Starting phenix.real_space_refine on Tue Mar 3 19:05:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7um7_26599/03_2026/7um7_26599.cif Found real_map, /net/cci-nas-00/data/ceres_data/7um7_26599/03_2026/7um7_26599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7um7_26599/03_2026/7um7_26599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7um7_26599/03_2026/7um7_26599.map" model { file = "/net/cci-nas-00/data/ceres_data/7um7_26599/03_2026/7um7_26599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7um7_26599/03_2026/7um7_26599.cif" } resolution = 2.75 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 54 5.16 5 C 5233 2.51 5 N 1367 2.21 5 O 1511 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-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8165 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1925 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 2 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 9, 'GLU:plan': 4, 'GLN:plan1': 3, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 91 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: 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: 125 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'GLN:plan1': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 93 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, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1712 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'H8D': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.93, per 1000 atoms: 0.24 Number of scatterers: 8165 At special positions: 0 Unit cell: (101.01, 115.57, 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 1511 8.00 N 1367 7.00 C 5233 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=2.04 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: 0.74 Conformation dependent library (CDL) restraints added in 331.0 milliseconds 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2038 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 12 sheets defined 35.4% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 40 through 66 Processing helix chain 'A' and resid 74 through 93 removed outlier: 4.401A pdb=" N LEU A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.578A pdb=" N HIS A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 145 removed outlier: 3.851A pdb=" N ALA A 119 " --> pdb=" O GLN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 179 removed outlier: 3.573A pdb=" N TRP A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 169 " --> pdb=" O THR A 165 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 199 through 207 removed outlier: 4.171A pdb=" N THR A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.539A pdb=" N VAL A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 311 removed outlier: 3.554A pdb=" N PHE A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Proline residue: A 300 - end of helix removed outlier: 3.740A pdb=" N THR A 304 " --> pdb=" O PRO A 300 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 308 " --> pdb=" O THR A 304 " (cutoff:3.500A) Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 316 through 339 removed outlier: 3.708A pdb=" N LYS A 320 " --> pdb=" O PRO A 316 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Proline residue: A 335 - end of helix removed outlier: 3.665A pdb=" N THR A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 349 Processing helix chain 'B' and resid 3 through 29 removed outlier: 3.928A pdb=" N LYS B 29 " --> pdb=" O ILE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 removed outlier: 4.418A pdb=" N ILE B 94 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N HIS B 95 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS B 96 " --> pdb=" O TRP B 93 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE B 97 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 3.600A 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: 3.878A pdb=" N ILE B 132 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 150 Processing helix chain 'B' and resid 168 through 181 removed outlier: 3.589A pdb=" N ALA B 172 " --> pdb=" O TYR B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 223 removed outlier: 3.571A pdb=" N ILE B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 25 removed outlier: 3.860A pdb=" N GLN C 9 " --> pdb=" O ASP C 5 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU C 10 " --> pdb=" O GLN C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.818A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 4.188A 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 23 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.682A pdb=" N TYR D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N CYS D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 removed outlier: 3.547A 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 'E' and resid 28 through 32 removed outlier: 3.782A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.994A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 