Starting phenix.real_space_refine on Wed Mar 12 19:10:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s8p_24900/03_2025/7s8p_24900.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s8p_24900/03_2025/7s8p_24900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s8p_24900/03_2025/7s8p_24900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s8p_24900/03_2025/7s8p_24900.map" model { file = "/net/cci-nas-00/data/ceres_data/7s8p_24900/03_2025/7s8p_24900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s8p_24900/03_2025/7s8p_24900.cif" } resolution = 2.6 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= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5182 2.51 5 N 1383 2.21 5 O 1474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8093 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1675 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 6, 'TRANS': 215} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 94 Chain: "C" Number of atoms: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2477 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 92 Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1730 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 1832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1832 Classifications: {'peptide': 247} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 44} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 86 Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'8IX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.14, per 1000 atoms: 0.64 Number of scatterers: 8093 At special positions: 0 Unit cell: (89.18, 117.39, 130.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1474 8.00 N 1383 7.00 C 5182 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.05 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 161 " - pdb=" SG CYS R 173 " distance=2.04 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: 2.11 Conformation dependent library (CDL) restraints added in 1.1 seconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2036 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 13 sheets defined 37.9% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'B' and resid 6 through 30 removed outlier: 3.680A pdb=" N ALA B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP B 26 " --> pdb=" O ASN B 22 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.500A pdb=" N THR B 48 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 101 removed outlier: 3.903A pdb=" N GLN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.548A pdb=" N LEU B 134 " --> pdb=" O ASN B 131 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 131 through 135' Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.740A pdb=" N LEU B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 150 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 164 through 168 removed outlier: 3.543A pdb=" N ALA B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 202 removed outlier: 3.733A pdb=" N ALA B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS B 195 " --> pdb=" O TYR B 191 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 243 removed outlier: 3.521A pdb=" N ASP B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 24 removed outlier: 3.514A pdb=" N ALA C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.859A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN C 132 " --> pdb=" O ARG C 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 128 through 132' Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.553A pdb=" N VAL D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 45 through 48 removed outlier: 4.249A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.866A pdb=" N ASN D 59 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.553A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.962A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 52 removed outlier: 3.507A pdb=" N ILE R 37 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL R 40 " --> pdb=" O ILE R 36 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY R 41 " --> pdb=" O ILE R 37 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU R 42 " --> pdb=" O SER R 38 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL R 47 " --> pdb=" O THR R 43 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL R 48 " --> pdb=" O GLY R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 86 removed outlier: 3.620A pdb=" N PHE R 75 " --> pdb=" O ALA R 71 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN R 79 " --> pdb=" O PHE R 75 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE R 80 " --> pdb=" O LEU R 76 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE R 81 " --> pdb=" O SER R 77 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU R 83 " --> pdb=" O GLN R 79 " (cutoff:3.500A) Proline residue: R 84 - end of helix Processing helix chain 'R' and resid 91 through 110 removed outlier: 3.975A pdb=" N LYS R 96 " --> pdb=" O HIS R 92 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE R 97 " --> pdb=" O LEU R 93 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL R 99 " --> pdb=" O ARG R 95 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL R 101 " --> pdb=" O ILE R 97 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE R 104 " --> pdb=" O SER R 100 " (cutoff:3.500A) Proline residue: R 105 - end of helix removed outlier: 3.726A pdb=" N THR