Starting phenix.real_space_refine on Wed Sep 17 14:53:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nzm_12665/09_2025/7nzm_12665.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nzm_12665/09_2025/7nzm_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_12665/09_2025/7nzm_12665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nzm_12665/09_2025/7nzm_12665.map" model { file = "/net/cci-nas-00/data/ceres_data/7nzm_12665/09_2025/7nzm_12665.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nzm_12665/09_2025/7nzm_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-2.0-5805/lib/python3.9/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 dihedrals: 6 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: 2.40, per 1000 atoms: 0.26 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: 0.87 Conformation dependent library (CDL) restraints added in 362.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.38 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: 1.76 Time building geometry restraints manager: 1.08 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: 5118 18.00 - 36.00: 402 36.00 - 54.00: 79 54.00 - 72.00: 19 72.00 - 90.00: 11 Dihedral angle restraints: 5629 sinusoidal: 2247 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 5626 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: 3.450 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.500 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5464 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 : 14.316 89.997 3445 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 aren 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 covalent geometry : bond 0.00662 ( 9305) covalent geometry : angle 1.12235 (12635) SS BOND : bond 0.00289 ( 2) SS BOND : angle 4.92792 ( 4) hydrogen bonds : bond 0.30250 ( 361) hydrogen bonds : angle 8.68867 ( 978) link_BETA1-4 : bond 0.01351 ( 1) link_BETA1-4 : angle 2.50220 ( 3) link_NAG-ASN : bond 0.00575 ( 1) link_NAG-ASN : angle 8.32327 ( 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 : 0.396 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: 0.1351 time to fit residues: 20.6457 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 : 0.375 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: E 59 ASN E 177 ASN B 117 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.029456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.021569 restraints weight = 106437.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.022413 restraints weight = 67007.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.023025 restraints weight = 47381.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.023447 restraints weight = 36381.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.023808 restraints weight = 29887.201| |-----------------------------------------------------------------------------| r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9309 Z= 0.157 Angle : 0.723 12.230 12645 Z= 0.374 Chirality : 0.046 0.270 1415 Planarity : 0.005 0.082 1627 Dihedral : 7.159 88.905 1345 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.56 % Allowed : 6.96 % Favored : 91.48 % 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 aren not related in a simple way. whole: -0.30 (0.24), residues: 1144 helix: 0.02 (0.24), residues: 442 sheet: -0.28 (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 B 144 PHE 0.020 0.001 PHE B 225 TRP 0.012 0.001 TRP A 356 HIS 0.007 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9305) covalent geometry : angle 0.71880 (12635) SS BOND : bond 0.00084 ( 2) SS BOND : angle 1.16227 ( 4) hydrogen bonds : bond 0.05062 ( 361) hydrogen bonds : angle 6.03097 ( 978) link_BETA1-4 : bond 0.01106 ( 1) link_BETA1-4 : angle 1.22387 ( 3) link_NAG-ASN : bond 0.00530 ( 1) link_NAG-ASN : angle 4.82695 ( 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 83 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.459 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: 0.9417 (tt0) cc_final: 0.9018 (mm-30) REVERT: E 130 PHE cc_start: 0.9635 (m-80) cc_final: 0.9344 (m-80) REVERT: E 152 PHE cc_start: 0.9233 (m-80) cc_final: 0.9020 (m-80) REVERT: A 44 MET cc_start: 0.8134 (tpp) cc_final: 0.7251 (tpp) REVERT: A 119 MET cc_start: 0.9252 (mtp) cc_final: 0.8989 (ptp) REVERT: A 132 MET cc_start: 0.9498 (ptm) cc_final: 0.9296 (ppp) REVERT: A 297 ASN cc_start: 0.9632 (t0) cc_final: 0.9195 (t0) REVERT: A 299 MET cc_start: 0.9105 (mtm) cc_final: 0.8865 (mmp) REVERT: A 305 MET cc_start: 