51 through 52 removed outlier: 3.577A pdb=" N VAL B 67 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LYS B 32 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ILE B 104 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU B 34 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N CYS B 106 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU B 36 " --> pdb=" O CYS B 106 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N ASP B 108 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE B 103 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N PHE B 139 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE B 105 " --> pdb=" O PHE B 139 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ASN B 141 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL B 107 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.663A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 6.865A 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: 3.980A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.908A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 153 removed outlier: 6.845A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.731A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.533A 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: 6.744A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.795A 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: 3.827A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.813A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TRP E 111 " --> pdb=" O ARG E 98 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ARG E 98 " --> pdb=" O TRP E 111 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLN E 113 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N CYS E 96 " --> pdb=" O GLN E 113 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.683A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 374 hydrogen bonds defined for protein. 1050 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2614 1.34 - 1.46: 2091 1.46 - 1.58: 3566 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 8345 Sorted by residual: bond pdb=" CA SER A 331 " pdb=" CB SER A 331 " ideal model delta sigma weight residual 1.531 1.478 0.053 1.72e-02 3.38e+03 9.39e+00 bond pdb=" N SER A 331 " pdb=" CA SER A 331 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.32e-02 5.74e+03 7.12e+00 bond pdb=" CA SER A 128 " pdb=" CB SER A 128 " ideal model delta sigma weight residual 1.529 1.492 0.037 1.55e-02 4.16e+03 5.70e+00 bond pdb=" N ASP A 86 " pdb=" CA ASP A 86 " ideal model delta sigma weight residual 1.458 1.486 -0.029 1.28e-02 6.10e+03 5.12e+00 bond pdb=" N SER A 128 " pdb=" CA SER A 128 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.81e+00 ... (remaining 8340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 11191 1.48 - 2.96: 139 2.96 - 4.45: 33 4.45 - 5.93: 8 5.93 - 7.41: 2 Bond angle restraints: 11373 Sorted by residual: angle pdb=" C GLY E 197 " pdb=" N THR E 198 " pdb=" CA THR E 198 " ideal model delta sigma weight residual 121.54 128.02 -6.48 1.91e+00 2.74e-01 1.15e+01 angle pdb=" C ARG A 73 " pdb=" N VAL A 74 " pdb=" CA VAL A 74 " ideal model delta sigma weight residual 120.33 122.97 -2.64 8.00e-01 1.56e+00 1.09e+01 angle pdb=" N SER A 331 " pdb=" CA SER A 331 " pdb=" C SER A 331 " ideal model delta sigma weight residual 113.20 109.29 3.91 1.21e+00 6.83e-01 1.05e+01 angle pdb=" C LEU B 224 " pdb=" N TYR B 225 " pdb=" CA TYR B 225 " ideal model delta sigma weight residual 121.70 116.24 5.46 1.80e+00 3.09e-01 9.20e+00 angle pdb=" N SER A 128 " pdb=" CA SER A 128 " pdb=" CB SER A 128 " ideal model delta sigma weight residual 110.01 114.21 -4.20 1.45e+00 4.76e-01 8.38e+00 ... (remaining 11368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.38: 4809 34.38 - 68.75: 67 68.75 - 103.13: 6 103.13 - 137.51: 0 137.51 - 171.88: 1 Dihedral angle restraints: 4883 sinusoidal: 1728 harmonic: 3155 Sorted by residual: dihedral pdb=" C21 H8D A 401 " pdb=" C19 H8D A 401 " pdb=" C20 H8D A 401 " pdb=" N3 H8D A 401 " ideal model delta sinusoidal sigma weight residual 62.30 -109.58 171.88 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CB CYS A 114 " pdb=" SG CYS A 114 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual 93.00 127.57 -34.57 1 1.00e+01 1.00e-02 1.70e+01 dihedral pdb=" CA TYR B 168 " pdb=" C TYR B 168 " pdb=" N GLU B 169 " pdb=" CA GLU B 169 " ideal model delta harmonic sigma weight residual -180.00 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 4880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 792 0.027 - 0.054: 324 0.054 - 0.082: 118 0.082 - 0.109: 66 0.109 - 0.136: 30 Chirality restraints: 1330 Sorted by residual: chirality pdb=" CA SER A 331 " pdb=" N SER A 331 " pdb=" C SER A 331 " pdb=" CB SER A 331 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE E 177 " pdb=" N ILE E 177 " pdb=" C ILE E 177 " pdb=" CB ILE E 177 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA ILE B 137 " pdb=" N