Starting phenix.real_space_refine on Thu Jul 2 09:40:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7um5_26597/07_2026/7um5_26597.cif Found real_map, /net/cci-nas-00/data/ceres_data/7um5_26597/07_2026/7um5_26597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7um5_26597/07_2026/7um5_26597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7um5_26597/07_2026/7um5_26597.map" model { file = "/net/cci-nas-00/data/ceres_data/7um5_26597/07_2026/7um5_26597.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7um5_26597/07_2026/7um5_26597.cif" } resolution = 2.73 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= 0.002 sd= 0.027 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 58 5.16 5 C 5287 2.51 5 N 1397 2.21 5 O 1535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8277 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2000 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain breaks: 1 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 4, 'ARG:plan': 7, 'GLU:plan': 6, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 100 Chain: "B" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2497 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'GLN:plan1': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 80 Chain: "D" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 372 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 49} 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, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1719 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'8K3': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 1.83, per 1000 atoms: 0.22 Number of scatterers: 8277 At special positions: 0 Unit cell: (91.91, 123.76, 126.49, 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 58 16.00 O 1535 8.00 N 1397 7.00 C 5287 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 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: 0.60 Conformation dependent library (CDL) restraints added in 420.9 milliseconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 36.6% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 41 through 68 removed outlier: 3.627A pdb=" N THR A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 55 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 59 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 61 " --> pdb=" O TRP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 93 removed outlier: 3.956A pdb=" N VAL A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 98 Processing helix chain 'A' and resid 110 through 145 removed outlier: 3.531A pdb=" N CYS A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 179 removed outlier: 3.657A pdb=" N LYS A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TRP A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER A 169 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 187 through 190 Processing helix chain 'A' and resid 197 through 209 removed outlier: 3.562A pdb=" N THR A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL A 206 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 231 removed outlier: 3.638A pdb=" N CYS A 214 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 308 removed outlier: 3.503A pdb=" N VAL A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TRP A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Proline residue: A 300 - end of helix removed outlier: 3.934A pdb=" N THR A 304 " --> pdb=" O PRO A 300 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 334 removed outlier: 3.500A pdb=" N SER A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.687A pdb=" N THR A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 352 removed outlier: 3.638A pdb=" N SER A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 29 removed outlier: 3.572A pdb=" N GLU B 11 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B 12 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS B 29 " --> pdb=" O ILE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 removed outlier: 3.768A pdb=" N LYS B 92 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE B 94 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N HIS B 95 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS B 96 " --> pdb=" O TRP B 93 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 97 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU B 98 " --> pdb=" O HIS B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 127 Processing helix chain 'B' and resid 128 through 132 removed outlier: 4.050A pdb=" N ILE B 132 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 167 through 181 Processing helix chain 'B' and resid 202 through 223 Processing helix chain 'C' and resid 4 through 25 removed outlier: 3.678A pdb=" N GLU C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN C 17 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.906A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 4.235A 