0.9592 (mmt) cc_final: 0.9078 (mmm) REVERT: A 345 ILE cc_start: 0.9837 (OUTLIER) cc_final: 0.9488 (pt) REVERT: A 346 LEU cc_start: 0.9867 (tp) cc_final: 0.9659 (tp) REVERT: D 16 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8851 (ttm) REVERT: D 69 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8848 (mm-30) outliers start: 15 outliers final: 7 residues processed: 80 average time/residue: 0.1067 time to fit residues: 12.1175 Evaluate side-chains 67 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain B residue 75 LEU 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 Chi-restraints excluded: chain C residue 602 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 59 optimal weight: 10.0000 chunk 105 optimal weight: 30.0000 chunk 39 optimal weight: 30.0000 chunk 94 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 33 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 40 HIS A 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.025740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.018609 restraints weight = 115490.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.019346 restraints weight = 71033.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.019898 restraints weight = 50117.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.020303 restraints weight = 38286.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.020608 restraints weight = 31149.011| |-----------------------------------------------------------------------------| r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9309 Z= 0.231 Angle : 0.700 9.241 12645 Z= 0.370 Chirality : 0.044 0.286 1415 Planarity : 0.005 0.073 1627 Dihedral : 6.874 86.211 1345 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.08 % Allowed : 8.21 % Favored : 89.71 % 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 aren not related in a simple way. whole: 0.03 (0.24), residues: 1144 helix: 0.11 (0.23), residues: 448 sheet: -0.12 (0.38), residues: 161 loop : 0.20 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 143 TYR 0.019 0.002 TYR D 32 PHE 0.019 0.002 PHE B 225 TRP 0.010 0.001 TRP B 149 HIS 0.009 0.002 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 9305) covalent geometry : angle 0.69607 (12635) SS BOND : bond 0.00240 ( 2) SS BOND : angle 1.22417 ( 4) hydrogen bonds : bond 0.04360 ( 361) hydrogen bonds : angle 5.77835 ( 978) link_BETA1-4 : bond 0.00401 ( 1) link_BETA1-4 : angle 2.33379 ( 3) link_NAG-ASN : bond 0.00620 ( 1) link_NAG-ASN : angle 4.24835 ( 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 77 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.395 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: E 81 TYR cc_start: 0.9114 (m-10) cc_final: 0.8802 (m-80) REVERT: E 127 GLU cc_start: 0.9422 (tt0) cc_final: 0.8982 (mm-30) REVERT: E 130 PHE cc_start: 0.9602 (m-80) cc_final: 0.9235 (m-80) REVERT: A 47 MET cc_start: 0.9399 (mmm) cc_final: 0.9161 (mmm) REVERT: A 123 MET cc_start: 0.9664 (mmm) cc_final: 0.9185 (tpp) REVERT: A 305 MET cc_start: 0.9534 (mmt) cc_final: 0.9169 (mmm) REVERT: A 325 MET cc_start: 0.8811 (tpp) cc_final: 0.8597 (tpp) REVERT: D 16 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8727 (ttm) REVERT: D 83 LEU cc_start: 0.9922 (mt) cc_final: 0.9518 (tp) REVERT: D 164 MET cc_start: 0.9674 (ppp) cc_final: 0.9441 (ppp) outliers start: 20 outliers final: 9 residues processed: 73 average time/residue: 0.1038 time to fit residues: 10.9266 Evaluate side-chains 64 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain A residue 152 VAL 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 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: 5.9990 chunk 15 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 104 optimal weight: 30.0000 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 78 optimal weight: 0.0670 overall best weight: 5.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 HIS E 177 ASN B 68 GLN B 239 HIS ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN D 156 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.024269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2403 r_free = 0.2403 target = 0.017378 restraints weight = 121306.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2440 r_free = 0.2440 target = 0.018107 restraints weight = 73030.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.018638 restraints weight = 50747.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.018990 restraints weight = 38580.