ILE B 137 " pdb=" C ILE B 137 " pdb=" CB ILE B 137 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 1327 not shown) Planarity restraints: 1429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C14 H8D A 401 " -0.179 2.00e-02 2.50e+03 2.76e-01 9.51e+02 pdb=" C16 H8D A 401 " 0.084 2.00e-02 2.50e+03 pdb=" C19 H8D A 401 " -0.325 2.00e-02 2.50e+03 pdb=" N3 H8D A 401 " 0.482 2.00e-02 2.50e+03 pdb=" O1 H8D A 401 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 198 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C THR E 198 " -0.035 2.00e-02 2.50e+03 pdb=" O THR E 198 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA E 199 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 330 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" C ASN A 330 " 0.032 2.00e-02 2.50e+03 pdb=" O ASN A 330 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A 331 " -0.011 2.00e-02 2.50e+03 ... (remaining 1426 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1022 2.76 - 3.29: 7178 3.29 - 3.83: 12217 3.83 - 4.36: 14601 4.36 - 4.90: 26300 Nonbonded interactions: 61318 Sorted by model distance: nonbonded pdb=" O PRO A 335 " pdb=" OG1 THR A 339 " model vdw 2.220 3.040 nonbonded pdb=" NH2 ARG A 230 " pdb=" OD1 ASP B 212 " model vdw 2.334 3.120 nonbonded pdb=" OG SER E 149 " pdb=" O LYS E 151 " model vdw 2.378 3.040 nonbonded pdb=" OD1 ASP A 138 " pdb=" OH TYR A 149 " model vdw 2.379 3.040 nonbonded pdb=" O SER E 85 " pdb=" OG SER E 85 " model vdw 2.398 3.040 ... (remaining 61313 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: 0.970 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.970 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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 : 0.002 0.053 8347 Z= 0.113 Angle : 0.477 7.409 11377 Z= 0.259 Chirality : 0.040 0.136 1330 Planarity : 0.008 0.276 1429 Dihedral : 13.052 171.882 2839 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: -0.25 (0.25), residues: 1069 helix: 0.51 (0.28), residues: 329 sheet: 1.06 (0.31), residues: 274 loop : -1.45 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 168 TYR 0.009 0.001 TYR E 178 PHE 0.008 0.001 PHE C 199 TRP 0.010 0.001 TRP C 63 HIS 0.002 0.000 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 8345) covalent geometry : angle 0.47594 (11373) SS BOND : bond 0.00422 ( 2) SS BOND : angle 1.37643 ( 4) hydrogen bonds : bond 0.29894 ( 374) hydrogen bonds : angle 7.30622 ( 1050) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.323 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.5039 time to fit residues: 96.6577 Evaluate side-chains 174 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 0.1980 chunk 97 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN B 183 ASN C 293 ASN E 167 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 = 0.3564 r_free = 0.3564 target = 0.117480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.102198 restraints weight = 11567.573| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.72 r_work: 0.3212 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8347 Z= 0.134 Angle : 0.548 7.629 11377 Z= 0.289 Chirality : 0.042 0.129 1330 Planarity : 0.004 0.031 1429 Dihedral : 5.634 92.575 1183 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.32 % Allowed : 8.53 % Favored : 90.14 % 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: 0.57 (0.25), residues: 1069 helix: 2.10 (0.29), residues: 332 sheet: 0.92 (0.30), residues: 282 loop : -1.37 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 168 TYR 0.013 0.001 TYR E 178 PHE 0.014 0.001 PHE E 29 TRP 0.011 0.001 TRP A 117 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8345) covalent geometry : angle 0.54710 (11373) SS BOND : bond 0.00987 ( 2) SS BOND : angle 1.89737 ( 4) hydrogen bonds : bond 0.06777 ( 374) hydrogen bonds : angle 4.71715 ( 1050) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.299 Fit side-chains REVERT: B 69 THR cc_start: 0.8745 (m) cc_final: 0.8501 (t) REVERT: C 189 SER cc_start: 0.8330 (t) cc_final: 0.8089 (p) REVERT: E 19 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8427 (ptmt) outliers start: 11 outliers final: 3 residues processed: 164 average time/residue: 0.4807 time to fit residues: 84.5774 Evaluate side-chains 161 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 157 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain E residue 19 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 0.0060 chunk 68 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.115059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.099713 restraints weight = 11424.075| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.70 r_work: 0.3179 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8347 Z= 0.163 Angle : 0.568 9.498 11377 Z= 0.297 Chirality : 0.043 0.139 1330 Planarity : 0.004 0.034 1429 Dihedral : 5.704 82.257 1183 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.40 % Allowed : 10.82 % Favored : 86.78 % 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: 