R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 126 removed outlier: 3.750A pdb=" N THR R 118 " --> pdb=" O SER R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 133 removed outlier: 3.544A pdb=" N ARG R 131 " --> pdb=" O PRO R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 155 removed outlier: 3.678A pdb=" N LEU R 151 " --> pdb=" O TRP R 147 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU R 152 " --> pdb=" O GLY R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 177 No H-bonds generated for 'chain 'R' and resid 175 through 177' Processing helix chain 'R' and resid 178 through 204 removed outlier: 3.782A pdb=" N ALA R 182 " --> pdb=" O PHE R 178 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TRP R 183 " --> pdb=" O ILE R 179 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG R 201 " --> pdb=" O VAL R 197 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE R 202 " --> pdb=" O LEU R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 210 No H-bonds generated for 'chain 'R' and resid 208 through 210' Processing helix chain 'R' and resid 211 through 229 removed outlier: 3.816A pdb=" N TYR R 215 " --> pdb=" O LEU R 211 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL R 216 " --> pdb=" O THR R 212 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR R 217 " --> pdb=" O ARG R 213 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL R 224 " --> pdb=" O LEU R 220 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE R 225 " --> pdb=" O THR R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 230 through 236 Processing helix chain 'R' and resid 248 through 267 removed outlier: 4.456A pdb=" N HIS R 252 " --> pdb=" O VAL R 248 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR R 254 " --> pdb=" O TYR R 250 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU R 255 " --> pdb=" O CYS R 251 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER R 265 " --> pdb=" O SER R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 273 Processing helix chain 'R' and resid 273 through 280 removed outlier: 3.710A pdb=" N GLN R 280 " --> pdb=" O GLY R 276 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 75 removed outlier: 3.572A pdb=" N PHE B 74 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N ALA B 105 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.663A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA C 328 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU C 318 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY C 330 " --> pdb=" O SER C 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.730A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN C 88 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.917A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.891A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN C 175 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.817A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.909A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.700A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.680A pdb=" N SER E 71 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.518A pdb=" N TRP E 111 " --> pdb=" O ARG E 98 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ARG E 98 " --> pdb=" O TRP E 111 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLN E 113 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N CYS E 96 " --> pdb=" O GLN E 113 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.415A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 143 through 148 Processing sheet with id=AB4, first strand: chain 'E' and resid 182 through 183 removed outlier: 6.782A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 942 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: 2.27 Time building geometry restraints manager: 2.39 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: 1288 1.31 - 1.44: 2305 1.44 - 1.57: 4591 1.57 - 1.70: 5 1.70 - 1.83: 74 Bond restraints: 8263 Sorted by residual: bond pdb=" C05 8IX R 401 " pdb=" N04 8IX R 401 " ideal model delta sigma weight residual 1.343 1.449 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" C14 8IX R 401 " pdb=" C15 8IX R 401 " ideal model delta sigma weight residual 1.532 1.609 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" N ILE R 81 " pdb=" CA ILE R 81 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.38e-02 5.25e+03 8.99e+00 bond pdb=" C14 8IX R 401 " pdb=" C16 8IX R 401 " ideal model delta sigma weight residual 1.522 1.462 0.060 2.00e-02 2.50e+03 8.91e+00 bond pdb=" N LEU R 83 " pdb=" CA LEU R 83 " ideal model delta sigma weight residual 1.461 1.487 -0.026 9.20e-03 1.18e+04 7.95e+00 ... (remaining 8258 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 11001 2.01 - 4.02: 209 4.02 - 6.03: 38 6.03 - 8.04: 12 8.04 - 10.06: 5 Bond angle restraints: 11265 Sorted by residual: angle pdb=" N ILE R 81 " pdb=" CA ILE R 81 " pdb=" C ILE R 81 " ideal model delta sigma weight residual 112.76 108.64 4.12 1.27e+00 6.20e-01 1.05e+01 angle pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta sigma weight residual 121.54 127.46 -5.92 1.91e+00 2.74e-01 9.60e+00 angle pdb=" N ASP C 153 " pdb=" CA ASP C 153 " pdb=" C ASP C 153 " ideal model delta sigma weight residual 110.80 104.41 6.39 2.13e+00 2.20e-01 9.01e+00 angle pdb=" N LEU R 230 " pdb=" CA LEU R 230 " pdb=" C LEU R 230 " ideal model delta sigma weight residual 109.81 116.43 -6.62 2.21e+00 