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.019288 restraints weight = 31568.253| |-----------------------------------------------------------------------------| r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 9309 Z= 0.222 Angle : 0.651 9.963 12645 Z= 0.342 Chirality : 0.042 0.164 1415 Planarity : 0.004 0.063 1627 Dihedral : 6.874 88.207 1345 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.87 % Allowed : 10.91 % Favored : 87.21 % 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 aren not related in a simple way. whole: 0.25 (0.24), residues: 1144 helix: 0.23 (0.24), residues: 442 sheet: 0.02 (0.41), residues: 146 loop : 0.35 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 143 TYR 0.020 0.002 TYR D 32 PHE 0.016 0.002 PHE B 225 TRP 0.009 0.001 TRP B 149 HIS 0.010 0.002 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 9305) covalent geometry : angle 0.64772 (12635) SS BOND : bond 0.00271 ( 2) SS BOND : angle 0.87618 ( 4) hydrogen bonds : bond 0.03892 ( 361) hydrogen bonds : angle 5.60166 ( 978) link_BETA1-4 : bond 0.00020 ( 1) link_BETA1-4 : angle 1.66174 ( 3) link_NAG-ASN : bond 0.00289 ( 1) link_NAG-ASN : angle 4.14746 ( 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 70 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 TYR cc_start: 0.9119 (m-10) cc_final: 0.8817 (m-80) REVERT: E 130 PHE cc_start: 0.9606 (m-80) cc_final: 0.9355 (m-80) REVERT: A 47 MET cc_start: 0.9541 (mmm) cc_final: 0.9321 (ppp) REVERT: A 123 MET cc_start: 0.9573 (mmm) cc_final: 0.9237 (tpp) REVERT: A 299 MET cc_start: 0.9291 (ttm) cc_final: 0.8611 (ppp) REVERT: A 305 MET cc_start: 0.9494 (mmt) cc_final: 0.9239 (tpp) REVERT: A 313 MET cc_start: 0.9820 (mmm) cc_final: 0.9372 (mmm) REVERT: D 16 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8845 (ttt) outliers start: 18 outliers final: 8 residues processed: 67 average time/residue: 0.1003 time to fit residues: 9.7547 Evaluate side-chains 59 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 152 VAL Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 133 LEU 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: 4.9990 chunk 74 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.023988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.017117 restraints weight = 119295.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.017836 restraints weight = 71549.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.018360 restraints weight = 49748.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.018741 restraints weight = 37981.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.019035 restraints weight = 30786.397| |-----------------------------------------------------------------------------| r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9309 Z= 0.163 Angle : 0.602 9.347 12645 Z= 0.312 Chirality : 0.042 0.161 1415 Planarity : 0.004 0.063 1627 Dihedral : 6.626 83.377 1345 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.66 % Allowed : 11.95 % 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 aren not related in a simple way. whole: 0.41 (0.25), residues: 1144 helix: 0.46 (0.24), residues: 451 sheet: -0.08 (0.40), residues: 163 loop : 0.44 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 181 TYR 0.016 0.001 TYR D 32 PHE 0.014 0.001 PHE B 225 TRP 0.011 0.001 TRP A 79 HIS 0.010 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9305) covalent geometry : angle 0.59807 (12635) SS BOND : bond 0.00236 ( 2) SS BOND : angle 0.87911 ( 4) hydrogen bonds : bond 0.03612 ( 361) hydrogen bonds : angle 5.38390 ( 978) link_BETA1-4 : bond 0.00192 ( 1) link_BETA1-4 : angle 1.67688 ( 3) link_NAG-ASN : bond 0.00179 ( 1) link_NAG-ASN : angle 4.19331 ( 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 69 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 TYR cc_start: 0.9225 (m-10) cc_final: 0.8880 (m-80) REVERT: E 130 PHE cc_start: 0.9549 (m-80) cc_final: 0.9254 (m-80) REVERT: A 44 MET cc_start: 0.8533 (tpp) cc_final: 0.8294 (tpp) REVERT: A 47 MET cc_start: 0.9537 (mmm) cc_final: 0.9197 (mmt) REVERT: A 119 MET cc_start: 0.9441 (ppp) cc_final: 0.9226 (ppp) REVERT: A 123 MET cc_start: 0.9513 (mmm) cc_final: 0.9245 (tpp) REVERT: A 299 MET cc_start: 0.9219 (ttm) cc_final: 0.8592 (tmm) REVERT: A 313 MET cc_start: 0.9808 (mmm) cc_final: 0.9231 (tpp) REVERT: D 16 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.9001 (ttt) REVERT: D 83 LEU cc_start: 0.9908 (mt) cc_final: 0.9444 (tp) REVERT: D 91 VAL cc_start: 0.9376 (OUTLIER) cc_final: 0.9150 (t) REVERT: D 102 