0.59 (0.26), residues: 1069 helix: 2.27 (0.30), residues: 333 sheet: 0.88 (0.29), residues: 288 loop : -1.48 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 168 TYR 0.014 0.002 TYR E 178 PHE 0.015 0.002 PHE E 29 TRP 0.017 0.002 TRP B 93 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8345) covalent geometry : angle 0.56640 (11373) SS BOND : bond 0.01241 ( 2) SS BOND : angle 2.29507 ( 4) hydrogen bonds : bond 0.06506 ( 374) hydrogen bonds : angle 4.51730 ( 1050) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.214 Fit side-chains REVERT: B 69 THR cc_start: 0.8794 (m) cc_final: 0.8476 (t) REVERT: C 189 SER cc_start: 0.8357 (t) cc_final: 0.8139 (p) REVERT: E 19 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8526 (ptmt) REVERT: E 87 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7530 (mtm-85) outliers start: 20 outliers final: 9 residues processed: 170 average time/residue: 0.5135 time to fit residues: 93.2135 Evaluate side-chains 173 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 154 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 25 optimal weight: 0.4980 chunk 58 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 0.0020 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.0770 chunk 64 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.3946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN C 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.118233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.102797 restraints weight = 11742.653| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.73 r_work: 0.3218 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8347 Z= 0.105 Angle : 0.496 8.744 11377 Z= 0.258 Chirality : 0.041 0.128 1330 Planarity : 0.003 0.029 1429 Dihedral : 5.400 77.606 1183 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.92 % Allowed : 12.86 % Favored : 85.22 % 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: 0.80 (0.26), residues: 1069 helix: 2.56 (0.30), residues: 332 sheet: 0.95 (0.29), residues: 286 loop : -1.40 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 168 TYR 0.014 0.001 TYR E 178 PHE 0.011 0.001 PHE C 199 TRP 0.020 0.001 TRP B 93 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 8345) covalent geometry : angle 0.49488 (11373) SS BOND : bond 0.00767 ( 2) SS BOND : angle 1.45304 ( 4) hydrogen bonds : bond 0.04689 ( 374) hydrogen bonds : angle 4.14237 ( 1050) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.321 Fit side-chains REVERT: B 69 THR cc_start: 0.8754 (m) cc_final: 0.8489 (t) REVERT: C 189 SER cc_start: 0.8337 (t) cc_final: 0.8130 (p) REVERT: C 256 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7312 (mtp180) outliers start: 16 outliers final: 10 residues processed: 160 average time/residue: 0.4770 time to fit residues: 81.7589 Evaluate side-chains 162 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 63 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 2 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 0.3980 chunk 3 optimal weight: 0.0670 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.117713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.102301 restraints weight = 11587.073| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.72 r_work: 0.3212 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8347 Z= 0.116 Angle : 0.501 6.900 11377 Z= 0.262 Chirality : 0.041 0.147 1330 Planarity : 0.003 0.031 1429 Dihedral : 5.335 75.561 1183 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.12 % Allowed : 13.34 % Favored : 83.53 % 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: 0.82 (0.26), residues: 1069 helix: 2.60 (0.30), residues: 332 sheet: 0.94 (0.30), residues: 282 loop : -1.37 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 111 TYR 0.014 0.001 TYR E 178 PHE 0.011 0.001 PHE E 29 TRP 0.021 0.001 TRP B 93 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8345) covalent geometry : angle 0.49987 (11373) SS BOND : bond 0.00902 ( 2) SS BOND : angle 1.64566 ( 4) hydrogen bonds : bond 0.04845 ( 374) hydrogen bonds : angle 4.10404 ( 1050) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.296 Fit side-chains REVERT: A 82 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7945 (ttm) REVERT: B 69 THR cc_start: 0.8771 (m) cc_final: 0.8462 (t) REVERT: B 188 LYS cc_start: 0.8565 (ttmm) cc_final: 0.8360 (ttmt) REVERT: C 189 SER cc_start: 0.8357 (t) cc_final: 0.8135 (p) REVERT: C 234 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8603 (m-80) REVERT: C 256 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7303 (mtp180) outliers start: 26 outliers final: 13 residues processed: 169 average time/residue: 0.4820 time to fit residues: 87.3575 Evaluate side-chains 170 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 39 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 3 optimal weight: 0.0070 chunk 77 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 56 optimal weight: 0.0370 chunk 36 optimal weight: 0.0770 chunk 33 optimal