Starting phenix.real_space_refine on Wed Mar 12 22:35:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dpf_27633/03_2025/8dpf_27633_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpf_27633/03_2025/8dpf_27633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dpf_27633/03_2025/8dpf_27633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpf_27633/03_2025/8dpf_27633.map" model { file = "/net/cci-nas-00/data/ceres_data/8dpf_27633/03_2025/8dpf_27633_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpf_27633/03_2025/8dpf_27633_trim.cif" } resolution = 2.84 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= 0.001 sd= 0.022 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: 5 Type Number sf(0) Gaussians S 56 5.16 5 Cl 1 4.86 5 C 5236 2.51 5 N 1368 2.21 5 O 1499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8160 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1939 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 9, 'TRANS': 254} Chain breaks: 4 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 80 Chain: "B" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1683 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 101 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 88 Chain: "C" Number of atoms: 2479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2479 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 9, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "D" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 284 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1734 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'CLR': 1, 'T4U': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.56, per 1000 atoms: 0.68 Number of scatterers: 8160 At special positions: 0 Unit cell: (90.09, 120.12, 134.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 56 16.00 O 1499 8.00 N 1368 7.00 C 5236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 207 " 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: 2.08 Conformation dependent library (CDL) restraints added in 1.0 seconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2048 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 38.8% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 61 through 80 removed outlier: 3.527A pdb=" N ILE A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 106 removed outlier: 5.138A pdb=" N PHE A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET A 93 " --> pdb=" O ASN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.692A pdb=" N SER A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 111 " --> pdb=" O MET A 107 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 112 " --> pdb=" O PRO A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 158 removed outlier: 4.304A pdb=" N SER A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 166 Processing helix chain 'A' and resid 167 through 185 removed outlier: 3.731A pdb=" N ALA A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 removed outlier: 3.925A pdb=" N VAL A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 200 removed outlier: 6.928A pdb=" N GLU A 198 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 223 removed outlier: 4.456A pdb=" N ILE A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N PHE A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 245 removed outlier: 3.506A pdb=" N THR A 228 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 337 removed outlier: 4.329A pdb=" N GLU A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Proline residue: A 326 - end of helix removed outlier: 3.851A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 360 removed outlier: 3.603A pdb=" N VAL A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TRP A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'B' and resid 6 through 31 removed outlier: 3.831A pdb=" N GLU B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.516A pdb=" N ILE B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 101 removed outlier: 3.595A pdb=" N CYS B 99 " --> pdb=" O TRP B 96 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.593A pdb=" N LEU B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 164 through 170 Processing helix chain 'B' and resid 185 through 203 removed outlier: 3.810A pdb=" N ALA B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 removed outlier: 3.581A pdb=" N ARG B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 24 removed outlier: 3.606A 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 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 17 through 24 removed outlier: 3.638A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.558A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76 removed outlier: 3.623A pdb=" N PHE B 74 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N GLY B 40 