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7661 (mp0) outliers start: 16 outliers final: 7 residues processed: 66 average time/residue: 0.0963 time to fit residues: 9.4459 Evaluate side-chains 61 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 124 LYS 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: 8.9990 chunk 1 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 59 optimal weight: 6.9990 chunk 14 optimal weight: 30.0000 chunk 16 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN ** D 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.022293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2340 r_free = 0.2340 target = 0.015948 restraints weight = 126472.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2377 r_free = 0.2377 target = 0.016625 restraints weight = 74899.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2402 r_free = 0.2402 target = 0.017113 restraints weight = 51467.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.017470 restraints weight = 39008.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.017731 restraints weight = 31651.086| |-----------------------------------------------------------------------------| r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.6233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 9309 Z= 0.287 Angle : 0.722 10.146 12645 Z= 0.379 Chirality : 0.043 0.191 1415 Planarity : 0.005 0.063 1627 Dihedral : 7.057 87.995 1345 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.08 % Allowed : 12.68 % Favored : 85.24 % 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 aren not related in a simple way. whole: 0.05 (0.25), residues: 1144 helix: 0.13 (0.24), residues: 449 sheet: -0.58 (0.37), residues: 176 loop : 0.41 (0.29), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 143 TYR 0.024 0.002 TYR D 32 PHE 0.016 0.002 PHE B 225 TRP 0.014 0.002 TRP B 149 HIS 0.009 0.003 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00571 ( 9305) covalent geometry : angle 0.71874 (12635) SS BOND : bond 0.00288 ( 2) SS BOND : angle 0.78797 ( 4) hydrogen bonds : bond 0.04014 ( 361) hydrogen bonds : angle 5.79571 ( 978) link_BETA1-4 : bond 0.00891 ( 1) link_BETA1-4 : angle 1.62178 ( 3) link_NAG-ASN : bond 0.00266 ( 1) link_NAG-ASN : angle 4.18344 ( 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 66 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 29 MET cc_start: 0.8926 (tmm) cc_final: 0.8722 (tmm) REVERT: E 81 TYR cc_start: 0.9362 (m-10) cc_final: 0.9008 (m-80) REVERT: E 130 PHE cc_start: 0.9586 (m-80) cc_final: 0.9343 (m-80) REVERT: B 117 ASN cc_start: 0.9182 (OUTLIER) cc_final: 0.7633 (t0) REVERT: B 283 MET cc_start: 0.8869 (tpp) cc_final: 0.8342 (tpp) REVERT: A 47 MET cc_start: 0.9611 (mmm) cc_final: 0.9364 (mmm) REVERT: A 49 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.9087 (tm-30) REVERT: A 123 MET cc_start: 0.9526 (mmm) cc_final: 0.9308 (tpp) REVERT: A 299 MET cc_start: 0.9261 (ttm) cc_final: 0.8657 (tmm) REVERT: A 313 MET cc_start: 0.9806 (mmm) cc_final: 0.9251 (tpp) REVERT: D 16 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.9009 (ttt) REVERT: D 102 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7842 (mp0) outliers start: 20 outliers final: 13 residues processed: 63 average time/residue: 0.0942 time to fit residues: 8.8998 Evaluate side-chains 62 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 124 LYS 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: 6.9990 chunk 8 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 106 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.022130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2335 r_free = 0.2335 target = 0.015735 restraints weight = 124327.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2371 r_free = 0.2371 target = 0.016402 restraints weight = 73701.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.016890 restraints weight = 51147.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2416 r_free = 0.2416 target = 0.017238 restraints weight = 38968.