weight: 0.8980 overall best weight: 0.3434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.118517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.103213 restraints weight = 11598.203| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.73 r_work: 0.3235 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8347 Z= 0.095 Angle : 0.471 9.042 11377 Z= 0.246 Chirality : 0.041 0.128 1330 Planarity : 0.003 0.029 1429 Dihedral : 5.120 72.090 1183 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.12 % Allowed : 14.18 % Favored : 82.69 % 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: 0.94 (0.26), residues: 1069 helix: 2.73 (0.30), residues: 332 sheet: 1.00 (0.30), residues: 281 loop : -1.32 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 184 TYR 0.014 0.001 TYR E 178 PHE 0.010 0.001 PHE C 199 TRP 0.025 0.001 TRP B 93 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00201 ( 8345) covalent geometry : angle 0.47034 (11373) SS BOND : bond 0.00679 ( 2) SS BOND : angle 1.23606 ( 4) hydrogen bonds : bond 0.04020 ( 374) hydrogen bonds : angle 3.90870 ( 1050) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.305 Fit side-chains REVERT: A 101 GLU cc_start: 0.5813 (OUTLIER) cc_final: 0.5528 (pm20) REVERT: B 69 THR cc_start: 0.8743 (m) cc_final: 0.8439 (t) REVERT: C 189 SER cc_start: 0.8341 (t) cc_final: 0.8137 (p) REVERT: C 234 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.8531 (m-80) REVERT: C 256 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7260 (mtp180) outliers start: 26 outliers final: 12 residues processed: 168 average time/residue: 0.4821 time to fit residues: 86.8022 Evaluate side-chains 166 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain E residue 63 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.101530 restraints weight = 11591.700| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.71 r_work: 0.3202 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8347 Z= 0.133 Angle : 0.530 10.593 11377 Z= 0.273 Chirality : 0.042 0.137 1330 Planarity : 0.003 0.031 1429 Dihedral : 5.233 62.019 1183 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.76 % Allowed : 14.54 % Favored : 82.69 % 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: 0.81 (0.26), residues: 1069 helix: 2.61 (0.30), residues: 333 sheet: 0.92 (0.29), residues: 282 loop : -1.40 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 184 TYR 0.012 0.001 TYR E 178 PHE 0.013 0.001 PHE C 234 TRP 0.027 0.001 TRP B 93 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8345) covalent geometry : angle 0.52907 (11373) SS BOND : bond 0.01021 ( 2) SS BOND : angle 1.82887 ( 4) hydrogen bonds : bond 0.05087 ( 374) hydrogen bonds : angle 4.08647 ( 1050) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.305 Fit side-chains REVERT: C 189 SER cc_start: 0.8386 (t) cc_final: 0.8166 (p) REVERT: C 234 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.8574 (m-80) REVERT: C 256 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7257 (mtp180) outliers start: 23 outliers final: 13 residues processed: 165 average time/residue: 0.4857 time to fit residues: 85.9694 Evaluate side-chains 168 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 63 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 40 optimal weight: 0.0170 chunk 94 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.117756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.102434 restraints weight = 11540.077| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.71 r_work: 0.3218 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8347 Z= 0.110 Angle : 0.501 11.097 11377 Z= 0.261 Chirality : 0.041 0.138 1330 Planarity : 0.003 0.030 1429 Dihedral : 4.925 46.921 1183 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.28 % Allowed : 15.38 % Favored : 82.33 % 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: 0.89 (0.26), residues: 1069 helix: 2.73 (0.30), residues: 332 sheet: 0.92 (0.29), residues: 282 loop : -1.35 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 184 TYR 0.013 0.001 TYR E 178 PHE 0.010 0.001 PHE E 29 TRP 0.028 0.001 TRP B 93 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8345) covalent geometry : angle 0.50038 (11373) SS BOND : bond 0.00829 ( 2) SS BOND : angle 1.51039 ( 4) hydrogen bonds : bond 0.04531 ( 374) hydrogen bonds : angle 3.97609 ( 1050) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.311 Fit side-chains REVERT: A 101 GLU cc_start: 0.5813 (OUTLIER) cc_final: 0.5525 (pm20) REVERT: B 69 THR cc_start: 0.8789 (m) cc_final: 0.8443 (t) REVERT: C 189 SER cc_start: 0.8375 (t) cc_final: 0.8156 (p) REVERT: C 234 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8566 (m-80) REVERT: C 256 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7239 (mtp180) REVERT: C 304 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8046 (ttt180) outliers start: 19 outliers final: 11 residues processed: 164 average time/residue: 0.4929 time to fit residues: 86.6304 Evaluate side-chains 168 