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 9 through 23 removed outlier: 3.693A pdb=" N GLU D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 43 removed outlier: 3.597A pdb=" N TYR D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 48 removed outlier: 3.863A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.682A pdb=" N ASN D 59 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.694A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.607A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 186 removed outlier: 3.689A pdb=" N SER A 186 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU A 191 " --> pdb=" O SER A 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 52 removed outlier: 6.365A pdb=" N VAL B 31 " --> pdb=" O ARG B 79 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N PHE B 81 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU B 33 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LYS B 32 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ILE B 104 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU B 34 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N CYS B 106 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU B 36 " --> pdb=" O CYS B 106 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N ASP B 108 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE B 103 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N PHE B 139 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE B 105 " --> pdb=" O PHE B 139 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASN B 141 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B 107 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.674A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.939A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.870A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 153 removed outlier: 6.885A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.816A 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: 7.701A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.825A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.599A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.799A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.200A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TRP E 111 " --> pdb=" O ARG E 98 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ARG E 98 " --> pdb=" O TRP E 111 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLN E 113 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N CYS E 96 " --> pdb=" O GLN E 113 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.601A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 136 removed outlier: 4.207A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 0.84 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: 1337 1.31 - 1.43: 2362 1.43 - 1.56: 4678 1.56 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 8457 Sorted by residual: bond pdb=" C13 8K3 A 401 " pdb=" N15 8K3 A 401 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" CA SER A 128 " pdb=" CB SER A 128 " ideal model delta sigma weight residual 1.528 1.468 0.061 1.59e-02 3.96e+03 1.46e+01 bond pdb=" C PRO A 335 " pdb=" O PRO A 335 " ideal model delta sigma weight residual 1.238 1.194 0.044 1.37e-02 5.33e+03 1.01e+01 bond pdb=" C ASN A 334 " pdb=" N PRO A 335 " ideal model delta sigma weight residual 1.337 1.369 -0.033 1.11e-02 8.12e+03 8.78e+00 bond pdb=" C07 8K3 A 401 " pdb=" C08 8K3 A 401 " ideal model delta sigma weight residual 1.414 1.368 0.046 2.00e-02 2.50e+03 5.39e+00 ... (remaining 8452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 11294 1.55 - 3.09: 177 3.09 - 4.64: 39 4.64 - 6.18: 8 6.18 - 7.73: 3 Bond angle restraints: 11521 Sorted by residual: angle pdb=" C PHE A 179 " pdb=" CA PHE A 179 " pdb=" CB PHE A 179 " ideal model delta sigma weight residual 110.42 118.15 -7.73 1.99e+00 2.53e-01 1.51e+01 angle pdb=" CA ASN A 334 " pdb=" C ASN A 334 " pdb=" N PRO A 335 " ideal model delta sigma weight residual 118.44 123.88 -5.44 1.59e+00 3.96e-01 1.17e+01 angle pdb=" CA PRO A 75 " pdb=" N PRO A 75 " pdb=" CD PRO A 75 " ideal model delta sigma weight residual 112.00 107.39 4.61 1.40e+00 5.10e-01 1.08e+01 angle pdb=" C ARG A 73 " pdb=" N VAL A 74 " pdb=" CA VAL A 74 " ideal model delta sigma weight residual 120.33 122.89 -2.56 8.00e-01 1.56e+00 1.02e+01 angle pdb=" N LEU A 336 " pdb=" CA LEU A 336 " pdb=" C LEU A 336 " ideal model delta sigma weight residual 113.16 109.40 3.76 1.24e+00 6.50e-01 9.20e+00 ... (remaining 11516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 4596 17.33 - 34.66: 275 34.66 - 52.00: 56 52.00 - 69.33: 6 69.33 - 86.66: 5 Dihedral angle restraints: 4938 sinusoidal: 1741 harmonic: 3197 Sorted by residual: dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 157.54 -64.54 1 1.00e+01 1.00e-02 5.47e+01 dihedral pdb=" CA LEU A 178 " pdb=" C LEU A 178 " pdb=" N PHE A 179 " pdb=" CA PHE A 179 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA HIS B 116 " pdb=" C HIS B 116 " pdb=" N GLU B 117 " pdb=" CA GLU B 117 " ideal model delta harmonic sigma weight residual 180.00 163.37 16.63 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 4935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 906 0.036 - 0.073: 313 0.073 - 0.109: 84 0.109 - 0.145: 34 0.145 - 0.182: 3 Chirality restraints: 1340 Sorted by residual: chirality pdb=" CA LEU A 177 " pdb=" N LEU A 177 " pdb=" C LEU A 177 " pdb=" CB LEU A 177 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CA LEU A 336 " pdb=" N LEU A 336 " pdb=" C LEU A 336 " pdb=" CB LEU A 336 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA TRP A 57 " pdb=" N TRP A 57 " pdb=" C TRP A 57 " pdb=" CB TRP A 57 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 1337 not shown) Planarity restraints: 1454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 74 " 0.044 5.00e-02 4.00e+02 6.54e-02 6.85e+00 pdb=" N PRO A 75 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 329 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.58e+00 pdb=" C SER A 329 " -0.041 2.00e-02 2.50e+03 pdb=" O SER A 329 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN A 330 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 333 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.82e+00 pdb=" C PHE A 333 " -0.034 2.00e-02 2.50e+03 pdb=" O PHE A 333 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN A 334 " 0.012 2.00e-02 2.50e+03 ... (remaining 1451 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2164 2.80 - 3.33: 6990 3.33 - 3.85: 12341 3.85 - 4.38: 14479 4.38 - 4.90: 26158 Nonbonded interactions: 62132 Sorted by model distance: nonbonded pdb=" O LEU A 42 " pdb=" OG1 THR A 45 " model vdw 2.281 3.040 nonbonded pdb=" NH1 ARG E 190 " pdb=" OD2 ASP E 211 " model vdw 2.285 3.120 nonbonded pdb=" O THR B 134 " pdb=" NZ LYS B 188 " model vdw 2.314 3.120 nonbonded pdb=" OD1 ASP C 254 " pdb=" N LEU C 255 " model vdw 2.331 3.120 nonbonded pdb=" OD1 ASP A 138 " pdb=" OH TYR A 149 " model vdw 2.354 3.040 ... (remaining 62127 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.620 Find NCS groups from input model: 0.050 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:5.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 : 0.003 0.106 8459 Z= 0.177 Angle : 0.531 7.725 11525 Z= 0.292 Chirality : 0.042 0.182 1340 Planarity : 0.004 0.065 1454 Dihedral : 11.904 86.660 2868 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.24), residues: 1086 helix: -0.26 (0.27), residues: 359 sheet: 0.98 (0.33), residues: 263 loop : -1.54 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 196 TYR 0.010 0.001 TYR E 178 PHE 0.015 0.001 PHE A 333 TRP 0.010 0.001 TRP C 63 HIS 0.004 0.001 HIS A 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.18 ( 8457) covalent geometry : angle 0.53132 / 0.29 (11521) SS BOND : bond 0.00250 / 0.14 ( 2) SS BOND : angle 0.29365 / 0.15 ( 4) hydrogen bonds : bond 0.29665 / 21.06 ( 375) hydrogen bonds : angle 7.38617 / 5.30 ( 1053) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.251 Fit side-chains REVERT: A 50 LEU cc_start: 0.7543 (tp) cc_final: 0.7274 (tt) REVERT: E 117 LEU cc_start: 0.8481 (tp) cc_final: 0.8275 (tp) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.3717 time to fit residues: 75.8171 Evaluate side-chains 178 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 38 optimal weight: 0.0970 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.109682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.095101 restraints weight = 12329.119| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.68 r_work: 0.3115 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8459 Z= 0.133 Angle : 0.551 7.692 11525 Z= 0.295 Chirality : 0.043 0.132 1340 Planarity : 0.004 0.037 1454 Dihedral : 4.557 55.058 1181 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.53 % Allowed : 9.09 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.25), residues: 1086 helix: 1.03 (0.28), residues: 356 sheet: 0.91 (0.31), residues: 285 loop : -1.52 (0.25), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 196 TYR 0.013 0.001 TYR E 178 PHE 0.011 0.001 PHE A 333 TRP 0.012 0.001 TRP C 297 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 8457) covalent geometry : angle 0.55110 / 0.29 (11521) SS BOND : bond 0.00287 / 0.16 ( 2) SS BOND : angle 0.37279 / 0.21 ( 4) hydrogen bonds : bond 0.06783 / 4.66 ( 375) hydrogen bonds : angle 4.68650 / 3.34 ( 1053) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.212 Fit side-chains REVERT: D 36 ASP cc_start: 0.8192 (m-30) cc_final: 0.7955 (m-30) REVERT: E 19 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8668 (tttm) outliers start: 13 outliers final: 4 residues processed: 186 average time/residue: 0.3756 time to fit residues: 75.5578 Evaluate side-chains 181 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 176 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain E residue 19 