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.017518 restraints weight = 31844.506| |-----------------------------------------------------------------------------| r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.6606 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= 0.218 Angle : 0.658 10.270 12645 Z= 0.342 Chirality : 0.042 0.172 1415 Planarity : 0.004 0.063 1627 Dihedral : 6.873 83.018 1345 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.77 % Allowed : 14.03 % Favored : 84.20 % 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 aren not related in a simple way. whole: 0.23 (0.25), residues: 1144 helix: 0.34 (0.24), residues: 448 sheet: -0.55 (0.40), residues: 163 loop : 0.45 (0.29), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 143 TYR 0.018 0.002 TYR D 32 PHE 0.012 0.002 PHE B 225 TRP 0.014 0.002 TRP A 79 HIS 0.009 0.002 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 9305) covalent geometry : angle 0.65389 (12635) SS BOND : bond 0.00293 ( 2) SS BOND : angle 0.74182 ( 4) hydrogen bonds : bond 0.03594 ( 361) hydrogen bonds : angle 5.60935 ( 978) link_BETA1-4 : bond 0.00293 ( 1) link_BETA1-4 : angle 1.89883 ( 3) link_NAG-ASN : bond 0.00200 ( 1) link_NAG-ASN : angle 4.23274 ( 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: 17 poor density : 46 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 29 MET cc_start: 0.8966 (tmm) cc_final: 0.8710 (tmm) REVERT: E 81 TYR cc_start: 0.9342 (m-10) cc_final: 0.8970 (m-80) REVERT: E 130 PHE cc_start: 0.9553 (m-80) cc_final: 0.9305 (m-80) REVERT: B 117 ASN cc_start: 0.9139 (OUTLIER) cc_final: 0.7704 (t0) REVERT: B 283 MET cc_start: 0.8894 (tpp) cc_final: 0.8456 (tpp) REVERT: A 47 MET cc_start: 0.9688 (mmm) cc_final: 0.9446 (mpp) REVERT: A 49 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.9012 (tm-30) REVERT: A 297 ASN cc_start: 0.9794 (OUTLIER) cc_final: 0.9536 (p0) REVERT: A 299 MET cc_start: 0.9282 (ttm) cc_final: 0.8488 (ttp) REVERT: A 313 MET cc_start: 0.9826 (mmm) cc_final: 0.9287 (tpp) REVERT: D 16 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.9061 (ttt) REVERT: D 102 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8140 (mp0) REVERT: D 245 MET cc_start: 0.9812 (mpp) cc_final: 0.9591 (ppp) outliers start: 17 outliers final: 7 residues processed: 60 average time/residue: 0.0944 time to fit residues: 8.5438 Evaluate side-chains 57 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain C residue 602 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 42 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.021652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2322 r_free = 0.2322 target = 0.015451 restraints weight = 127761.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2359 r_free = 0.2359 target = 0.016119 restraints weight = 75368.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2386 r_free = 0.2386 target = 0.016608 restraints weight = 51856.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2405 r_free = 0.2405 target = 0.016966 restraints weight = 39114.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.017232 restraints weight = 31555.030| |-----------------------------------------------------------------------------| r_work (final): 0.2402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.7106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9309 Z= 0.238 Angle : 0.705 11.112 12645 Z= 0.364 Chirality : 0.042 0.180 1415 Planarity : 0.005 0.060 1627 Dihedral : 7.057 89.476 1345 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.98 % Allowed : 14.24 % Favored : 83.78 % 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 aren not related in a simple way. whole: 0.02 (0.25), residues: 1144 helix: 0.25 (0.24), residues: 448 sheet: -0.74 (0.39), residues: 163 loop : 0.28 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 246 TYR 0.021 0.002 TYR D 32 PHE 0.014 0.002 PHE B 225 TRP 0.013 0.002 TRP C 582 HIS 0.010 0.002 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 9305) covalent geometry : angle 0.70169 (12635) SS BOND : bond 0.00105 ( 2) SS BOND : angle 1.38588 ( 4) hydrogen bonds : bond 0.03646 ( 361) hydrogen bonds : angle 5.70137 ( 978) link_BETA1-4 : bond 0.00107 ( 1) link_BETA1-4 : angle 1.90467 ( 3) link_NAG-ASN : bond 0.00245 ( 1) link_NAG-ASN : angle 4.22820 ( 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 64 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 29 MET cc_start: 0.8998 (tmm) cc_final: 0.8745 (tmm) REVERT: E 81 TYR cc_start: 0.9381 (m-10) cc_final: 0.9040 (m-80) REVERT: E 130 PHE cc_start: 0.9555 (m-80) cc_final: 0.9279 (m-80) REVERT: B 117 ASN cc_start: 0.9159 (OUTLIER) cc_final: 0.7670 (t0) REVERT: B 283 MET cc_start: 0.8882 (tpp) cc_final: 0.8478 (tpp) REVERT: A 47 MET cc_start: 0.9602 (mmm) cc_final: 0.9375 (mmp) REVERT: A 49 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8886 (tm-30) REVERT: A 176 MET cc_start: 0.8186 (tmm) cc_final: 0.7421 (tmm) REVERT: A 297 ASN cc_start: 0.9778 (OUTLIER) cc_final: 0.9505 (p0) REVERT: A 299 MET cc_start: 0.9228 (ttm) cc_final: 0.8633 (tmm) REVERT: A 313 MET cc_start: 0.9812 (mmm) cc_final: 0.9240 (tpp) REVERT: D 16 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.9063 (ttt) REVERT: D 102 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.8015 (mp0) REVERT: D 245 MET cc_start: 0.9811 (mpp) cc_final: 0.9605 (ppp) outliers start: 19 outliers final: 11 residues processed: 61 average time/residue: 0.0850 time to fit residues: 8.0542 Evaluate side-chains 60 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain C residue 560 GLU Chi-restraints excluded: chain C residue 602 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 HIS ** D 56 ASN ** 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 = 0.2660 r_free = 0.2660 target = 0.021562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2321 r_free = 0.2321 target = 0.015366 restraints weight = 126613.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2358 r_free = 0.2358 target = 0.016032 restraints weight = 74398.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2385 r_free = 0.2385 target = 0.016526 restraints weight = 51045.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.016883 restraints weight = 38455.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2418 r_free = 0.2418 target = 0.017142 restraints weight = 31112.224| |-----------------------------------------------------------------------------| r_work (final): 0.2399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.7284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9309 Z= 0.213 Angle : 0.672 10.661 12645 Z= 0.346 Chirality : 0.042 0.168 1415 Planarity : 0.004 0.060 1627 Dihedral : 6.926 84.409 1345 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.98 % Allowed : 14.35 % Favored : 83.68 % 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 aren not related in a simple way. whole: 0.11 (0.25), residues: 1144 helix: 0.31 (0.24), residues: 448 sheet: -0.77 (0.39), residues: 168 loop : 0.38 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 246 TYR 0.024 0.002 TYR E 149 PHE 0.042 0.002 PHE E 152 TRP 0.016 0.002 TRP C 582 HIS 0.010 0.002 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 9305) covalent geometry : angle 0.66837 (12635) SS BOND : bond 0.00625 ( 2) SS BOND : angle 1.36584 ( 4) hydrogen bonds : bond 0.03508 ( 361) hydrogen bonds : angle 5.55824 ( 978) link_BETA1-4 : bond 0.00152 ( 1) link_BETA1-4 : angle 1.76498 ( 3) link_NAG-ASN : bond 0.00231 ( 1) link_NAG-ASN : angle 4.27193 ( 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 64 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 44 MET cc_start: 0.8599 (tpp) cc_final: 0.8304 (mmm) REVERT: E 81 TYR cc_start: 0.9368 (m-10) cc_final: 0.9005 (m-80) REVERT: E 130 PHE cc_start: 0.9528 (m-80) cc_final: 0.9239 (m-80) REVERT: B 117 ASN cc_start: 0.9167 (OUTLIER) cc_final: 0.7708 (t0) REVERT: B 283 MET cc_start: 0.8892 (tpp) cc_final: 0.8503 (tpp) REVERT: A 47 MET cc_start: 0.9637 (mmm) cc_final: 0.9418 (mpp) REVERT: A 49 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8838 (tm-30) REVERT: A 132 MET cc_start: 0.9528 (tmm) cc_final: 0.9313 (tmm) REVERT: A 140 LEU cc_start: 0.9805 (OUTLIER) cc_final: 0.9587 (mm) REVERT: A 176 MET cc_start: 0.8227 (tmm) cc_final: 0.7460 (tmm) REVERT: A 297 ASN cc_start: 0.9769 (OUTLIER) cc_final: 0.9481 (p0) REVERT: A 299 MET cc_start: 0.9218 (ttm) cc_final: 0.8564 (ttp) REVERT: A 313 MET cc_start: 0.9812 (mmm) cc_final: 0.9251 (tpp) REVERT: D 16 MET cc_start: 0.9320 (OUTLIER) cc_final: 0.8351 (ttt) REVERT: D 245 MET cc_start: 0.9815 (mpp) cc_final: 0.9595 (ppp) outliers start: 19 outliers final: 10 residues processed: 61 average time/residue: 0.0840 time to fit residues: 7.9398 Evaluate side-chains 60 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain C residue 560 GLU Chi-restraints excluded: chain C residue 602 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 106 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 74 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.021709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2325 r_free = 0.2325 target = 0.015363 restraints weight = 122400.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2362 r_free = 0.2362 target = 0.016049 restraints weight = 72637.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2388 r_free = 0.2388 target = 0.016537 restraints weight = 49923.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.016899 restraints weight = 37881.