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.714A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.784A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.054A 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: 7.002A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.769A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.251A 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: 3.850A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C 203 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.335A 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: 3.942A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.960A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.538A 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 removed outlier: 3.817A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.302A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.302A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.767A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.767A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN E 219 " --> pdb=" O THR E 226 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1149 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: 2.57 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2618 1.34 - 1.46: 1981 1.46 - 1.58: 3645 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 8328 Sorted by residual: bond pdb=" N ILE A 156 " pdb=" CA ILE A 156 " ideal model delta sigma weight residual 1.460 1.507 -0.047 1.32e-02 5.74e+03 1.26e+01 bond pdb=" C ASN A 158 " pdb=" N PRO A 159 " ideal model delta sigma weight residual 1.335 1.369 -0.034 1.36e-02 5.41e+03 6.29e+00 bond pdb=" C08 T4U A 501 " pdb=" C11 T4U A 501 " ideal model delta sigma weight residual 1.520 1.563 -0.043 2.00e-02 2.50e+03 4.53e+00 bond pdb=" C04 T4U A 501 " pdb=" C09 T4U A 501 " ideal model delta sigma weight residual 1.508 1.548 -0.040 2.00e-02 2.50e+03 3.90e+00 bond pdb=" C GLU E 222 " pdb=" N TYR E 223 " ideal model delta sigma weight residual 1.331 1.290 0.041 2.07e-02 2.33e+03 3.85e+00 ... (remaining 8323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 11184 2.43 - 4.86: 145 4.86 - 7.29: 16 7.29 - 9.72: 2 9.72 - 12.15: 4 Bond angle restraints: 11351 Sorted by residual: angle pdb=" CA ASN A 158 " pdb=" C ASN A 158 " pdb=" N PRO A 159 " ideal model delta sigma weight residual 117.73 123.68 -5.95 1.04e+00 9.25e-01 3.28e+01 angle pdb=" O ALA A 155 " pdb=" C ALA A 155 " pdb=" N ILE A 156 " ideal model delta sigma weight residual 122.22 117.21 5.01 1.17e+00 7.31e-01 1.83e+01 angle pdb=" C07 T4U A 501 " pdb=" C08 T4U A 501 " pdb=" C11 T4U A 501 " ideal model delta sigma weight residual 111.70 123.85 -12.15 3.00e+00 1.11e-01 1.64e+01 angle pdb=" CA ASN A 158 " pdb=" C ASN A 158 " pdb=" O ASN A 158 " ideal model delta sigma weight residual 120.80 115.72 5.08 1.32e+00 5.74e-01 1.48e+01 angle pdb=" CA ALA A 155 " pdb=" C ALA A 155 " pdb=" N ILE A 156 " ideal model delta sigma weight residual 117.63 122.36 -4.73 1.25e+00 6.40e-01 1.43e+01 ... (remaining 11346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.66: 4850 28.66 - 57.32: 56 57.32 - 85.98: 9 85.98 - 114.64: 2 114.64 - 143.30: 2 Dihedral angle restraints: 4919 sinusoidal: 1755 harmonic: 3164 Sorted by residual: dihedral pdb=" CA ALA E 131 " pdb=" C ALA E 131 " pdb=" N THR E 132 " pdb=" CA THR E 132 " ideal model delta harmonic sigma weight residual 180.00 135.65 44.35 0 5.00e+00 4.00e-02 7.87e+01 dihedral pdb=" C11 T4U A 501 " pdb=" C07 T4U A 501 " pdb=" C08 T4U A 501 " pdb=" N13 T4U A 501 " ideal model delta sinusoidal sigma weight residual -82.85 60.45 -143.30 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" CA PHE A 223 " pdb=" C PHE A 223 " pdb=" N PHE A 224 " pdb=" CA PHE A 224 " ideal model delta harmonic sigma weight residual -180.00 -158.42 -21.58 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 4916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.322: 1345 0.322 - 0.644: 0 0.644 - 0.965: 0 0.965 - 1.287: 0 1.287 - 1.609: 1 Chirality restraints: 1346 Sorted by residual: chirality pdb=" C08 T4U A 501 " pdb=" C01 T4U A 501 " pdb=" C07 T4U A 501 " pdb=" C11 T4U A 501 " both_signs ideal model delta sigma weight residual False -2.50 -0.89 -1.61 2.00e-01 2.50e+01 6.47e+01 chirality pdb=" CB ILE A 156 " pdb=" CA ILE A 156 " pdb=" CG1 ILE A 156 " pdb=" CG2 ILE A 156 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CA PRO C 236 " pdb=" N PRO C 236 " pdb=" C PRO C 236 " pdb=" CB PRO C 236 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 1343 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 155 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.42e+00 pdb=" C ALA A 155 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA A 155 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE A 156 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 