Starting phenix.real_space_refine on Thu Jul 2 16:09:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nzm_12665/07_2026/7nzm_12665.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nzm_12665/07_2026/7nzm_12665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nzm_12665/07_2026/7nzm_12665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nzm_12665/07_2026/7nzm_12665.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7nzm_12665/07_2026/7nzm_12665.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nzm_12665/07_2026/7nzm_12665.cif" model { file = "/net/cci-nas-00/data/ceres_data/7nzm_12665/07_2026/7nzm_12665.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nzm_12665/07_2026/7nzm_12665.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 4 5.49 5 S 53 5.16 5 C 5776 2.51 5 N 1538 2.21 5 O 1737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9109 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1392 Classifications: {'peptide': 178} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 173} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2312 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 279} 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: {'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2884 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2024 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "C" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 437 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.04, per 1000 atoms: 0.22 Number of scatterers: 9109 At special positions: 0 Unit cell: (95.192, 110.84, 112.144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 53 16.00 P 4 15.00 O 1737 8.00 N 1538 7.00 C 5776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 69 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG F 1 " - " ASN D 18 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 346.3 milliseconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 13 sheets defined 46.8% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'E' and resid 55 through 66 removed outlier: 4.279A pdb=" N ILE E 58 " --> pdb=" O ILE E 55 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE E 62 " --> pdb=" O ASN E 59 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG E 63 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY E 65 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 118 removed outlier: 3.824A pdb=" N LYS E 96 " --> pdb=" O GLU E 92 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL E 117 " --> pdb=" O HIS E 113 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 133 Processing helix chain 'E' and resid 133 through 142 Processing helix chain 'E' and resid 145 through 155 removed outlier: 3.789A pdb=" N TYR E 149 " --> pdb=" O GLY E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 157 No H-bonds generated for 'chain 'E' and resid 156 through 157' Processing helix chain 'E' and resid 158 through 163 Processing helix chain 'E' and resid 168 through 181 removed outlier: 3.529A pdb=" N VAL E 174 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE E 179 " --> pdb=" O LEU E 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 19 removed outlier: 3.767A pdb=" N ILE B 12 " --> pdb=" O ASN B 8 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 42 through 49 removed outlier: 4.549A pdb=" N PHE B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 80 removed outlier: 3.788A pdb=" N GLU B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 114 Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 135 through 144 Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.545A pdb=" N THR B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP B 154 " --> pdb=" O LYS B 150 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'B' and resid 199 through 207 removed outlier: 3.595A pdb=" N LEU B 205 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 239 removed outlier: 3.525A pdb=" N LYS B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 235 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS B 239 " --> pdb=" O PHE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.645A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.568A pdb=" N LYS A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.614A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 197 removed outlier: 3.594A pdb=" N GLY A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 207 Processing helix chain 'A' and resid 207 through 217 removed outlier: 4.074A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.661A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 Proline residue: A 258 - end of helix removed outlier: 4.486A pdb=" N LEU A 261 " --> pdb=" O CYS A 257 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.564A pdb=" N CYS A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.928A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.533A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.880A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 368 through 374 removed outlier: 4.078A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 18 removed outlier: 3.833A pdb=" N ASN D 18 " --> pdb=" O THR D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 31 removed outlier: 3.645A pdb=" N ARG D 31 " --> pdb=" O ARG D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 56 Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 139 through 159 removed outlier: 4.237A pdb=" N TYR D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASP D 149 " --> pdb=" O ASN D 145 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL D 150 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU D 152 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS D 157 " --> pdb=" O ASP D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 183 removed outlier: 3.881A pdb=" N SER D 182 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 189 Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 234 through 240 Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'C' and resid 582 through 604 removed outlier: 3.564A pdb=" N ARG C 587 " --> pdb=" O GLU C 583 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP C 588 " --> pdb=" O GLN C 584 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C 591 " --> pdb=" O ARG C 587 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR C 597 " --> pdb=" O ALA C 593 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU C 602 " --> pdb=" O GLN C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 607 No H-bonds generated for 'chain 'C' and resid 605 through 607' Processing helix chain 'C' and resid 608 through 618 removed outlier: 3.743A pdb=" N ARG C 614 " --> pdb=" O ALA C 610 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TRP C 616 " --> pdb=" O ARG C 612 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA C 617 " --> pdb=" O ALA C 613 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 18 through 27 removed outlier: 6.708A pdb=" N TYR E 32 " --> pdb=" O ARG E 24 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ILE E 26 " --> pdb=" O GLY E 30 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLY E 30 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA E 31 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE E 82 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR E 81 " --> pdb=" O VAL E 75 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL E 75 " --> pdb=" O TYR E 81 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP E 83 " --> pdb=" O ILE E 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 118 through 120 removed outlier: 3.876A pdb=" N LEU B 59 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B 285 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N THR C 563 " --> pdb=" O CYS B 291 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE B 293 " --> pdb=" O THR C 563 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N HIS C 565 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE B 295 " --> pdb=" O HIS C 565 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 162 through 165 Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 209 removed outlier: 6.813A pdb=" N ASP B 208 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 244 through 246 removed outlier: 3.508A pdb=" N VAL B 264 " --> pdb=" O ILE B 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.656A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.745A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 42 through 44 removed outlier: 6.453A pdb=" N VAL A 43 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG D 79 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU D 39 " --> pdb=" O ARG D 79 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL D 40 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N THR D 10 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 255 " --> pdb=" O ALA D 5 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU D 256 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA D 231 " --> pdb=" O GLU D 256 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.650A pdb=" N ASN A 162 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET A 176 " --> pdb=" O ASN A 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.236A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 238 through 241 removed outlier: 3.501A pdb=" N LYS A 238 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR A 240 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 248 " --> pdb=" O TYR A 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 90 through 96 removed outlier: 7.459A pdb=" N LYS D 117 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N THR D 94 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL D 115 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA D 114 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE D 118 " --> pdb=" O PHE D 128 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE D 128 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N MET D 164 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ALA D 129 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N MET D 166 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N VAL D 131 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ASP D 168 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU D 133 " --> pdb=" O ASP D 168 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG D 213 " --> pdb=" O GLY D 167 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL D 216 " --> pdb=" O GLN D 193 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN D 193 " --> pdb=" O VAL D 216 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2587 1.33 - 1.45: 1632 1.45 - 1.57: 4997 1.57 - 1.70: 9 1.70 - 1.82: 80 Bond restraints: 9305 Sorted by residual: bond pdb=" C4 ATP A 401 " pdb=" C5 ATP A 401 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.11e+01 bond pdb=" C5 ATP A 401 " pdb=" C6 ATP A 401 " ideal model delta sigma weight residual 1.409 1.469 -0.060 1.00e-02 1.00e+04 3.61e+01 bond pdb=" C4 ATP A 