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.0070 chunk 38 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 13 optimal weight: 0.1980 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.110026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.095335 restraints weight = 12214.739| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.67 r_work: 0.3119 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8459 Z= 0.119 Angle : 0.518 8.409 11525 Z= 0.272 Chirality : 0.042 0.179 1340 Planarity : 0.003 0.038 1454 Dihedral : 4.182 39.672 1181 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.13 % Allowed : 11.92 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.25), residues: 1086 helix: 1.65 (0.29), residues: 350 sheet: 0.85 (0.31), residues: 293 loop : -1.36 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 196 TYR 0.011 0.001 TYR E 178 PHE 0.011 0.001 PHE A 203 TRP 0.012 0.001 TRP A 117 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 8457) covalent geometry : angle 0.51789 / 0.27 (11521) SS BOND : bond 0.00228 / 0.13 ( 2) SS BOND : angle 0.13767 / 0.07 ( 4) hydrogen bonds : bond 0.05695 / 3.92 ( 375) hydrogen bonds : angle 4.29783 / 3.09 ( 1053) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.314 Fit side-chains REVERT: B 77 HIS cc_start: 0.8537 (t-170) cc_final: 0.8270 (t-170) REVERT: B 83 VAL cc_start: 0.8552 (p) cc_final: 0.8242 (m) REVERT: C 258 ASP cc_start: 0.8118 (t0) cc_final: 0.7789 (t0) REVERT: E 19 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8684 (tttm) outliers start: 18 outliers final: 9 residues processed: 187 average time/residue: 0.3647 time to fit residues: 74.2539 Evaluate side-chains 187 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.0870 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 40 optimal weight: 0.0770 chunk 66 optimal weight: 0.7980 chunk 61 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.110748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.096031 restraints weight = 12474.417| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.69 r_work: 0.3138 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8459 Z= 0.106 Angle : 0.499 5.997 11525 Z= 0.263 Chirality : 0.042 0.253 1340 Planarity : 0.003 0.036 1454 Dihedral : 3.997 32.505 1181 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.65 % Allowed : 13.70 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.26), residues: 1086 helix: 1.99 (0.29), residues: 350 sheet: 0.98 (0.31), residues: 287 loop : -1.33 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 196 TYR 0.011 0.001 TYR E 178 PHE 0.010 0.001 PHE E 80 TRP 0.011 0.001 TRP A 117 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 ( 8457) covalent geometry : angle 0.49917 / 0.26 (11521) SS BOND : bond 0.00202 / 0.11 ( 2) SS BOND : angle 0.15827 / 0.08 ( 4) hydrogen bonds : bond 0.04808 / 3.30 ( 375) hydrogen bonds : angle 4.09226 / 2.95 ( 1053) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.237 Fit side-chains REVERT: C 258 ASP cc_start: 0.8048 (t0) cc_final: 0.7738 (t0) outliers start: 14 outliers final: 6 residues processed: 181 average time/residue: 0.3280 time to fit residues: 64.5175 Evaluate side-chains 177 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 171 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 90 optimal weight: 0.0570 chunk 42 optimal weight: 0.2980 chunk 46 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 68 optimal weight: 0.0980 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 259 GLN C 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.111460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.096740 restraints weight = 12377.480| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.69 r_work: 0.3145 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8459 Z= 0.100 Angle : 0.492 7.172 11525 Z= 0.256 Chirality : 0.042 0.309 1340 Planarity : 0.003 0.035 1454 Dihedral : 3.900 27.303 1181 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.01 % Allowed : 13.58 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.26), residues: 1086 helix: 2.23 (0.29), residues: 349 sheet: 0.98 (0.31), residues: 287 loop : -1.31 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 196 TYR 0.011 0.001 TYR E 178 PHE 0.011 0.001 PHE A 55 TRP 0.010 0.001 TRP A 117 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 ( 8457) covalent geometry : angle 0.49190 / 0.26 (11521) SS BOND : bond 0.00201 / 0.11 ( 2) SS BOND : angle 0.21947 / 0.12 ( 4) hydrogen bonds : bond 0.04396 / 3.02 ( 375) hydrogen bonds : angle 3.95423 / 2.87 ( 1053) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.319 Fit side-chains REVERT: A 139 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7647 (mtt180) REVERT: B 83 VAL cc_start: 0.8547 (p) cc_final: 0.8284 (m) REVERT: C 258 ASP cc_start: 0.8013 (t0) cc_final: 0.7694 (t0) REVERT: E 19 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8666 (tttm) outliers start: 17 outliers final: 