151 " 0.014 2.00e-02 2.50e+03 1.19e-02 2.47e+00 pdb=" CG PHE C 151 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE C 151 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE C 151 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 151 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 151 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 151 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 193 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO C 194 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 194 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 194 " -0.022 5.00e-02 4.00e+02 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 47 2.65 - 3.22: 7116 3.22 - 3.78: 11459 3.78 - 4.34: 15933 4.34 - 4.90: 27135 Nonbonded interactions: 61690 Sorted by model distance: nonbonded pdb=" OD2 ASP A 151 " pdb=" OH TYR B 243 " model vdw 2.093 3.040 nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.274 3.040 nonbonded pdb=" OG SER E 134 " pdb=" OE1 GLU E 234 " model vdw 2.328 3.040 nonbonded pdb=" NH2 ARG E 98 " pdb=" OD2 ASP E 109 " model vdw 2.346 3.120 nonbonded pdb=" OE1 GLN C 176 " pdb=" OG1 THR C 179 " model vdw 2.367 3.040 ... (remaining 61685 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: 1.390 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.890 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:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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 : 0.004 0.047 8328 Z= 0.296 Angle : 0.745 12.153 11351 Z= 0.410 Chirality : 0.064 1.609 1346 Planarity : 0.005 0.039 1424 Dihedral : 11.289 143.302 2865 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.12 % Allowed : 0.37 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 1.40 (0.25), residues: 1065 helix: 1.51 (0.29), residues: 326 sheet: 1.31 (0.30), residues: 271 loop : 0.40 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 63 HIS 0.008 0.002 HIS E 220 PHE 0.027 0.003 PHE C 151 TYR 0.017 0.002 TYR A 375 ARG 0.007 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 364 ASN cc_start: 0.7338 (m110) cc_final: 0.7025 (m110) REVERT: B 195 LYS cc_start: 0.7640 (tttt) cc_final: 0.6974 (tttm) REVERT: C 289 TYR cc_start: 0.8201 (m-80) cc_final: 0.8000 (m-80) REVERT: C 340 ASN cc_start: 0.7537 (t0) cc_final: 0.7296 (t0) REVERT: D 50 LEU cc_start: 0.8569 (mt) cc_final: 0.8174 (mt) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.9521 time to fit residues: 198.4373 Evaluate side-chains 172 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0570 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 chunk 84 optimal weight: 0.0270 chunk 32 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 0.0970 chunk 98 optimal weight: 3.9990 overall best weight: 0.1754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 223 ASN B 244 ASN C 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.129605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.115415 restraints weight = 12179.496| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.81 r_work: 0.3420 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8328 Z= 0.152 Angle : 0.561 6.140 11351 Z= 0.306 Chirality : 0.044 0.154 1346 Planarity : 0.004 0.046 1424 Dihedral : 8.870 150.161 1236 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.59 % Allowed : 7.68 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.63 (0.26), residues: 1065 helix: 2.07 (0.29), residues: 344 sheet: 1.29 (0.30), residues: 283 loop : 0.21 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 297 HIS 0.005 0.001 HIS B 209 PHE 0.016 0.001 PHE C 199 TYR 0.015 0.001 TYR E 178 ARG 0.006 0.001 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 366 LEU cc_start: 0.8022 (mt) cc_final: 0.7739 (mp) REVERT: B 22 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.7995 (OUTLIER) REVERT: C 189 SER cc_start: 0.8384 (p) cc_final: 0.8181 (t) REVERT: C 190 LEU cc_start: 0.7638 (mt) cc_final: 0.7430 (mp) REVERT: C 258 ASP cc_start: 0.6497 (t0) cc_final: 0.6237 (t0) REVERT: C 289 TYR cc_start: 0.8249 (m-80) cc_final: 0.7775 (m-80) REVERT: E 207 LEU cc_start: 0.8494 (tp) cc_final: 0.8293 (tp) outliers start: 13 outliers final: 6 residues processed: 171 average time/residue: 1.0050 time to fit residues: 183.9390 Evaluate side-chains 168 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 162 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 58 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 75 optimal weight: 0.0570 chunk 78 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 244 ASN C 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.126513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.112213 restraints weight = 12372.380| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.83 r_work: 0.3387 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8328 