Starting phenix.real_space_refine on Wed Mar 12 18:54:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7um7_26599/03_2025/7um7_26599.cif Found real_map, /net/cci-nas-00/data/ceres_data/7um7_26599/03_2025/7um7_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_2025/7um7_26599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7um7_26599/03_2025/7um7_26599.map" model { file = "/net/cci-nas-00/data/ceres_data/7um7_26599/03_2025/7um7_26599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7um7_26599/03_2025/7um7_26599.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.027 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 9} 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: {'GLU:plan': 1, 'ARG: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: {'GLN:plan1': 4, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7} 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, 'GLU:plan': 2, 'ARG:plan': 1, '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: {'GLN:plan1': 1, 'GLU:plan': 7, '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: 5.68, per 1000 atoms: 0.70 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: 2.30 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.09 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: 2.41 Time building geometry restraints manager: 2.67 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.820 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.670 ------------------------------------------------------------------------------- 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 8345 Z= 0.139 Angle : 0.476 7.409 11373 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (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 TRP 0.010 0.001 TRP C 63 HIS 0.002 0.000 HIS E 35 PHE 0.008 0.001 PHE C 199 TYR 0.009 0.001 TYR E 178 ARG 0.007 0.000 ARG E 168 *********************** 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 : 0.884 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 1.0796 time to fit residues: 208.4574 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 : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 97 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.116548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.101309 restraints weight = 11419.476| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.70 r_work: 0.3196 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8345 Z= 0.226 Angle : 0.569 7.417 11373 Z= 0.300 Chirality : 0.043 0.132 1330 Planarity : 0.004 0.034 1429 Dihedral : 5.753 95.242 1183 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.56 % Allowed : 8.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.25), residues: 1069 helix: 2.01 (0.29), residues: 332 sheet: 0.92 (0.30), residues: 282 loop : -1.42 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 117 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.001 PHE E 29 TYR 0.014 0.001 TYR E 178 ARG 0.006 0.000 ARG E 168 *********************** 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 179 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.961 Fit side-chains REVERT: B 69 THR cc_start: 0.8760 (m) cc_final: 0.8497 (t) REVERT: C 189 SER cc_start: 0.8321 (t) cc_final: 0.8096 (p) REVERT: E 19 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8467 (ptmt) outliers start: 13 outliers final: 5 residues processed: 169 average time/residue: 1.0447 time to fit residues: 189.3336 Evaluate side-chains 169 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 163 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 84 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 Chi-restraints excluded: chain E residue 63 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 77 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.0980 chunk 71 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 ASN E 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.117399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.101961 restraints weight = 11600.844| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.72 r_work: 0.3208 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8345 Z= 0.167 Angle : 0.514 9.917 11373 Z= 0.268 Chirality : 0.041 0.131 1330 Planarity : 0.003 0.031 1429 Dihedral : 5.498 79.197 1183 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.80 % Allowed : 11.30 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1069 helix: 2.48 (0.30), residues: 332 sheet: 0.98 (0.29), residues: 286 loop : -1.43 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 93 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE E 29 TYR 0.014 0.001 TYR E 178 ARG 0.003 0.000 ARG E 168 *********************** 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 166 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.943 Fit side-chains REVERT: B 69 THR cc_start: 0.8782 (m) cc_final: 0.8500 (t) REVERT: C 189 SER cc_start: 0.8328 (t) cc_final: 0.8117 (p) REVERT: E 19 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8477 (ptmt) outliers start: 15 outliers final: 8 residues processed: 156 average time/residue: 1.1942 time to fit residues: 199.6654 Evaluate side-chains 158 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 25 ILE 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 227 SER Chi-restraints excluded: chain E residue 19 LYS 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 53 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 46 optimal weight: 0.0270 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 0.0270 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 GLN E 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.118949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.103522 restraints weight = 11510.104| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.72 r_work: 0.3228 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 0.002 0.034 8345 Z= 0.138 Angle : 0.481 7.413 11373 Z= 0.251 Chirality : 0.041 0.140 1330 Planarity : 0.003 0.028 1429 Dihedral : 5.305 75.565 1183 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.92 % Allowed : 12.62 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.26), residues: 1069 helix: 2.67 (0.30), residues: 332 sheet: 0.97 (0.29), residues: 286 loop : -1.37 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 93 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE A 55 TYR 0.014 0.001 TYR E 178 ARG 0.003 0.000 ARG E 168 *********************** 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 168 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.999 