: 0.0970 chunk 91 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.110729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.096159 restraints weight = 15314.302| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.05 r_work: 0.3160 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9102 Z= 0.148 Angle : 0.618 8.327 12424 Z= 0.301 Chirality : 0.043 0.207 1463 Planarity : 0.005 0.042 1523 Dihedral : 8.163 73.295 1311 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.16 % Allowed : 14.39 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.27), residues: 1118 helix: 1.31 (0.21), residues: 694 sheet: -0.65 (0.87), residues: 34 loop : -1.51 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 52 TYR 0.006 0.001 TYR C 71 PHE 0.012 0.001 PHE B 3 TRP 0.016 0.001 TRP F 55 HIS 0.007 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9102) covalent geometry : angle 0.61810 (12424) hydrogen bonds : bond 0.03367 ( 489) hydrogen bonds : angle 4.20765 ( 1404) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.349 Fit side-chains REVERT: B 71 ARG cc_start: 0.8479 (ttp80) cc_final: 0.8219 (ttp80) REVERT: E 163 ASP cc_start: 0.8831 (t0) cc_final: 0.8606 (t0) outliers start: 29 outliers final: 21 residues processed: 187 average time/residue: 0.1050 time to fit residues: 26.5429 Evaluate side-chains 183 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 56 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain D residue 8 TRP Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 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 117 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3496 r_free = 0.3496 target = 0.111478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.096913 restraints weight = 15040.183| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.03 r_work: 0.3175 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2033 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= 0.125 Angle : 0.599 7.041 12424 Z= 0.294 Chirality : 0.041 0.160 1463 Planarity : 0.004 0.042 1523 Dihedral : 8.039 72.169 1311 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.62 % Allowed : 17.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.27), residues: 1118 helix: 1.42 (0.21), residues: 693 sheet: -0.40 (0.90), residues: 34 loop : -1.48 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 52 TYR 0.007 0.001 TYR C 139 PHE 0.014 0.001 PHE B 3 TRP 0.016 0.001 TRP F 55 HIS 0.005 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9102) covalent geometry : angle 0.59912 (12424) hydrogen bonds : bond 0.03145 ( 489) hydrogen bonds : angle 4.14033 ( 1404) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.445 Fit side-chains REVERT: B 71 ARG cc_start: 0.8447 (ttp80) cc_final: 0.8074 (ttp80) outliers start: 24 outliers final: 18 residues processed: 180 average time/residue: 0.1108 time to fit residues: 27.0249 Evaluate side-chains 179 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 117 MET 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 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 3 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.111569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.096719 restraints weight = 14962.246| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.05 r_work: 0.3159 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2131 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= 0.141 Angle : 0.604 6.576 12424 Z= 0.298 Chirality : 0.042 0.148 1463 Planarity : 0.004 0.041 1523 Dihedral : 7.960 71.322 1311 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.05 % Allowed : 17.45 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.27), residues: 1118 helix: 1.51 (0.21), residues: 688 sheet: -0.44 (0.90), residues: 34 loop : -1.56 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 52 TYR 0.006 0.001 TYR C 71 PHE 0.014 0.001 PHE B 3 TRP 0.016 0.001 TRP F 55 HIS 0.005 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9102) covalent geometry : angle 0.60432 (12424) hydrogen bonds : bond 0.03208 ( 489) hydrogen bonds : angle 4.11401 ( 1404) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.333 Fit side-chains REVERT: B 71 ARG cc_start: 0.8420 (ttp80) cc_final: 0.8024 (ttp80) outliers start: 28 outliers final: 24 residues processed: 186 average time/residue: 0.1122 time to fit residues: 27.9223 Evaluate side-chains 187 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 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 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 58 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 Chi-restraints excluded: chain F residue 117 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.3462 r_free = 0.3462 target = 0.108975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.094399 restraints weight = 15257.838| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.04 r_work: 0.3136 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9102 Z= 0.170 Angle : 0.634 7.431 12424 Z= 0.312 Chirality : 0.043 0.153 1463 Planarity : 0.005 0.040 1523 Dihedral : 8.004 71.607 1311 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.49 % Allowed : 17.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.27), residues: 1118 helix: 1.50 (0.21), residues: 687 sheet: -0.41 (0.93), residues: 34 loop : -1.56 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 52 TYR 0.008 0.001 TYR C 139 PHE 0.013 0.001 PHE B 3 TRP 0.016 0.001 TRP F 55 HIS 0.007 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 9102) covalent geometry : angle 0.63416 (12424) hydrogen bonds : bond 0.03414 ( 489) hydrogen bonds : angle 4.14553 ( 1404) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.344 Fit side-chains REVERT: B 2 MET cc_start: 0.7869 (ttt) cc_final: 0.7361 (ttm) REVERT: B 71 ARG cc_start: 0.8385 (ttp80) cc_final: 0.7998 (ttp80) REVERT: B 174 ILE cc_start: 0.8673 (mt) cc_final: 0.8473 (mp) REVERT: C 48 TYR cc_start: 0.7151 (p90) cc_final: 0.6399 (p90) REVERT: C 71 TYR cc_start: 0.8994 (t80) cc_final: 0.8749 (t80) REVERT: D 14 MET cc_start: 0.6888 (pmm) cc_final: 0.6579 (ptm) outliers start: 32 outliers final: 26 residues processed: 189 average time/residue: 0.1104 time to fit residues: 28.2083 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 : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 