Z= 0.205 Angle : 0.566 6.926 11351 Z= 0.307 Chirality : 0.044 0.146 1346 Planarity : 0.004 0.051 1424 Dihedral : 8.291 153.599 1236 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.83 % Allowed : 9.63 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.59 (0.26), residues: 1065 helix: 2.25 (0.29), residues: 347 sheet: 1.25 (0.31), residues: 282 loop : -0.02 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 130 HIS 0.010 0.002 HIS B 209 PHE 0.016 0.002 PHE C 199 TYR 0.010 0.001 TYR E 178 ARG 0.005 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 1.405 Fit side-chains revert: symmetry clash REVERT: A 366 LEU cc_start: 0.8195 (mt) cc_final: 0.7977 (mp) REVERT: B 22 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.7980 (m110) REVERT: B 32 ARG cc_start: 0.8235 (mtt180) cc_final: 0.7970 (mtt-85) REVERT: C 49 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8430 (tpp-160) REVERT: C 189 SER cc_start: 0.8447 (p) cc_final: 0.8239 (t) REVERT: C 190 LEU cc_start: 0.7797 (mt) cc_final: 0.7590 (mp) REVERT: C 258 ASP cc_start: 0.6599 (t0) cc_final: 0.6217 (t0) REVERT: C 289 TYR cc_start: 0.8375 (m-80) cc_final: 0.8041 (m-80) REVERT: E 93 MET cc_start: 0.8135 (tpt) cc_final: 0.7786 (tpt) REVERT: E 132 THR cc_start: 0.8099 (t) cc_final: 0.7612 (m) REVERT: E 207 LEU cc_start: 0.8507 (tp) cc_final: 0.8303 (tp) outliers start: 15 outliers final: 7 residues processed: 175 average time/residue: 1.4502 time to fit residues: 270.9720 Evaluate side-chains 173 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 3.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 51 optimal weight: 0.0370 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 244 ASN C 75 GLN C 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.126345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.112011 restraints weight = 12338.977| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.83 r_work: 0.3373 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 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 : 0.003 0.045 8328 Z= 0.198 Angle : 0.553 7.346 11351 Z= 0.298 Chirality : 0.043 0.143 1346 Planarity : 0.004 0.054 1424 Dihedral : 7.474 136.981 1236 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.56 % Allowed : 10.61 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.63 (0.26), residues: 1065 helix: 2.43 (0.29), residues: 342 sheet: 1.22 (0.31), residues: 287 loop : -0.09 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 130 HIS 0.009 0.001 HIS B 209 PHE 0.015 0.002 PHE C 151 TYR 0.010 0.001 TYR E 178 ARG 0.006 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.7306 (mmm) cc_final: 0.6943 (mtm) REVERT: B 22 ASN cc_start: 0.8203 (m-40) cc_final: 0.7936 (m110) REVERT: C 49 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8427 (tpp-160) REVERT: C 98 SER cc_start: 0.8474 (p) cc_final: 0.8146 (t) REVERT: C 258 ASP cc_start: 0.6720 (t0) cc_final: 0.6321 (t0) REVERT: C 289 TYR cc_start: 0.8395 (m-80) cc_final: 0.8021 (m-80) REVERT: E 132 THR cc_start: 0.8222 (t) cc_final: 0.7813 (m) outliers start: 21 outliers final: 9 residues processed: 177 average time/residue: 1.0697 time to fit residues: 202.2041 Evaluate side-chains 175 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 233 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 51 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 82 optimal weight: 0.0980 chunk 48 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 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 331 ASN B 244 ASN C 75 GLN C 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.124779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.110486 restraints weight = 12186.053| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.83 r_work: 0.3348 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8328 Z= 0.242 Angle : 0.587 8.235 11351 Z= 0.314 Chirality : 0.044 0.156 1346 Planarity : 0.004 0.057 1424 Dihedral : 7.369 132.188 1236 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.44 % Allowed : 11.83 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.51 (0.26), residues: 1065 helix: 2.41 (0.29), residues: 341 sheet: 1.13 (0.31), residues: 289 loop : -0.21 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 130 HIS 0.010 0.002 HIS B 209 PHE 0.018 0.002 PHE C 151 TYR 0.010 0.002 TYR E 178 ARG 0.006 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.7380 (mmm) cc_final: 0.7052 (mtm) REVERT: B 22 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7956 (m110) REVERT: C 49 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8317 (mmt-90) REVERT: C 98 SER cc_start: 0.8493 (p) cc_final: 0.8200 (t) REVERT: C 258 ASP cc_start: 0.6905 (t0) cc_final: 0.6470 (t0) REVERT: C 289 TYR cc_start: 0.8444 (m-80) cc_final: 0.8123 (m-80) REVERT: E 132 THR cc_start: 0.8228 (t) cc_final: 