7 residues processed: 179 average time/residue: 0.3498 time to fit residues: 68.2320 Evaluate side-chains 176 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 167 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 96 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 86 optimal weight: 0.0870 chunk 17 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.109007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.094231 restraints weight = 12273.782| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.67 r_work: 0.3108 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8459 Z= 0.131 Angle : 0.535 8.160 11525 Z= 0.280 Chirality : 0.043 0.317 1340 Planarity : 0.003 0.038 1454 Dihedral : 4.068 26.377 1181 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.36 % Allowed : 14.29 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.26), residues: 1086 helix: 2.16 (0.29), residues: 350 sheet: 1.01 (0.32), residues: 274 loop : -1.28 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 68 TYR 0.010 0.001 TYR E 178 PHE 0.015 0.001 PHE A 203 TRP 0.012 0.001 TRP C 211 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 8457) covalent geometry : angle 0.53547 / 0.28 (11521) SS BOND : bond 0.00163 / 0.09 ( 2) SS BOND : angle 0.34318 / 0.17 ( 4) hydrogen bonds : bond 0.05245 / 3.62 ( 375) hydrogen bonds : angle 4.06256 / 2.95 ( 1053) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.279 Fit side-chains REVERT: A 139 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7766 (mtt180) REVERT: A 318 ILE cc_start: 0.6517 (OUTLIER) cc_final: 0.6298 (pp) REVERT: E 19 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8701 (tttm) outliers start: 20 outliers final: 8 residues processed: 179 average time/residue: 0.3886 time to fit residues: 75.4944 Evaluate side-chains 179 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 39 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 87 optimal weight: 0.0670 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.094122 restraints weight = 12378.462| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.69 r_work: 0.3096 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8459 Z= 0.132 Angle : 0.541 8.958 11525 Z= 0.281 Chirality : 0.044 0.333 1340 Planarity : 0.003 0.040 1454 Dihedral : 4.099 26.106 1181 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.89 % Allowed : 14.88 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.26), residues: 1086 helix: 2.17 (0.29), residues: 350 sheet: 1.00 (0.32), residues: 269 loop : -1.30 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 68 TYR 0.010 0.001 TYR E 178 PHE 0.014 0.001 PHE A 203 TRP 0.011 0.001 TRP C 211 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 8457) covalent geometry : angle 0.54100 / 0.28 (11521) SS BOND : bond 0.00162 / 0.09 ( 2) SS BOND : angle 0.31871 / 0.16 ( 4) hydrogen bonds : bond 0.05269 / 3.63 ( 375) hydrogen bonds : angle 4.06864 / 2.95 ( 1053) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.217 Fit side-chains REVERT: A 139 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7825 (mtt180) REVERT: A 318 ILE cc_start: 0.6484 (OUTLIER) cc_final: 0.6276 (pp) REVERT: C 258 ASP cc_start: 0.8150 (t0) cc_final: 0.7807 (t0) REVERT: E 19 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8700 (tttm) outliers start: 16 outliers final: 9 residues processed: 178 average time/residue: 0.3862 time to fit residues: 74.3083 Evaluate side-chains 179 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 55 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 60 optimal weight: 0.0010 chunk 79 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.108906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.094036 restraints weight = 12284.942| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.68 r_work: 0.3104 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8459 Z= 0.124 Angle : 0.534 9.469 11525 Z= 0.277 Chirality : 0.043 0.336 1340 Planarity : 0.003 0.039 1454 Dihedral : 4.041 21.425 1181 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.89 % Allowed : 15.58 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.26), residues: 1086 helix: 2.21 (0.29), residues: 350 sheet: 0.99 (0.32), residues: 275 loop : -1.32 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 196 TYR 0.010 0.001 TYR E 178 PHE 0.014 0.001 PHE E 80 TRP 0.011 0.001 TRP C 211 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 8457) covalent geometry : angle 0.53358 / 0.28 (11521) SS BOND : bond 0.00168 / 0.09 ( 2) SS BOND : angle 0.31407 / 0.16 ( 4) hydrogen bonds : bond 0.05046 / 3.48 ( 375) hydrogen bonds : angle 4.05627 / 2.94 ( 1053) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.309 Fit side-chains REVERT: A 139 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7810 (mtt180) REVERT: A 318 ILE cc_start: 0.6396 (OUTLIER) cc_final: 0.6184 (pp) REVERT: C 61 MET cc_start: 0.8827 (ppp) cc_final: 0.8618 (ppp) REVERT: E 19 