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.017161 restraints weight = 30722.503| |-----------------------------------------------------------------------------| r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.7307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9309 Z= 0.151 Angle : 0.643 10.461 12645 Z= 0.325 Chirality : 0.042 0.153 1415 Planarity : 0.004 0.059 1627 Dihedral : 6.703 82.579 1345 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.35 % Allowed : 14.76 % Favored : 83.89 % 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 aren not related in a simple way. whole: 0.25 (0.25), residues: 1144 helix: 0.48 (0.24), residues: 448 sheet: -0.64 (0.41), residues: 161 loop : 0.36 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 246 TYR 0.014 0.001 TYR D 32 PHE 0.041 0.001 PHE E 152 TRP 0.015 0.001 TRP C 582 HIS 0.009 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9305) covalent geometry : angle 0.63911 (12635) SS BOND : bond 0.00090 ( 2) SS BOND : angle 1.33291 ( 4) hydrogen bonds : bond 0.03295 ( 361) hydrogen bonds : angle 5.37976 ( 978) link_BETA1-4 : bond 0.00307 ( 1) link_BETA1-4 : angle 1.51254 ( 3) link_NAG-ASN : bond 0.00030 ( 1) link_NAG-ASN : angle 4.17542 ( 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 58 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 81 TYR cc_start: 0.9347 (m-10) cc_final: 0.8988 (m-80) REVERT: E 130 PHE cc_start: 0.9518 (m-80) cc_final: 0.9220 (m-80) REVERT: B 283 MET cc_start: 0.8896 (tpp) cc_final: 0.8511 (tpp) REVERT: A 47 MET cc_start: 0.9631 (mmm) cc_final: 0.9339 (mpp) REVERT: A 49 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8857 (tm-30) REVERT: A 123 MET cc_start: 0.9480 (tpp) cc_final: 0.9196 (tmm) REVERT: A 124 PHE cc_start: 0.9488 (OUTLIER) cc_final: 0.9202 (t80) REVERT: A 140 LEU cc_start: 0.9779 (OUTLIER) cc_final: 0.9543 (mm) REVERT: A 176 MET cc_start: 0.8134 (tmm) cc_final: 0.7341 (tmm) REVERT: A 297 ASN cc_start: 0.9796 (OUTLIER) cc_final: 0.9494 (p0) REVERT: A 299 MET cc_start: 0.9197 (ttm) cc_final: 0.8529 (ttp) REVERT: A 313 MET cc_start: 0.9823 (mmm) cc_final: 0.9244 (tpp) REVERT: D 16 MET cc_start: 0.9423 (OUTLIER) cc_final: 0.9079 (ttt) REVERT: D 245 MET cc_start: 0.9816 (mpp) cc_final: 0.9605 (ppp) outliers start: 13 outliers final: 8 residues processed: 55 average time/residue: 0.0869 time to fit residues: 7.4417 Evaluate side-chains 57 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 49 GLN Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain C residue 602 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 99 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.021899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2334 r_free = 0.2334 target = 0.015472 restraints weight = 119189.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2371 r_free = 0.2371 target = 0.016154 restraints weight = 70223.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.016654 restraints weight = 48633.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2416 r_free = 0.2416 target = 0.017017 restraints weight = 36860.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2430 r_free = 0.2430 target = 0.017296 restraints weight = 29930.351| |-----------------------------------------------------------------------------| r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.7316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9309 Z= 0.126 Angle : 0.642 10.345 12645 Z= 0.322 Chirality : 0.042 0.191 1415 Planarity : 0.004 0.059 1627 Dihedral : 6.465 81.428 1345 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.25 % Allowed : 14.86 % Favored : 83.89 % 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 aren not related in a simple way. whole: 0.37 (0.26), residues: 1144 helix: 0.63 (0.24), residues: 451 sheet: -0.52 (0.41), residues: 163 loop : 0.37 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 246 TYR 0.012 0.001 TYR D 32 PHE 0.017 0.001 PHE E 152 TRP 0.015 0.001 TRP A 79 HIS 0.008 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9305) covalent geometry : angle 0.63849 (12635) SS BOND : bond 0.00108 ( 2) SS BOND : angle 0.97872 ( 4) hydrogen bonds : bond 0.03174 ( 361) hydrogen bonds : angle 5.27957 ( 978) link_BETA1-4 : bond 0.00269 ( 1) link_BETA1-4 : angle 1.29110 ( 3) link_NAG-ASN : bond 0.00093 ( 1) link_NAG-ASN : angle 4.33224 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1657.50 seconds wall clock time: 29 minutes 38.38 seconds (1778.38 seconds total)