0.7849 (m) outliers start: 20 outliers final: 13 residues processed: 175 average time/residue: 1.0553 time to fit residues: 197.2197 Evaluate side-chains 182 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 5 optimal weight: 0.0270 chunk 95 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 18 optimal weight: 0.0770 chunk 49 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 244 ASN C 75 GLN C 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.126605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.112548 restraints weight = 12107.264| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.81 r_work: 0.3374 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8328 Z= 0.176 Angle : 0.545 8.797 11351 Z= 0.291 Chirality : 0.043 0.137 1346 Planarity : 0.004 0.056 1424 Dihedral : 7.215 130.319 1236 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.32 % Allowed : 12.32 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.59 (0.27), residues: 1065 helix: 2.48 (0.29), residues: 342 sheet: 1.15 (0.31), residues: 290 loop : -0.15 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 130 HIS 0.007 0.001 HIS B 209 PHE 0.014 0.001 PHE C 151 TYR 0.011 0.001 TYR E 178 ARG 0.006 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.7208 (mmm) cc_final: 0.6990 (mtm) REVERT: B 22 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7870 (m110) REVERT: C 49 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8434 (tpp-160) REVERT: C 98 SER cc_start: 0.8502 (p) cc_final: 0.8200 (t) REVERT: C 258 ASP cc_start: 0.6888 (t0) cc_final: 0.6435 (t0) REVERT: C 289 TYR cc_start: 0.8420 (m-80) cc_final: 0.8059 (m-80) REVERT: E 132 THR cc_start: 0.8137 (t) cc_final: 0.7740 (m) REVERT: E 180 MET cc_start: 0.7833 (ttp) cc_final: 0.7476 (ttp) outliers start: 19 outliers final: 12 residues processed: 178 average time/residue: 1.1192 time to fit residues: 214.3008 Evaluate side-chains 184 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 58 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 33 optimal weight: 0.0470 chunk 8 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 244 ASN C 75 GLN C 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.124743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.110446 restraints weight = 12275.574| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.83 r_work: 0.3361 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8328 Z= 0.241 Angle : 0.589 9.581 11351 Z= 0.312 Chirality : 0.044 0.148 1346 Planarity : 0.004 0.058 1424 Dihedral : 7.321 132.818 1236 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.80 % Allowed : 12.68 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.40 (0.26), residues: 1065 helix: 2.28 (0.29), residues: 345 sheet: 1.13 (0.32), residues: 277 loop : -0.27 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 130 HIS 0.009 0.002 HIS B 209 PHE 0.018 0.002 PHE C 151 TYR 0.010 0.001 TYR E 178 ARG 0.006 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 323 MET cc_start: 0.7325 (mmm) cc_final: 0.7064 (mtm) REVERT: B 22 ASN cc_start: 0.8236 (OUTLIER) cc_final: 0.7951 (m110) REVERT: C 49 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8451 (tpp-160) REVERT: C 98 SER cc_start: 0.8507 (p) cc_final: 0.8210 (t) REVERT: C 258 ASP cc_start: 0.6970 (t0) cc_final: 0.6465 (t0) REVERT: C 289 TYR cc_start: 0.8445 (m-80) cc_final: 0.8104 (m-80) REVERT: E 132 THR cc_start: 0.8152 (t) cc_final: 0.7732 (m) outliers start: 23 outliers final: 14 residues processed: 182 average time/residue: 1.0363 time to fit residues: 201.4181 Evaluate side-chains 185 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 107 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 87 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 57 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 244 ASN C 75 GLN C 155 ASN C 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.125387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.111331 restraints weight = 12401.683| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.82 r_work: 0.3369 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8328 Z= 0.208 Angle : 0.571 9.861 11351 Z= 0.302 Chirality : 0.043 0.143 1346 Planarity : 0.004 0.056 1424 Dihedral : 7.254 132.254 1236 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.80 % Allowed : 13.17 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.44 (0.27), residues: 1065 helix: 2.37 (0.29), residues: 344 sheet: 1.15 (0.31), residues: 290 loop : -0.33 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 130 HIS 0.007 0.001 HIS B 209 PHE 0.016 0.002 PHE C 151 TYR 0.011 0.001 TYR E 178 ARG 0.006 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: B 22 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7897 (m110) REVERT: C 49 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8461 (tpp-160) REVERT: C 98 SER cc_start: 0.8491 (p) cc_final: 0.8197 (t) REVERT: C 155 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.7836 (t0) REVERT: C 258 ASP cc_start: 0.7009 (t0) cc_final: 0.6486 (t0) REVERT: C 289 TYR cc_start: 0.8448 (m-80) cc_final: 0.8026 (m-80) REVERT: E 132 THR cc_start: 0.8140 (t) cc_final: 0.7754 (m) REVERT: E 198 THR cc_start: 0.7689 (p) cc_final: 0.7471 (p) outliers start: 23 outliers final: 13 residues processed: 178 average time/residue: 1.0734 time to fit residues: 203.6964 Evaluate side-chains 187 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 79 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 244 ASN C 75 GLN C 155 ASN C 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.124843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.110744 restraints weight = 12560.159| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.83 r_work: 0.3359 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8328 Z= 0.233 Angle : 0.593 10.241 11351 Z= 0.312 Chirality : 0.044 0.147 1346 Planarity : 0.004 0.056 1424 Dihedral : 7.296 132.837 1236 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.32 % Allowed : 13.66 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.37 (0.27), residues: 1065 helix: 2.26 (0.29), residues: 345 sheet: 1.10 (0.32), residues: 279 loop : -0.29 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 130 HIS 0.009 0.001 HIS B 209 PHE 0.017 0.002 PHE C 151 TYR 0.010 0.002 TYR E 178 ARG 0.007 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: B 22 ASN cc_start: 0.8215 (OUTLIER) cc_final: 0.7936 (m110) REVERT: C 49 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8475 (tpp-160) REVERT: C 98 SER cc_start: 0.8484 (p) cc_final: 0.8210 (t) REVERT: C 155 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.7788 (t0) REVERT: C 258 ASP cc_start: 0.7050 (t0) cc_final: 0.6478 (t0) REVERT: C 314 ARG cc_start: 0.8205 (ttp80) cc_final: 0.7986 (ttp80) REVERT: E 132 THR cc_start: 0.8180 (t) cc_final: 0.7797 (m) outliers start: 19 outliers final: 15 residues processed: 175 average time/residue: 1.0778 time to fit residues: 201.1200 Evaluate side-chains 189 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 103 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 244 ASN C 75 GLN C 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.124580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.110582 restraints weight = 12253.127| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.81 r_work: 0.3358 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8328 Z= 0.237 Angle : 0.599 10.534 11351 Z= 0.315 Chirality : 0.044 0.151 1346 Planarity : 0.004 0.056 1424 Dihedral : 7.297 133.149 1236 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.07 % Allowed : 14.02 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.32 (0.26), residues: 1065 helix: 2.25 (0.29), residues: 345 sheet: 1.04 (0.32), residues: 279 loop : -0.34 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 130 HIS 0.009 0.002 HIS B 209 PHE 0.019 0.002 PHE C 151 TYR 0.011 0.002 TYR E 178 ARG 0.007 0.000 ARG B 185 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: B 22 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7939 (m110) REVERT: C 49 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8462 (tpp-160) REVERT: C 98 SER cc_start: 0.8497 (p) cc_final: 0.8213 (t) REVERT: C 258 ASP cc_start: 0.7097 (t0) cc_final: 0.6514 (t0) REVERT: C 289 TYR cc_start: 0.8385 (m-80) cc_final: 0.8127 (m-80) REVERT: C 314 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7999 (ttp80) outliers start: 17 outliers final: 15 residues processed: 176 average time/residue: 1.1079 time to fit residues: 207.5070 Evaluate side-chains 186 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 101 optimal weight: 0.0770 chunk 107 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN C 75 GLN C 155 ASN C 239 ASN E 35 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.126110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.112089 restraints weight = 12393.959| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.83 r_work: 0.3379 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8328 Z= 0.183 Angle : 0.566 10.509 11351 Z= 0.296 Chirality : 0.043 0.152 1346 Planarity : 0.004 0.056 1424 Dihedral : 7.180 131.690 1236 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.32 % Allowed : 14.15 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.42 (0.27), residues: 1065 helix: 2.42 (0.29), residues: 343 sheet: 1.08 (0.31), residues: 291 loop : -0.37 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 130 HIS 0.007 0.001 HIS B 209 PHE 0.015 0.001 PHE C 151 TYR 0.012 0.001 TYR E 178 ARG 0.007 0.000 ARG B 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6803.52 seconds wall clock time: 117 minutes 46.99 seconds (7066.99 seconds total)