401 " pdb=" N9 ATP A 401 " ideal model delta sigma weight residual 1.374 1.324 0.050 1.00e-02 1.00e+04 2.53e+01 bond pdb=" C5 ATP A 401 " pdb=" N7 ATP A 401 " ideal model delta sigma weight residual 1.387 1.337 0.050 1.00e-02 1.00e+04 2.51e+01 bond pdb=" C8 ATP A 401 " pdb=" N7 ATP A 401 " ideal model delta sigma weight residual 1.310 1.352 -0.042 1.00e-02 1.00e+04 1.80e+01 ... (remaining 9300 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.30: 12532 4.30 - 8.59: 94 8.59 - 12.89: 6 12.89 - 17.18: 1 17.18 - 21.48: 2 Bond angle restraints: 12635 Sorted by residual: angle pdb=" PA ATP A 401 " pdb=" O3A ATP A 401 " pdb=" PB ATP A 401 " ideal model delta sigma weight residual 136.83 115.35 21.48 1.00e+00 1.00e+00 4.61e+02 angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 118.69 21.18 1.00e+00 1.00e+00 4.49e+02 angle pdb=" C5 ATP A 401 " pdb=" C4 ATP A 401 " pdb=" N3 ATP A 401 " ideal model delta sigma weight residual 126.80 118.75 8.05 1.00e+00 1.00e+00 6.48e+01 angle pdb=" N3 ATP A 401 " pdb=" C4 ATP A 401 " pdb=" N9 ATP A 401 " ideal model delta sigma weight residual 127.04 134.93 -7.89 1.15e+00 7.59e-01 4.72e+01 angle pdb=" C ARG B 96 " pdb=" N GLY B 97 " pdb=" CA GLY B 97 " ideal model delta sigma weight residual 121.67 114.60 7.07 1.43e+00 4.89e-01 2.45e+01 ... (remaining 12630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 5072 18.00 - 36.00: 389 36.00 - 54.00: 68 54.00 - 72.00: 17 72.00 - 90.00: 10 Dihedral angle restraints: 5556 sinusoidal: 2174 harmonic: 3382 Sorted by residual: dihedral pdb=" CA LEU D 133 " pdb=" C LEU D 133 " pdb=" N HIS D 134 " pdb=" CA HIS D 134 " ideal model delta harmonic sigma weight residual 180.00 155.94 24.06 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CB CYS E 69 " pdb=" SG CYS E 69 " pdb=" SG CYS E 97 " pdb=" CB CYS E 97 " ideal model delta sinusoidal sigma weight residual 93.00 55.62 37.38 1 1.00e+01 1.00e-02 1.97e+01 dihedral pdb=" CA VAL A 43 " pdb=" C VAL A 43 " pdb=" N MET A 44 " pdb=" CA MET A 44 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 5553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1078 0.065 - 0.129: 295 0.129 - 0.194: 36 0.194 - 0.259: 4 0.259 - 0.323: 2 Chirality restraints: 1415 Sorted by residual: chirality pdb=" CA ARG B 96 " pdb=" N ARG B 96 " pdb=" C ARG B 96 " pdb=" CB ARG B 96 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA CYS A 257 " pdb=" N CYS A 257 " pdb=" C CYS A 257 " pdb=" CB CYS A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA GLU E 16 " pdb=" N GLU E 16 " pdb=" C GLU E 16 " pdb=" CB GLU E 16 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1412 not shown) Planarity restraints: 1628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 90 " 0.076 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO E 91 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO E 91 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO E 91 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 111 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO A 112 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 76 " 0.024 2.00e-02 2.50e+03 1.86e-02 6.91e+00 pdb=" CG TYR D 76 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR D 76 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR D 76 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 76 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 76 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 76 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 76 " 0.001 2.00e-02 2.50e+03 ... (remaining 1625 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 21 2.40 - 3.02: 5360 3.02 - 3.65: 12874 3.65 - 4.27: 19327 4.27 - 4.90: 32191 Nonbonded interactions: 69773 Sorted by model distance: nonbonded pdb=" OD2 ASP B 92 " pdb="MN MN B 401 " model vdw 1.774 2.320 nonbonded pdb=" ND1 HIS B 248 " pdb="MN MN B 401 " model vdw 1.926 2.400 nonbonded pdb=" NE2 HIS B 173 " pdb="MN MN B 401 " model vdw 1.993 2.400 nonbonded pdb=" CE1 HIS B 248 " pdb="MN MN B 401 " model vdw 1.999 2.540 nonbonded pdb=" O LEU B 38 " pdb=" OG SER B 42 " model vdw 2.110 3.040 ... (remaining 69768 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 group one per residue 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: 2.900 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.530 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5143 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 : 0.007 0.071 9309 Z= 0.317 Angle : 1.133 21.476 12645 Z= 0.687 Chirality : 0.058 0.323 1415 Planarity : 0.006 0.114 1627 Dihedral : 13.937 89.997 3372 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.22), residues: 1144 helix: -1.35 (0.21), residues: 406 sheet: -0.40 (0.37), residues: 166 loop : -0.87 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 132 TYR 0.045 0.004 TYR D 76 PHE 0.023 0.003 PHE D 109 TRP 0.040 0.004 TRP C 616 HIS 0.008 0.002 HIS B 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.32 ( 9305) covalent geometry : angle 1.12235 / 0.68 (12635) SS BOND : bond 0.00289 / 0.15 ( 2) SS BOND : angle 4.92792 / 2.46 ( 4) hydrogen bonds : bond 0.30250 / 20.24 ( 361) hydrogen bonds : angle 8.68867 / 5.98 ( 978) link_BETA1-4 : bond 0.01351 / 0.71 ( 1) link_BETA1-4 : angle 2.50220 / 1.28 ( 3) link_NAG-ASN : bond 0.00575 / 0.30 ( 1) link_NAG-ASN : angle 8.32327 / 4.69 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 603 LEU cc_start: 0.6489 (tp) cc_final: 0.6282 (tp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1167 time to fit residues: 18.0319 Evaluate side-chains 67 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 177 ASN B 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.039892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.033762 restraints weight = 113104.