Fit side-chains REVERT: B 69 THR cc_start: 0.8762 (m) cc_final: 0.8479 (t) REVERT: C 189 SER cc_start: 0.8327 (t) cc_final: 0.8100 (p) REVERT: C 256 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7283 (mtp180) REVERT: E 19 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8435 (ttmm) outliers start: 16 outliers final: 9 residues processed: 158 average time/residue: 0.9679 time to fit residues: 164.4290 Evaluate side-chains 161 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 227 SER Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 74 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS E 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.113016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.097927 restraints weight = 11382.424| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.68 r_work: 0.3137 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 8345 Z= 0.461 Angle : 0.689 8.891 11373 Z= 0.359 Chirality : 0.049 0.163 1330 Planarity : 0.004 0.045 1429 Dihedral : 5.973 76.283 1183 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.37 % Allowed : 13.22 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1069 helix: 1.95 (0.29), residues: 334 sheet: 0.75 (0.29), residues: 287 loop : -1.60 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 93 HIS 0.008 0.002 HIS E 35 PHE 0.022 0.003 PHE E 68 TYR 0.016 0.002 TYR A 220 ARG 0.006 0.001 ARG E 179 *********************** 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 194 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.937 Fit side-chains REVERT: B 30 ASP cc_start: 0.8168 (m-30) cc_final: 0.7968 (m-30) REVERT: C 256 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7305 (mtp180) REVERT: E 5 VAL cc_start: 0.8570 (t) cc_final: 0.8368 (t) REVERT: E 19 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8559 (ptmt) REVERT: E 87 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7511 (mtm-85) outliers start: 28 outliers final: 11 residues processed: 177 average time/residue: 0.9720 time to fit residues: 184.7802 Evaluate side-chains 178 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 324 LEU 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 C residue 256 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 77 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.115437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.100171 restraints weight = 11405.003| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.69 r_work: 0.3180 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8345 Z= 0.226 Angle : 0.555 9.433 11373 Z= 0.290 Chirality : 0.043 0.138 1330 Planarity : 0.004 0.038 1429 Dihedral : 5.566 77.558 1183 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.00 % Allowed : 14.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1069 helix: 2.29 (0.29), residues: 333 sheet: 0.76 (0.29), residues: 288 loop : -1.56 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 93 HIS 0.005 0.001 HIS E 35 PHE 0.013 0.001 PHE E 29 TYR 0.015 0.001 TYR E 178 ARG 0.004 0.000 ARG B 184 *********************** 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 183 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.874 Fit side-chains REVERT: B 30 ASP cc_start: 0.8060 (m-30) cc_final: 0.7837 (m-30) REVERT: C 234 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8570 (m-80) REVERT: C 256 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7280 (mtp180) REVERT: E 19 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8513 (ptmt) REVERT: E 87 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7464 (mtm-85) outliers start: 25 outliers final: 14 residues processed: 168 average time/residue: 0.9348 time to fit residues: 169.0019 Evaluate side-chains 175 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 324 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 40 VAL 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 7 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 80 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.115784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.100484 restraints weight = 11419.170| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.70 r_work: 0.3182 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8345 Z= 0.224 Angle : 0.547 10.898 11373 Z= 0.286 Chirality : 0.043 0.140 1330 Planarity : 0.004 0.036 1429 Dihedral : 5.431 72.307 1183 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.12 % Allowed : 15.38 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.26), residues: 1069 helix: 2.39 (0.29), residues: 333 sheet: 0.74 (0.29), residues: 288 loop : -1.51 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 93 HIS 0.005 0.001 HIS E 35 PHE 0.013 0.001 PHE E 29 TYR 0.014 0.001 TYR E 178 ARG 0.004 0.000 ARG B 184 *********************** 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 180 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.885 Fit side-chains REVERT: A 101 GLU cc_start: 0.5835 (OUTLIER) cc_final: 0.5551 (pm20) REVERT: B 30 ASP cc_start: 0.8041 (m-30) cc_final: 0.7818 (m-30) REVERT: C 234 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8569 (m-80) REVERT: C 256 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7280 (mtp180) REVERT: C 304 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8057 (ttt180) REVERT: E 19 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8494 (ttmm) REVERT: E 87 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7471 (mtm-85) REVERT: E 118 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8163 (p) outliers start: 26 outliers final: 14 residues processed: 166 average time/residue: 0.9994 time to fit residues: 178.1000 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 : 0.970 ------------------------------------------------------------------------------- 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 84 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 40 VAL 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 19 LYS Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 154 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 102 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 46 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 56 optimal weight: 0.0670 chunk 78 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 85 optimal weight: 0.3980 chunk 90 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.117056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.101684 restraints weight = 11547.100| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.72 r_work: 0.3203 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 : 0.003 0.040 8345 Z= 0.172 Angle : 0.515 10.667 11373 Z= 0.269 Chirality : 0.042 0.134 1330 Planarity : 0.003 0.033 1429 Dihedral : 5.252 62.642 1183 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.12 % Allowed : 15.