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 63 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 102 optimal weight: 0.3980 chunk 70 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 44 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.117711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.102287 restraints weight = 11536.484| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.72 r_work: 0.3207 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8347 Z= 0.119 Angle : 0.522 10.624 11377 Z= 0.268 Chirality : 0.041 0.138 1330 Planarity : 0.003 0.031 1429 Dihedral : 4.773 35.882 1183 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.52 % Allowed : 15.62 % Favored : 81.85 % 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: 1069 helix: 2.72 (0.30), residues: 332 sheet: 0.95 (0.29), residues: 282 loop : -1.37 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 184 TYR 0.012 0.001 TYR E 178 PHE 0.011 0.001 PHE E 29 TRP 0.030 0.001 TRP B 93 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8345) covalent geometry : angle 0.52084 (11373) SS BOND : bond 0.00888 ( 2) SS BOND : angle 1.60821 ( 4) hydrogen bonds : bond 0.04682 ( 374) hydrogen bonds : angle 4.00693 ( 1050) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.320 Fit side-chains REVERT: A 101 GLU cc_start: 0.5830 (OUTLIER) cc_final: 0.5545 (pm20) REVERT: C 189 SER cc_start: 0.8385 (t) cc_final: 0.8161 (p) REVERT: C 234 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8583 (m-80) REVERT: C 256 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7248 (mtp180) REVERT: C 304 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8080 (ttt180) outliers start: 21 outliers final: 12 residues processed: 164 average time/residue: 0.4894 time to fit residues: 86.1330 Evaluate side-chains 168 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 63 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 50 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.117072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.101780 restraints weight = 11352.737| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.70 r_work: 0.3201 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8347 Z= 0.129 Angle : 0.528 10.331 11377 Z= 0.276 Chirality : 0.042 0.143 1330 Planarity : 0.003 0.032 1429 Dihedral : 4.761 35.695 1183 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.76 % Allowed : 15.50 % Favored : 81.73 % 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: 0.81 (0.26), residues: 1069 helix: 2.66 (0.30), residues: 332 sheet: 0.94 (0.30), residues: 277 loop : -1.42 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 184 TYR 0.012 0.001 TYR E 178 PHE 0.018 0.001 PHE A 55 TRP 0.030 0.001 TRP B 93 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8345) covalent geometry : angle 0.52756 (11373) SS BOND : bond 0.00975 ( 2) SS BOND : angle 1.73242 ( 4) hydrogen bonds : bond 0.04966 ( 374) hydrogen bonds : angle 4.05362 ( 1050) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.195 Fit side-chains REVERT: A 101 GLU cc_start: 0.5830 (OUTLIER) cc_final: 0.5546 (pm20) REVERT: C 189 SER cc_start: 0.8376 (t) cc_final: 0.8165 (p) REVERT: C 234 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8610 (m-80) REVERT: C 256 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7254 (mtp180) REVERT: C 304 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8071 (ttt180) REVERT: E 5 VAL cc_start: 0.8534 (t) cc_final: 0.8307 (t) REVERT: E 118 THR cc_start: 0.8383 (OUTLIER) cc_final: 0.8138 (p) outliers start: 23 outliers final: 13 residues processed: 166 average time/residue: 0.5053 time to fit residues: 89.9228 Evaluate side-chains 172 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 63 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 55 optimal weight: 0.1980 chunk 79 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.117080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.101751 restraints weight = 11448.780| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.71 r_work: 0.3198 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8347 Z= 0.130 Angle : 0.543 11.374 11377 Z= 0.281 Chirality : 0.042 0.142 1330 Planarity : 0.003 0.032 1429 Dihedral : 4.782 36.224 1183 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.76 % Allowed : 15.62 % Favored : 81.61 % 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: 0.81 (0.26), residues: 1069 helix: 2.65 (0.30), residues: 332 sheet: 0.92 (0.29), residues: 281 loop : -1.41 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 184 TYR 0.013 0.001 TYR E 178 PHE 0.023 0.001 PHE A 55 TRP 0.032 0.001 TRP B 93 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8345) covalent geometry : angle 0.54189 (11373) SS BOND : bond 0.00964 ( 2) SS BOND : angle 1.71427 ( 4) hydrogen bonds : bond 0.04951 ( 374) hydrogen bonds : angle 4.05736 ( 1050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3426.15 seconds wall clock time: 58 minutes 49.60 seconds (3529.60 seconds total)