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.034672 restraints weight = 54493.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.035316 restraints weight = 32134.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.035720 restraints weight = 20835.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.035994 restraints weight = 14807.003| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9309 Z= 0.155 Angle : 0.724 12.079 12645 Z= 0.375 Chirality : 0.046 0.263 1415 Planarity : 0.005 0.081 1627 Dihedral : 5.464 52.703 1272 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.66 % Allowed : 6.44 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.24), residues: 1144 helix: 0.05 (0.24), residues: 442 sheet: -0.29 (0.35), residues: 169 loop : -0.18 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 612 TYR 0.016 0.002 TYR D 32 PHE 0.021 0.002 PHE B 225 TRP 0.011 0.001 TRP B 149 HIS 0.006 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 9305) covalent geometry : angle 0.72040 / 0.37 (12635) SS BOND : bond 0.00251 / 0.13 ( 2) SS BOND : angle 1.09111 / 0.59 ( 4) hydrogen bonds : bond 0.04980 / 3.29 ( 361) hydrogen bonds : angle 6.01922 / 4.20 ( 978) link_BETA1-4 : bond 0.00194 / 0.10 ( 1) link_BETA1-4 : angle 1.03793 / 0.50 ( 3) link_NAG-ASN : bond 0.00263 / 0.14 ( 1) link_NAG-ASN : angle 4.46560 / 2.40 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 GLU cc_start: 0.9369 (tt0) cc_final: 0.9007 (mm-30) REVERT: E 130 PHE cc_start: 0.9510 (m-80) cc_final: 0.9228 (m-80) REVERT: E 152 PHE cc_start: 0.9065 (m-80) cc_final: 0.8857 (m-80) REVERT: A 44 MET cc_start: 0.8036 (tpp) cc_final: 0.7685 (tpp) REVERT: A 119 MET cc_start: 0.9168 (mtp) cc_final: 0.8921 (ptp) REVERT: A 283 MET cc_start: 0.9247 (mmm) cc_final: 0.9041 (mmm) REVERT: A 297 ASN cc_start: 0.9447 (t0) cc_final: 0.8883 (t0) REVERT: A 305 MET cc_start: 0.9473 (OUTLIER) cc_final: 0.9061 (mmm) REVERT: A 345 ILE cc_start: 0.9843 (OUTLIER) cc_final: 0.9481 (pt) REVERT: A 346 LEU cc_start: 0.9886 (tp) cc_final: 0.9680 (tp) REVERT: D 16 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8660 (ttm) outliers start: 16 outliers final: 6 residues processed: 79 average time/residue: 0.1033 time to fit residues: 11.6411 Evaluate side-chains 68 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 156 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 59 optimal weight: 9.9990 chunk 105 optimal weight: 30.0000 chunk 39 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 46 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.026681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.019308 restraints weight = 110216.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.020019 restraints weight = 69270.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.020592 restraints weight = 50102.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.021021 restraints weight = 38457.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.021318 restraints weight = 31270.042| |-----------------------------------------------------------------------------| r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9309 Z= 0.194 Angle : 0.658 8.723 12645 Z= 0.344 Chirality : 0.043 0.184 1415 Planarity : 0.004 0.070 1627 Dihedral : 5.237 53.731 1272 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.08 % Allowed : 7.90 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.24), residues: 1144 helix: 0.23 (0.24), residues: 454 sheet: 0.08 (0.38), residues: 156 loop : 0.05 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 256 TYR 0.015 0.002 TYR D 32 PHE 0.017 0.002 PHE B 225 TRP 0.009 0.001 TRP B 149 HIS 0.007 0.002 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 ( 9305) covalent geometry : angle 0.65406 / 0.34 (12635) SS BOND : bond 0.00215 / 0.11 ( 2) SS BOND : angle 1.10866 / 0.62 ( 4) hydrogen bonds : bond 0.04243 / 2.87 ( 361) hydrogen bonds : angle 5.61207 / 3.89 ( 978) link_BETA1-4 : bond 0.01224 / 0.64 ( 1) link_BETA1-4 : angle 2.23107 / 1.20 ( 3) link_NAG-ASN : bond 0.00436 / 0.23 ( 1) link_NAG-ASN : angle 4.00416 / 2.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 44 MET cc_start: 0.8856 (tpp) cc_final: 0.8209 (tpp) REVERT: E 81 TYR cc_start: 0.9046 (m-10) cc_final: 0.8760 (m-80) REVERT: E 127 GLU cc_start: 0.9411 (tt0) cc_final: 0.9045 (mm-30) REVERT: E 130 PHE cc_start: 0.9577 (m-80) cc_final: 0.9193 (m-80) REVERT: A 123 MET cc_start: 0.9559 (mmm) cc_final: 0.9136 (tpp) REVERT: A 176 MET cc_start: 0.7660 (tmm) cc_final: 0.7185 (tmm) REVERT: A 190 MET cc_start: 0.9372 (ptm) cc_final: 0.9113 (ppp) REVERT: A 283 MET cc_start: 0.9424 (mmm) cc_final: 0.9199 (mmm) REVERT: A 305 MET cc_start: 0.9539 (OUTLIER) cc_final: 0.9174 (mmm) REVERT: A 313 MET cc_start: 0.9465 (mmm) cc_final: 0.9173 (mmm) REVERT: D 16 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8763 (ttm) REVERT: D 164 MET cc_start: 0.9672 (ppp) cc_final: 0.9434 (tmm) outliers start: 20 outliers final: 9 residues processed: 71 average time/residue: 0.0950 time to fit residues: 9.8225 Evaluate side-chains 63 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 156 GLN Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain C residue 561 LYS Chi-restraints excluded: chain C residue 602 GLU Chi-restraints excluded: chain C residue 607 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 9 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 33 optimal weight: 30.0000 chunk 59 optimal weight: 5.9990 chunk 104 optimal weight: 30.0000 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 0.0870 chunk 100 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 68 GLN D 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.025514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.018331 restraints weight = 112871.