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 58 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 117 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3494 r_free = 0.3494 target = 0.111340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.096792 restraints weight = 15075.946| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.03 r_work: 0.3169 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2357 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= 0.126 Angle : 0.611 7.350 12424 Z= 0.301 Chirality : 0.042 0.304 1463 Planarity : 0.004 0.040 1523 Dihedral : 7.783 70.518 1311 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.73 % Allowed : 18.65 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.27), residues: 1118 helix: 1.62 (0.21), residues: 687 sheet: -0.27 (0.89), residues: 34 loop : -1.51 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 156 TYR 0.005 0.001 TYR A 98 PHE 0.013 0.001 PHE B 3 TRP 0.017 0.001 TRP F 55 HIS 0.004 0.001 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9102) covalent geometry : angle 0.61104 (12424) hydrogen bonds : bond 0.03073 ( 489) hydrogen bonds : angle 4.06167 ( 1404) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.335 Fit side-chains REVERT: B 71 ARG cc_start: 0.8358 (ttp80) cc_final: 0.8021 (ttp80) REVERT: C 71 TYR cc_start: 0.8946 (t80) cc_final: 0.8736 (t80) REVERT: D 14 MET cc_start: 0.6892 (pmm) cc_final: 0.6589 (ptm) REVERT: E 95 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9034 (mt) outliers start: 25 outliers final: 20 residues processed: 183 average time/residue: 0.1102 time to fit residues: 27.0210 Evaluate side-chains 184 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 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 E residue 30 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 117 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.111318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.096800 restraints weight = 15005.312| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.02 r_work: 0.3174 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2426 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= 0.128 Angle : 0.618 9.970 12424 Z= 0.302 Chirality : 0.042 0.228 1463 Planarity : 0.004 0.040 1523 Dihedral : 7.667 69.836 1311 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.94 % Allowed : 18.54 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.27), residues: 1118 helix: 1.69 (0.21), residues: 686 sheet: -1.53 (0.70), residues: 52 loop : -1.36 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 54 TYR 0.007 0.001 TYR C 139 PHE 0.014 0.001 PHE B 3 TRP 0.014 0.001 TRP F 55 HIS 0.005 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9102) covalent geometry : angle 0.61841 (12424) hydrogen bonds : bond 0.03065 ( 489) hydrogen bonds : angle 4.03018 ( 1404) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.326 Fit side-chains REVERT: B 71 ARG cc_start: 0.8362 (ttp80) cc_final: 0.8085 (ttp80) REVERT: C 48 TYR cc_start: 0.7112 (p90) cc_final: 0.6892 (p90) REVERT: C 49 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8161 (mm-40) REVERT: C 71 TYR cc_start: 0.8926 (t80) cc_final: 0.8720 (t80) REVERT: D 14 MET cc_start: 0.6918 (pmm) cc_final: 0.6619 (ptm) REVERT: E 95 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9012 (mt) outliers start: 27 outliers final: 21 residues processed: 181 average time/residue: 0.1075 time to fit residues: 26.0655 Evaluate side-chains 186 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 107 optimal weight: 0.0020 chunk 76 optimal weight: 0.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.112596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.098029 restraints weight = 14988.135| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.03 r_work: 0.3188 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 : 0.003 0.032 9102 Z= 0.118 Angle : 0.607 9.394 12424 Z= 0.297 Chirality : 0.041 0.228 1463 Planarity : 0.004 0.040 1523 Dihedral : 7.528 68.614 1311 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.72 % Favored : 94.19 % Rotamer: Outliers : 2.62 % Allowed : 19.19 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.27), residues: 1118 helix: 1.76 (0.21), residues: 686 sheet: -1.39 (0.70), residues: 52 loop : -1.35 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 54 TYR 0.010 0.001 TYR C 48 PHE 0.014 0.001 PHE B 3 TRP 0.012 0.001 TRP C 66 HIS 0.005 0.001 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9102) covalent geometry : angle 0.60724 (12424) hydrogen bonds : bond 0.02910 ( 489) hydrogen bonds : angle 3.96746 ( 1404) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.337 Fit side-chains REVERT: B 71 ARG cc_start: 0.8341 (ttp80) cc_final: 0.8067 (ttp80) REVERT: D 14 MET cc_start: 0.6881 (pmm) cc_final: 0.6542 (mtp) REVERT: E 95 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8992 (mt) outliers start: 24 outliers final: 21 residues processed: 182 average time/residue: 0.1025 time to fit residues: 25.2363 Evaluate side-chains 184 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 1 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 108 optimal weight: 0.0670 chunk 7 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.107211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.092582 restraints weight = 15074.400| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.05 r_work: 0.3106 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9102 Z= 0.224 Angle : 0.697 9.596 12424 Z= 0.342 Chirality : 0.045 0.242 1463 Planarity : 0.005 0.040 1523 Dihedral : 7.873 71.065 1311 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.53 % Favored : 93.29 % Rotamer: Outliers : 2.84 % Allowed : 19.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.26), residues: 1118 helix: 1.53 (0.21), residues: 686 sheet: -1.71 (0.71), residues: 52 loop : -1.45 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 100 TYR 0.008 0.001 TYR C 71 PHE 0.013 0.002 PHE B 3 TRP 0.013 0.001 TRP C 180 HIS 0.008 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 9102) covalent geometry : angle 0.69739 (12424) hydrogen bonds : bond 0.03726 ( 489) hydrogen bonds : angle 4.19658 ( 1404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2321.90 seconds wall clock time: 40 minutes 29.03 seconds (2429.03 seconds total)