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1069 helix: 2.56 (0.30), residues: 333 sheet: 0.80 (0.29), residues: 288 loop : -1.43 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 93 HIS 0.004 0.001 HIS E 35 PHE 0.010 0.001 PHE C 199 TYR 0.014 0.001 TYR E 178 ARG 0.003 0.000 ARG B 184 *********************** 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 179 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.883 Fit side-chains REVERT: A 101 GLU cc_start: 0.5833 (OUTLIER) cc_final: 0.5546 (pm20) REVERT: B 30 ASP cc_start: 0.7993 (m-30) cc_final: 0.7772 (m-30) REVERT: C 234 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8575 (m-80) REVERT: C 256 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7250 (mtp180) REVERT: C 304 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8050 (ttt180) REVERT: E 118 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8153 (p) outliers start: 26 outliers final: 15 residues processed: 167 average time/residue: 0.9502 time to fit residues: 171.1213 Evaluate side-chains 173 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 84 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 40 VAL 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 7 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 203 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 0.0970 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 71 optimal weight: 0.7980 chunk 82 optimal weight: 0.0070 chunk 101 optimal weight: 0.0980 chunk 23 optimal weight: 2.9990 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.119218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.103925 restraints weight = 11743.725| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.73 r_work: 0.3243 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8345 Z= 0.130 Angle : 0.483 10.579 11373 Z= 0.251 Chirality : 0.041 0.131 1330 Planarity : 0.003 0.030 1429 Dihedral : 4.732 41.209 1183 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.40 % Allowed : 16.47 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.26), residues: 1069 helix: 2.70 (0.30), residues: 332 sheet: 0.88 (0.30), residues: 278 loop : -1.31 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 93 HIS 0.003 0.000 HIS E 35 PHE 0.012 0.001 PHE A 55 TYR 0.014 0.001 TYR E 178 ARG 0.003 0.000 ARG B 184 *********************** 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 172 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.864 Fit side-chains REVERT: A 62 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6654 (mm) REVERT: A 101 GLU cc_start: 0.5799 (OUTLIER) cc_final: 0.5538 (pm20) REVERT: C 234 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.8532 (m-80) REVERT: C 256 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7207 (mtp180) REVERT: C 258 ASP cc_start: 0.8126 (t0) cc_final: 0.7848 (t0) REVERT: C 304 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8057 (ttt180) REVERT: E 118 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8157 (p) outliers start: 20 outliers final: 7 residues processed: 161 average time/residue: 0.9851 time to fit residues: 170.1752 Evaluate side-chains 164 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 40 VAL 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 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 66 optimal weight: 0.0370 chunk 70 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 64 optimal weight: 0.0670 chunk 69 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.118499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.103187 restraints weight = 11511.350| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.72 r_work: 0.3233 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8345 Z= 0.149 Angle : 0.503 10.337 11373 Z= 0.259 Chirality : 0.041 0.138 1330 Planarity : 0.003 0.031 1429 Dihedral : 4.650 34.718 1183 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.92 % Allowed : 17.31 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1069 helix: 2.71 (0.30), residues: 333 sheet: 0.84 (0.30), residues: 284 loop : -1.26 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 93 HIS 0.002 0.001 HIS E 35 PHE 0.013 0.001 PHE A 55 TYR 0.013 0.001 TYR E 178 ARG 0.003 0.000 ARG C 219 ********************** 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 166 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.890 Fit side-chains REVERT: A 62 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6669 (mm) REVERT: A 101 GLU cc_start: 0.5797 (OUTLIER) cc_final: 0.5538 (pm20) REVERT: C 234 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8531 (m-80) REVERT: C 256 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7252 (mtp180) REVERT: C 258 ASP cc_start: 0.8097 (t0) cc_final: 0.7812 (t0) REVERT: C 304 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8092 (ttt180) REVERT: E 118 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8144 (p) outliers start: 16 outliers final: 8 residues processed: 160 average time/residue: 1.0033 time to fit residues: 172.3162 Evaluate side-chains 164 residues out of total 929 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 40 VAL 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 Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 101 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 52 optimal weight: 0.1980 chunk 85 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.116906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.101499 restraints weight = 11629.182| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.72 r_work: 0.3201 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8345 Z= 0.195 Angle : 0.526 10.098 11373 Z= 0.275 Chirality : 0.042 0.139 1330 Planarity : 0.003 0.032 1429 Dihedral : 4.792 35.617 1183 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.92 % Allowed : 17.55 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1069 helix: 2.59 (0.30), residues: 333 sheet: 0.85 (0.30), residues: 282 loop : -1.36 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 93 HIS 0.005 0.001 HIS E 35 PHE 0.014 0.001 PHE A 55 TYR 0.012 0.001 TYR E 178 ARG 0.003 0.000 ARG B 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7183.02 seconds wall clock time: 125 minutes 32.92 seconds (7532.92 seconds total)