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8693 (tttm) outliers start: 16 outliers final: 10 residues processed: 180 average time/residue: 0.3831 time to fit residues: 74.7789 Evaluate side-chains 183 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 6 optimal weight: 0.1980 chunk 61 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 90 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.109456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.094580 restraints weight = 12337.340| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.69 r_work: 0.3109 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8459 Z= 0.119 Angle : 0.534 9.465 11525 Z= 0.276 Chirality : 0.043 0.326 1340 Planarity : 0.003 0.038 1454 Dihedral : 4.011 19.238 1181 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.65 % Allowed : 16.41 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.26), residues: 1086 helix: 2.26 (0.29), residues: 350 sheet: 1.01 (0.32), residues: 275 loop : -1.31 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 196 TYR 0.010 0.001 TYR E 178 PHE 0.014 0.001 PHE E 80 TRP 0.010 0.001 TRP C 211 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 8457) covalent geometry : angle 0.53389 / 0.28 (11521) SS BOND : bond 0.00169 / 0.09 ( 2) SS BOND : angle 0.30659 / 0.15 ( 4) hydrogen bonds : bond 0.04879 / 3.36 ( 375) hydrogen bonds : angle 4.01541 / 2.92 ( 1053) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 0.253 Fit side-chains REVERT: A 139 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7805 (mtt180) REVERT: A 318 ILE cc_start: 0.6355 (OUTLIER) cc_final: 0.6151 (pp) REVERT: E 19 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8706 (tttm) outliers start: 14 outliers final: 10 residues processed: 178 average time/residue: 0.3435 time to fit residues: 66.4014 Evaluate side-chains 183 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 90 optimal weight: 0.0970 chunk 24 optimal weight: 0.3980 chunk 7 optimal weight: 0.0470 chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 80 optimal weight: 0.0270 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.111864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.097050 restraints weight = 12410.633| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.69 r_work: 0.3151 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8459 Z= 0.096 Angle : 0.504 10.272 11525 Z= 0.259 Chirality : 0.042 0.343 1340 Planarity : 0.003 0.035 1454 Dihedral : 3.789 20.228 1181 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.53 % Allowed : 16.65 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.26), residues: 1086 helix: 2.39 (0.29), residues: 350 sheet: 0.95 (0.31), residues: 291 loop : -1.21 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 196 TYR 0.010 0.001 TYR E 178 PHE 0.011 0.001 PHE E 80 TRP 0.012 0.001 TRP C 63 HIS 0.005 0.001 HIS A 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.10 ( 8457) covalent geometry : angle 0.50364 / 0.26 (11521) SS BOND : bond 0.00200 / 0.11 ( 2) SS BOND : angle 0.28747 / 0.15 ( 4) hydrogen bonds : bond 0.03940 / 2.71 ( 375) hydrogen bonds : angle 3.88830 / 2.83 ( 1053) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 0.310 Fit side-chains REVERT: A 130 TRP cc_start: 0.8707 (m100) cc_final: 0.8481 (m100) REVERT: B 18 LYS cc_start: 0.8643 (tttm) cc_final: 0.8428 (tttm) REVERT: C 61 MET cc_start: 0.8825 (ppp) cc_final: 0.8576 (pp-130) REVERT: E 19 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8672 (tttm) outliers start: 13 outliers final: 10 residues processed: 179 average time/residue: 0.3315 time to fit residues: 64.6524 Evaluate side-chains 182 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 93 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 chunk 19 optimal weight: 7.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.108523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.093722 restraints weight = 12308.013| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.68 r_work: 0.3094 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8459 Z= 0.148 Angle : 0.574 9.387 11525 Z= 0.298 Chirality : 0.045 0.334 1340 Planarity : 0.004 0.039 1454 Dihedral : 4.038 17.429 1181 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.53 % Allowed : 17.00 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.26), residues: 1086 helix: 2.28 (0.29), residues: 350 sheet: 0.98 (0.32), residues: 275 loop : -1.33 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 68 TYR 0.013 0.001 TYR C 105 PHE 0.016 0.002 PHE A 203 TRP 0.012 0.002 TRP C 211 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 8457) covalent geometry : angle 0.57363 / 0.30 (11521) SS BOND : bond 0.00142 / 0.08 ( 2) SS BOND : angle 0.44151 / 0.22 ( 4) hydrogen bonds : bond 0.05409 / 3.74 ( 375) hydrogen bonds : angle 4.09026 / 2.97 ( 1053) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2750.83 seconds wall clock time: 47 minutes 27.13 seconds (2847.13 seconds total)