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.019076 restraints weight = 70179.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.019624 restraints weight = 49618.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.020028 restraints weight = 38089.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.020337 restraints weight = 31035.222| |-----------------------------------------------------------------------------| r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9309 Z= 0.152 Angle : 0.590 9.090 12645 Z= 0.305 Chirality : 0.042 0.161 1415 Planarity : 0.004 0.064 1627 Dihedral : 4.979 61.230 1272 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.08 % Allowed : 9.56 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.25), residues: 1144 helix: 0.57 (0.25), residues: 447 sheet: 0.04 (0.40), residues: 156 loop : 0.35 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 6 TYR 0.014 0.001 TYR D 32 PHE 0.016 0.001 PHE B 225 TRP 0.015 0.002 TRP E 135 HIS 0.006 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 ( 9305) covalent geometry : angle 0.58707 / 0.30 (12635) SS BOND : bond 0.00252 / 0.13 ( 2) SS BOND : angle 0.83365 / 0.47 ( 4) hydrogen bonds : bond 0.03517 / 2.40 ( 361) hydrogen bonds : angle 5.29116 / 3.65 ( 978) link_BETA1-4 : bond 0.00425 / 0.22 ( 1) link_BETA1-4 : angle 1.19578 / 0.65 ( 3) link_NAG-ASN : bond 0.00138 / 0.07 ( 1) link_NAG-ASN : angle 3.86126 / 2.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 44 MET cc_start: 0.9024 (tpp) cc_final: 0.8641 (tpp) REVERT: E 81 TYR cc_start: 0.9047 (m-10) cc_final: 0.8752 (m-80) REVERT: E 127 GLU cc_start: 0.9369 (tt0) cc_final: 0.9088 (mm-30) REVERT: E 130 PHE cc_start: 0.9471 (m-80) cc_final: 0.9204 (m-80) REVERT: E 152 PHE cc_start: 0.9411 (m-80) cc_final: 0.9206 (m-80) REVERT: A 123 MET cc_start: 0.9580 (mmm) cc_final: 0.9181 (tpp) REVERT: A 190 MET cc_start: 0.9400 (ptm) cc_final: 0.9122 (ppp) REVERT: A 299 MET cc_start: 0.9305 (mmm) cc_final: 0.8423 (tpp) REVERT: A 305 MET cc_start: 0.9598 (mmt) cc_final: 0.9210 (mmm) REVERT: A 313 MET cc_start: 0.9662 (mmm) cc_final: 0.9312 (mmm) REVERT: D 91 VAL cc_start: 0.9378 (OUTLIER) cc_final: 0.9151 (t) REVERT: C 560 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8405 (pm20) outliers start: 20 outliers final: 7 residues processed: 74 average time/residue: 0.0988 time to fit residues: 10.5189 Evaluate side-chains 62 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 156 GLN Chi-restraints excluded: chain C residue 560 GLU Chi-restraints excluded: chain C residue 602 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 61 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 85 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 overall best weight: 4.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 113 HIS E 177 ASN B 239 HIS D 155 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.024412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.017400 restraints weight = 117599.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.018139 restraints weight = 72058.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.018633 restraints weight = 50346.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.019032 restraints weight = 39015.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.019303 restraints weight = 31870.305| |-----------------------------------------------------------------------------| r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9309 Z= 0.206 Angle : 0.646 9.268 12645 Z= 0.333 Chirality : 0.042 0.166 1415 Planarity : 0.004 0.064 1627 Dihedral : 5.061 61.610 1272 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.04 % Allowed : 12.37 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.25), residues: 1144 helix: 0.51 (0.24), residues: 458 sheet: 0.03 (0.42), residues: 147 loop : 0.35 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 79 TYR 0.016 0.002 TYR D 175 PHE 0.014 0.001 PHE B 225 TRP 0.011 0.001 TRP B 149 HIS 0.006 0.001 HIS B 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.21 ( 9305) covalent geometry : angle 0.64261 / 0.33 (12635) SS BOND : bond 0.00232 / 0.12 ( 2) SS BOND : angle 0.84102 / 0.48 ( 4) hydrogen bonds : bond 0.03756 / 2.59 ( 361) hydrogen bonds : angle 5.38681 / 3.71 ( 978) link_BETA1-4 : bond 0.00413 / 0.22 ( 1) link_BETA1-4 : angle 1.78509 / 0.98 ( 3) link_NAG-ASN : bond 0.00373 / 0.20 ( 1) link_NAG-ASN : angle 3.89227 / 2.