2.05e-01 8.98e+00 angle pdb=" N LEU R 83 " pdb=" CA LEU R 83 " pdb=" C LEU R 83 " ideal model delta sigma weight residual 112.75 108.75 4.00 1.36e+00 5.41e-01 8.64e+00 ... (remaining 11260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.19: 4372 15.19 - 30.37: 375 30.37 - 45.56: 93 45.56 - 60.74: 15 60.74 - 75.93: 7 Dihedral angle restraints: 4862 sinusoidal: 1709 harmonic: 3153 Sorted by residual: dihedral pdb=" CA TYR B 243 " pdb=" C TYR B 243 " pdb=" N ASN B 244 " pdb=" CA ASN B 244 " ideal model delta harmonic sigma weight residual 180.00 159.76 20.24 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA GLU C 130 " pdb=" C GLU C 130 " pdb=" N GLY C 131 " pdb=" CA GLY C 131 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA LYS C 78 " pdb=" C LYS C 78 " pdb=" N LEU C 79 " pdb=" CA LEU C 79 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 4859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1117 0.062 - 0.125: 197 0.125 - 0.187: 14 0.187 - 0.250: 0 0.250 - 0.312: 2 Chirality restraints: 1330 Sorted by residual: chirality pdb=" C14 8IX R 401 " pdb=" C13 8IX R 401 " pdb=" C15 8IX R 401 " pdb=" C17 8IX R 401 " both_signs ideal model delta sigma weight residual False -2.85 -3.17 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C10 8IX R 401 " pdb=" C09 8IX R 401 " pdb=" C11 8IX R 401 " pdb=" C15 8IX R 401 " both_signs ideal model delta sigma weight residual False 2.70 2.99 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA LEU R 230 " pdb=" N LEU R 230 " pdb=" C LEU R 230 " pdb=" CB LEU R 230 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 1327 not shown) Planarity restraints: 1417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 106 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO E 107 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 107 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 107 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 212 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO B 213 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 48 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO D 49 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " -0.024 5.00e-02 4.00e+02 ... (remaining 1414 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 334 2.73 - 3.27: 7462 3.27 - 3.81: 11748 3.81 - 4.36: 14691 4.36 - 4.90: 26319 Nonbonded interactions: 60554 Sorted by model distance: nonbonded pdb=" OH TYR R 106 " pdb=" O GLY R 229 " model vdw 2.183 3.040 nonbonded pdb=" O TYR B 170 " pdb=" NH1 ARG B 188 " model vdw 2.208 3.120 nonbonded pdb=" O ASP C 163 " pdb=" OG1 THR C 164 " model vdw 2.253 3.040 nonbonded pdb=" OD1 ASP B 20 " pdb=" NZ LYS C 89 " model vdw 2.289 3.120 nonbonded pdb=" NH2 ARG E 67 " pdb=" OD2 ASP E 90 " model vdw 2.305 3.120 ... (remaining 60549 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.790 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 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 0.106 8263 Z= 0.351 Angle : 0.749 10.056 11265 Z= 0.389 Chirality : 0.049 0.312 1330 Planarity : 0.004 0.045 1417 Dihedral : 12.741 75.928 2817 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.01 (0.23), residues: 1071 helix: -1.79 (0.24), residues: 350 sheet: 0.15 (0.32), residues: 253 loop : -1.72 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 63 HIS 0.007 0.002 HIS B 209 PHE 0.014 0.002 PHE R 225 TYR 0.013 0.002 TYR C 105 ARG 0.005 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.876 Fit side-chains REVERT: B 223 ASN cc_start: 0.7663 (m-40) cc_final: 0.7419 (m110) REVERT: B 230 ASP cc_start: 0.7601 (m-30) cc_final: 0.7286 (m-30) REVERT: C 135 VAL cc_start: 0.8325 (t) cc_final: 0.8062 (p) REVERT: R 67 ASN cc_start: 0.6652 (m110) cc_final: 0.6383 (m-40) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 1.1373 time to fit residues: 217.5518 Evaluate side-chains 165 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 0.0980 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 97 optimal weight: 0.0030 overall best weight: 1.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN C 156 GLN C 340 ASN E 39 GLN E 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.114226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.095971 restraints weight = 11480.756| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.69 r_work: 0.3147 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8263 Z= 0.314 Angle : 0.714 11.082 11265 Z= 0.371 Chirality : 0.047 0.172 1330 Planarity : 0.005 0.043 1417 Dihedral : 5.286 31.252 1217 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.24 % Allowed : 9.70 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.93 (0.24), residues: 1071 helix: -0.04 (0.26), residues: 357 sheet: 0.28 (0.30), residues: 278 loop : -1.66 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 63 HIS 0.008 0.002 HIS B 209 PHE 0.018 0.002 PHE R 225 TYR 0.020 0.002 TYR R 106 ARG 0.007 0.000 ARG R 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.872 Fit side-chains REVERT: B 199 ASP cc_start: 0.7034 (p0) cc_final: 0.6831 (p0) REVERT: B 239 ASN cc_start: 0.8461 (m-40) cc_final: 0.8183 (m110) REVERT: C 61 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8314 (ppp) REVERT: R 226 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8108 (mp) REVERT: R 241 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.6155 (mpp-170) outliers start: 18 outliers final: 9 residues processed: 164 average