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 LYS cc_start: 0.9515 (ttmt) cc_final: 0.9261 (mmtt) REVERT: E 81 TYR cc_start: 0.9242 (m-10) cc_final: 0.8909 (m-80) REVERT: E 127 GLU cc_start: 0.9433 (tt0) cc_final: 0.8997 (mm-30) REVERT: E 130 PHE cc_start: 0.9528 (m-80) cc_final: 0.9109 (m-80) REVERT: A 47 MET cc_start: 0.9504 (mmm) cc_final: 0.9247 (ppp) REVERT: A 123 MET cc_start: 0.9566 (mmm) cc_final: 0.9248 (tpp) REVERT: A 176 MET cc_start: 0.7719 (tmm) cc_final: 0.7428 (tmm) REVERT: A 299 MET cc_start: 0.9281 (mmm) cc_final: 0.8721 (mmm) REVERT: A 305 MET cc_start: 0.9551 (mmt) cc_final: 0.9248 (mmm) REVERT: A 313 MET cc_start: 0.9676 (mmm) cc_final: 0.9306 (mmm) REVERT: D 83 LEU cc_start: 0.9919 (mt) cc_final: 0.9487 (tp) REVERT: D 91 VAL cc_start: 0.9380 (OUTLIER) cc_final: 0.9166 (t) REVERT: D 102 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: D 164 MET cc_start: 0.9658 (ppp) cc_final: 0.9456 (tmm) outliers start: 10 outliers final: 5 residues processed: 63 average time/residue: 0.1022 time to fit residues: 9.2553 Evaluate side-chains 61 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain C residue 602 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 11 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 59 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 294 GLN ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.022907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2363 r_free = 0.2363 target = 0.016302 restraints weight = 122645.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2400 r_free = 0.2400 target = 0.017002 restraints weight = 73127.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.017520 restraints weight = 50500.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.017898 restraints weight = 38256.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.018187 restraints weight = 30898.683| |-----------------------------------------------------------------------------| r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.5938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9309 Z= 0.246 Angle : 0.686 9.212 12645 Z= 0.358 Chirality : 0.043 0.177 1415 Planarity : 0.005 0.063 1627 Dihedral : 5.386 65.339 1272 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.87 % Allowed : 11.75 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.25), residues: 1144 helix: 0.24 (0.24), residues: 450 sheet: -0.32 (0.41), residues: 157 loop : 0.51 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 79 TYR 0.022 0.002 TYR D 32 PHE 0.019 0.002 PHE B 293 TRP 0.012 0.002 TRP B 206 HIS 0.008 0.002 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.25 ( 9305) covalent geometry : angle 0.68327 / 0.36 (12635) SS BOND : bond 0.00276 / 0.15 ( 2) SS BOND : angle 0.76414 / 0.43 ( 4) hydrogen bonds : bond 0.03793 / 2.62 ( 361) hydrogen bonds : angle 5.67853 / 3.89 ( 978) link_BETA1-4 : bond 0.00548 / 0.29 ( 1) link_BETA1-4 : angle 1.67645 / 0.90 ( 3) link_NAG-ASN : bond 0.00161 / 0.08 ( 1) link_NAG-ASN : angle 3.98560 / 2.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 TYR cc_start: 0.9350 (m-10) cc_final: 0.8937 (m-80) REVERT: E 127 GLU cc_start: 0.9443 (OUTLIER) cc_final: 0.9241 (pp20) REVERT: E 130 PHE cc_start: 0.9525 (m-80) cc_final: 0.9322 (m-80) REVERT: B 117 ASN cc_start: 0.9190 (OUTLIER) cc_final: 0.7707 (t0) REVERT: B 283 MET cc_start: 0.8800 (tpp) cc_final: 0.8365 (tpp) REVERT: A 47 MET cc_start: 0.9608 (mmm) cc_final: 0.9337 (mmm) REVERT: A 123 MET cc_start: 0.9585 (mmm) cc_final: 0.9274 (tpp) REVERT: A 299 MET cc_start: 0.9201 (mmm) cc_final: 0.8647 (mmm) REVERT: A 305 MET cc_start: 0.9568 (mmt) cc_final: 0.9244 (mmm) REVERT: A 313 MET cc_start: 0.9674 (mmm) cc_final: 0.9296 (mmm) REVERT: D 102 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7797 (mp0) outliers start: 18 outliers final: 9 residues processed: 66 average time/residue: 0.0924 time to fit residues: 9.0783 Evaluate side-chains 61 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 173 CYS Chi-restraints excluded: chain C residue 602 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 34 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 112 optimal weight: 0.0670 chunk 82 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.023007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2365 r_free = 0.2365 target = 0.016327 restraints weight = 121677.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2405 r_free = 0.2405 target = 0.017051 restraints weight = 72020.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.017572 restraints weight = 49710.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.017958 restraints weight = 37679.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.018244 restraints weight = 30509.961| |-----------------------------------------------------------------------------| r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.6168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9309 Z= 0.173 Angle : 0.639 9.828 12645 Z= 0.325 Chirality : 0.042 0.184 1415 Planarity : 0.004 0.063 1627 Dihedral : 5.143 67.367 1272 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.25 % Allowed : 13.41 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.25), residues: 1144 helix: 0.52 (0.24), residues: 454 sheet: -0.31 (0.41), residues: 155 loop : 0.49 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 28 TYR 0.016 0.001 TYR D 175 PHE 0.013 0.001 PHE B 225 TRP 0.012 0.001 TRP C 582 HIS 0.007 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 ( 9305) covalent geometry : angle 0.63572 / 0.32 (12635) SS BOND : bond 0.00306 / 0.16 ( 2) SS BOND : angle 0.64085 / 0.36 ( 4) hydrogen bonds : bond 0.03457 / 2.35 ( 361) hydrogen bonds : angle 5.49172 / 3.77 ( 978) link_BETA1-4 : bond 0.00146 / 0.08 ( 1) link_BETA1-4 : angle 1.16218 / 0.64 ( 3) link_NAG-ASN : bond 0.00241 / 0.13 ( 1) link_NAG-ASN : angle 4.11222 / 2.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 44 MET cc_start: 0.8944 (mmm) cc_final: 0.8375 (mmm) REVERT: E 81 TYR cc_start: 0.9370 (m-10) cc_final: 0.8969 (m-80) REVERT: E 84 LEU cc_start: 0.9544 (mp) cc_final: 0.9172 (mp) REVERT: E 127 GLU cc_start: 0.9425 (OUTLIER) cc_final: 0.9211 (pp20) REVERT: E 130 PHE cc_start: 0.9481 (m-80) cc_final: 0.9248 (m-80) REVERT: B 283 MET cc_start: 0.8842 (tpp) cc_final: 0.8441 (tpp) REVERT: A 123 MET cc_start: 0.9482 (mmm) cc_final: 0.9212 (tpp) REVERT: A 176 MET cc_start: 0.7866 (tmm) cc_final: 0.7578 (tmm) REVERT: A 299 MET cc_start: 0.9216 (mmm) cc_final: 0.8692 (mmm) REVERT: A 305 MET cc_start: 0.9552 (mmt) cc_final: 0.9254 (mmm) REVERT: A 313 MET cc_start: 0.9660 (mmm) cc_final: 0.9255 (mmm) outliers start: 12 outliers final: 6 residues processed: 62 average time/residue: 0.0873 time to fit residues: 8.1644 Evaluate side-chains 56 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain C residue 602 GLU Chi-restraints excluded: chain C residue 603 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 42 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 82 optimal weight: 0.0770 chunk 6 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.023210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2371 r_free = 0.2371 target = 0.016414 restraints weight = 119772.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.017163 restraints weight = 71631.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.017694 restraints weight = 49205.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.018083 restraints weight = 37396.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.018377 restraints weight = 30329.660| |-----------------------------------------------------------------------------| r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.6272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9309 Z= 0.126 Angle : 0.632 10.182 12645 Z= 0.315 Chirality : 0.042 0.144 1415 Planarity : 0.004 0.064 1627 Dihedral : 4.935 66.532 1272 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.25 % Allowed : 13.83 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.25), residues: 1144 helix: 0.72 (0.25), residues: 455 sheet: -0.29 (0.42), residues: 155 loop : 0.47 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 79 TYR 0.012 0.001 TYR D 175 PHE 0.012 0.001 PHE B 225 TRP 0.017 0.001 TRP A 79 HIS 0.008 0.001 HIS B 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 9305) covalent geometry : angle 0.62858 / 0.31 (12635) SS BOND : bond 0.00302 / 0.16 ( 2) SS BOND : angle 0.55033 / 0.31 ( 4) hydrogen bonds : bond 0.03208 / 2.20 ( 361) hydrogen bonds : angle 5.22137 / 3.57 ( 978) link_BETA1-4 : bond 0.00284 / 0.15 ( 1) link_BETA1-4 : angle 1.40663 / 0.76 ( 3) link_NAG-ASN : bond 0.00028 / 0.01 ( 1) link_NAG-ASN : angle 3.85837 / 2.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 TYR cc_start: 0.9369 (m-10) cc_final: 0.8979 (m-80) REVERT: E 130 PHE cc_start: 0.9468 (m-80) cc_final: 0.9224 (m-80) REVERT: B 283 MET cc_start: 0.8862 (tpp) cc_final: 0.8493 (tpp) REVERT: A 140 LEU cc_start: 0.9744 (OUTLIER) cc_final: 0.9501 (mm) REVERT: A 176 MET cc_start: 0.7805 (tmm) cc_final: 0.7490 (tmm) REVERT: A 190 MET cc_start: 0.9483 (ptm) cc_final: 0.9189 (ppp) REVERT: A 299 MET cc_start: 0.9280 (mmm) cc_final: 0.8761 (mmm) REVERT: A 305 MET cc_start: 0.9582 (mmt) cc_final: 0.9246 (mmm) REVERT: D 16 MET cc_start: 0.9074 (ppp) cc_final: 0.8804 (ppp) outliers start: 12 outliers final: 8 residues processed: 63 average time/residue: 0.0885 time to fit residues: 8.0753 Evaluate side-chains 60 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain C residue 602 GLU Chi-restraints excluded: chain C residue 603 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.022675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2361 r_free = 0.2361 target = 0.016109 restraints weight = 122367.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2399 r_free = 0.2399 target = 0.016822 restraints weight = 73344.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.017335 restraints weight = 50721.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.017700 restraints weight = 38617.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.017997 restraints weight = 31406.966| |-----------------------------------------------------------------------------| r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.6660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9309 Z= 0.177 Angle : 0.674 9.985 12645 Z= 0.336 Chirality : 0.042 0.161 1415 Planarity : 0.004 0.062 1627 Dihedral : 5.064 66.285 1272 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.14 % Allowed : 14.35 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.25), residues: 1144 helix: 0.62 (0.24), residues: 457 sheet: -0.39 (0.41), residues: 162 loop : 0.38 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 143 TYR 0.016 0.001 TYR D 32 PHE 0.013 0.002 PHE B 225 TRP 0.014 0.001 TRP A 79 HIS 0.008 0.002 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 ( 9305) covalent geometry : angle 0.67079 / 0.34 (12635) SS BOND : bond 0.00315 / 0.17 ( 2) SS BOND : angle 0.55752 / 0.32 ( 4) hydrogen bonds : bond 0.03298 / 2.27 ( 361) hydrogen bonds : angle 5.36482 / 3.67 ( 978) link_BETA1-4 : bond 0.00207 / 0.11 ( 1) link_BETA1-4 : angle 1.48318 / 0.82 ( 3) link_NAG-ASN : bond 0.00235 / 0.12 ( 1) link_NAG-ASN : angle 3.93487 / 2.17 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 TYR cc_start: 0.9423 (m-10) cc_final: 0.8947 (m-80) REVERT: E 130 PHE cc_start: 0.9503 (m-80) cc_final: 0.9180 (m-80) REVERT: B 282 MET cc_start: 0.8377 (tmm) cc_final: 0.7256 (tmm) REVERT: B 283 MET cc_start: 0.8860 (tpp) cc_final: 0.8400 (tpp) REVERT: A 140 LEU cc_start: 0.9780 (OUTLIER) cc_final: 0.9555 (mm) REVERT: A 176 MET cc_start: 0.7939 (tmm) cc_final: 0.7615 (tmm) REVERT: A 299 MET cc_start: 0.9202 (mmm) cc_final: 0.8685 (mmm) REVERT: A 305 MET cc_start: 0.9566 (mmt) cc_final: 0.9249 (mmm) REVERT: A 313 MET cc_start: 0.9715 (mmm) cc_final: 0.9245 (mmm) REVERT: D 16 MET cc_start: 0.9006 (ppp) cc_final: 0.8723 (ppp) REVERT: C 588 ASP cc_start: 0.9486 (p0) cc_final: 0.9190 (p0) outliers start: 11 outliers final: 9 residues processed: 56 average time/residue: 0.0840 time to fit residues: 7.1730 Evaluate side-chains 57 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain C residue 602 GLU Chi-restraints excluded: chain C residue 603 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 106 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 14 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.023324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2381 r_free = 0.2381 target = 0.016462 restraints weight = 116698.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.017204 restraints weight = 70419.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.017736 restraints weight = 48766.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.018139 restraints weight = 37141.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.018434 restraints weight = 30117.105| |-----------------------------------------------------------------------------| r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.6593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 9309 Z= 0.104 Angle : 0.655 10.252 12645 Z= 0.316 Chirality : 0.042 0.144 1415 Planarity : 0.003 0.060 1627 Dihedral : 4.791 67.258 1272 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.94 % Allowed : 14.45 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.25), residues: 1144 helix: 0.95 (0.25), residues: 448 sheet: -0.24 (0.42), residues: 160 loop : 0.37 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 28 TYR 0.011 0.001 TYR A 306 PHE 0.011 0.001 PHE B 225 TRP 0.016 0.001 TRP A 79 HIS 0.007 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 ( 9305) covalent geometry : angle 0.65234 / 0.32 (12635) SS BOND : bond 0.00324 / 0.17 ( 2) SS BOND : angle 0.48203 / 0.27 ( 4) hydrogen bonds : bond 0.03057 / 2.08 ( 361) hydrogen bonds : angle 5.06165 / 3.48 ( 978) link_BETA1-4 : bond 0.00479 / 0.25 ( 1) link_BETA1-4 : angle 1.07045 / 0.59 ( 3) link_NAG-ASN : bond 0.00047 / 0.02 ( 1) link_NAG-ASN : angle 3.89403 / 2.13 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 TYR cc_start: 0.9369 (m-10) cc_final: 0.8999 (m-80) REVERT: E 130 PHE cc_start: 0.9429 (m-80) cc_final: 0.9171 (m-80) REVERT: B 282 MET cc_start: 0.8321 (tmm) cc_final: 0.7226 (tmm) REVERT: B 283 MET cc_start: 0.8835 (tpp) cc_final: 0.8388 (tpp) REVERT: A 140 LEU cc_start: 0.9725 (OUTLIER) cc_final: 0.9460 (mm) REVERT: A 176 MET cc_start: 0.7832 (tmm) cc_final: 0.7497 (tmm) REVERT: A 190 MET cc_start: 0.9485 (ptm) cc_final: 0.9184 (ppp) REVERT: A 299 MET cc_start: 0.9298 (mmm) cc_final: 0.8815 (mmm) REVERT: A 305 MET cc_start: 0.9569 (mmt) cc_final: 0.9262 (mmm) REVERT: A 325 MET cc_start: 0.8955 (tpp) cc_final: 0.8695 (tpp) REVERT: D 16 MET cc_start: 0.8953 (ppp) cc_final: 0.8653 (ppp) outliers start: 9 outliers final: 8 residues processed: 60 average time/residue: 0.0892 time to fit residues: 8.0896 Evaluate side-chains 57 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain C residue 602 GLU Chi-restraints excluded: chain C residue 603 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 63 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 26 optimal weight: 0.5980 chunk 90 optimal weight: 30.0000 chunk 102 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.022789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2364 r_free = 0.2364 target = 0.016111 restraints weight = 117607.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2402 r_free = 0.2402 target = 0.016821 restraints weight = 71303.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.017341 restraints weight = 49606.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.017718 restraints weight = 37892.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.017995 restraints weight = 30818.791| |-----------------------------------------------------------------------------| r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.6751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9309 Z= 0.138 Angle : 0.657 9.566 12645 Z= 0.324 Chirality : 0.042 0.151 1415 Planarity : 0.004 0.061 1627 Dihedral : 4.800 66.166 1272 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.04 % Allowed : 14.55 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.25), residues: 1144 helix: 0.90 (0.25), residues: 451 sheet: -0.22 (0.41), residues: 162 loop : 0.45 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 595 TYR 0.011 0.001 TYR D 32 PHE 0.011 0.001 PHE B 225 TRP 0.016 0.001 TRP A 79 HIS 0.007 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 9305) covalent geometry : angle 0.65389 / 0.32 (12635) SS BOND : bond 0.00482 / 0.25 ( 2) SS BOND : angle 0.58509 / 0.34 ( 4) hydrogen bonds : bond 0.03190 / 2.21 ( 361) hydrogen bonds : angle 5.18895 / 3.55 ( 978) link_BETA1-4 : bond 0.00148 / 0.08 ( 1) link_BETA1-4 : angle 1.20556 / 0.67 ( 3) link_NAG-ASN : bond 0.00126 / 0.07 ( 1) link_NAG-ASN : angle 3.92957 / 2.13 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1493.58 seconds wall clock time: 26 minutes 41.26 seconds (1601.26 seconds total)