time/residue: 1.4769 time to fit residues: 256.4667 Evaluate side-chains 161 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 178 PHE Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 241 ARG Chi-restraints excluded: chain R residue 275 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 0.0770 chunk 61 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 144 ASN C 340 ASN E 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.116106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.097600 restraints weight = 11667.954| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.71 r_work: 0.3180 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8263 Z= 0.198 Angle : 0.598 9.919 11265 Z= 0.312 Chirality : 0.043 0.157 1330 Planarity : 0.004 0.037 1417 Dihedral : 4.765 25.509 1217 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.36 % Allowed : 12.19 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.30 (0.25), residues: 1071 helix: 0.82 (0.28), residues: 360 sheet: 0.55 (0.31), residues: 272 loop : -1.56 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 PHE 0.013 0.001 PHE B 228 TYR 0.015 0.001 TYR R 106 ARG 0.008 0.000 ARG R 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.895 Fit side-chains REVERT: B 194 ARG cc_start: 0.8113 (ttp80) cc_final: 0.7865 (ttm-80) REVERT: B 199 ASP cc_start: 0.7096 (p0) cc_final: 0.6888 (p0) REVERT: B 239 ASN cc_start: 0.8383 (m-40) cc_final: 0.8124 (m110) REVERT: C 61 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8194 (ppp) outliers start: 27 outliers final: 14 residues processed: 171 average time/residue: 1.3614 time to fit residues: 246.0341 Evaluate side-chains 174 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain R residue 178 PHE Chi-restraints excluded: chain R residue 239 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 144 ASN C 340 ASN E 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.115102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.096764 restraints weight = 11589.670| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.70 r_work: 0.3168 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8263 Z= 0.226 Angle : 0.614 10.244 11265 Z= 0.320 Chirality : 0.044 0.160 1330 Planarity : 0.004 0.041 1417 Dihedral : 4.771 29.001 1217 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.86 % Allowed : 13.93 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.15 (0.25), residues: 1071 helix: 1.01 (0.28), residues: 360 sheet: 0.60 (0.31), residues: 272 loop : -1.52 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 63 HIS 0.004 0.001 HIS E 35 PHE 0.016 0.002 PHE B 228 TYR 0.015 0.002 TYR R 106 ARG 0.010 0.000 ARG R 201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.897 Fit side-chains REVERT: B 21 LYS cc_start: 0.8535 (ttpp) cc_final: 0.8208 (ttpp) REVERT: B 25 GLU cc_start: 0.7606 (mp0) cc_final: 0.7259 (mp0) REVERT: B 194 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7845 (ttm-80) REVERT: B 199 ASP cc_start: 0.7131 (p0) cc_final: 0.6895 (p0) REVERT: B 239 ASN cc_start: 0.8414 (m-40) cc_final: 0.8098 (m110) REVERT: C 61 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8311 (ppp) outliers start: 31 outliers final: 21 residues processed: 175 average time/residue: 1.1664 time to fit residues: 216.5426 Evaluate side-chains 176 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 178 PHE Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 252 HIS Chi-restraints excluded: chain R residue 275 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.4433 > 50: distance: 55 - 58: 9.440 distance: 58 - 59: 17.354 distance: 59 - 60: 26.515 distance: 59 - 62: 25.454 distance: 60 - 61: 27.496 distance: 60 - 66: 16.253 distance: 62 - 63: 12.709 distance: 62 - 64: 17.038 distance: 63 - 65: 11.331 distance: 66 - 67: 10.527 distance: 67 - 68: 11.456 distance: 67 - 70: 20.465 distance: 68 - 69: 17.897 distance: 68 - 72: 8.073 distance: 70 - 71: 26.497 distance: 72 - 73: 4.754 distance: 73 - 76: 6.054 distance: 74 - 75: 3.780 distance: 74 - 83: 5.423 distance: 77 - 79: 3.888 distance: 78 - 80: 4.540 distance: 81 - 82: 4.769 distance: 83 - 84: 7.527 distance: 84 - 85: 4.711 distance: 84 - 87: 3.362 distance: 85 - 94: 8.952 distance: 87 - 88: 6.465 distance: 88 - 89: 3.284 distance: 89 - 91: 5.637 distance: 90 - 92: 5.827 distance: 91 - 93: 4.068 distance: 92 - 93: 4.210 distance: 94 - 95: 4.056 distance: 94 - 100: 13.173 distance: 95 - 98: 10.016 distance: 96 - 97: 4.772 distance: 96 - 101: 6.034 distance: 98 - 99: 7.357 distance: 99 - 100: 13.835 distance: 101 - 102: 10.049 distance: 102 - 103: 18.811 distance: 103 - 104: 19.203 distance: 103 - 109: 13.716 distance: 105 - 106: 5.935 distance: 106 - 107: 10.194 distance: 109 - 110: 18.754 distance: 110 - 111: 8.562 distance: 111 - 112: 26.704 distance: 111 - 113: 12.316 distance: 113 - 114: 14.742 distance: 114 - 115: 6.713 distance: 114 - 117: 8.819 distance: 115 - 116: 5.274 distance: 115 - 121: 13.225 distance: 117 - 118: 6.200 distance: 118 - 119: 8.390 distance: 118 - 120: 17.858 distance: 121 - 122: 8.661 distance: 122 - 123: 4.244 distance: 122 - 125: 6.894 distance: 123 - 124: 3.695 distance: 123 - 126: 5.766 distance: 126 - 127: 3.200 distance: 127 - 130: 3.355 distance: 128 - 129: 3.858 distance: 129 - 156: 6.250 distance: 131 - 132: 4.827 distance: 131 - 133: 4.519 distance: 132 - 134: 5.573 distance: 133 - 135: 3.374 distance: 134 - 136: 5.991 distance: 135 - 136: 6.318