Starting phenix.real_space_refine on Thu Mar 13 20:54:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nzm_12665/03_2025/7nzm_12665.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nzm_12665/03_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_12665/03_2025/7nzm_12665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nzm_12665/03_2025/7nzm_12665.map" model { file = "/net/cci-nas-00/data/ceres_data/7nzm_12665/03_2025/7nzm_12665.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nzm_12665/03_2025/7nzm_12665.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 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, 'GLN:plan1': 2, 'ARG:plan': 2, 'TRP:plan': 1} 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: 5.73, per 1000 atoms: 0.63 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: 2.33 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.05 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: 2.38 Time building geometry restraints manager: 2.75 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.830 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.060 ------------------------------------------------------------------------------- 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 9305 Z= 0.440 Angle : 1.122 21.476 12635 Z= 0.685 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (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 TRP 0.040 0.004 TRP C 616 HIS 0.008 0.002 HIS B 248 PHE 0.023 0.003 PHE D 109 TYR 0.045 0.004 TYR D 76 ARG 0.015 0.001 ARG B 132 *********************** 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 : 0.981 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: 0.2703 time to fit residues: 41.6168 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 : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.040725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.034626 restraints weight = 110135.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.035506 restraints weight = 53275.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.036121 restraints weight = 31912.789| |-----------------------------------------------------------------------------| r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9305 Z= 0.205 Angle : 0.716 12.210 12635 Z= 0.369 Chirality : 0.046 0.275 1415 Planarity : 0.004 0.081 1627 Dihedral : 7.098 89.868 1345 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.56 % Allowed : 6.65 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.24), residues: 1144 helix: 0.00 (0.24), residues: 442 sheet: -0.25 (0.37), residues: 161 loop : -0.21 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 356 HIS 0.007 0.001 HIS B 173 PHE 0.019 0.001 PHE B 225 TYR 0.015 0.002 TYR D 32 ARG 0.006 0.001 ARG C 612 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 LYS cc_start: 0.9536 (ttmt) cc_final: 0.9322 (mmtt) REVERT: E 127 GLU cc_start: 0.9385 (tt0) cc_final: 0.9091 (mm-30) REVERT: E 130 PHE cc_start: 0.9516 (m-80) cc_final: 0.9248 (m-80) REVERT: E 152 PHE cc_start: 0.9119 (m-80) cc_final: 0.8896 (m-80) REVERT: A 119 MET cc_start: 0.9195 (mtp) cc_final: 0.8961 (ptp) REVERT: A 132 MET cc_start: 0.9379 (ptm) cc_final: 0.9166 (ppp) REVERT: A 297 ASN cc_start: 0.9484 (t0) cc_final: 0.9082 (t0) REVERT: A 305 MET cc_start: 0.9519 (mmt) cc_final: 0.9062 (mmm) REVERT: A 313 MET cc_start: 0.9122 (mmm) cc_final: 0.8898 (mmm) REVERT: A 345 ILE cc_start: 0.9825 (OUTLIER) cc_final: 0.9450 (pt) REVERT: A 346 LEU cc_start: 0.9888 (tp) cc_final: 0.9683 (tp) REVERT: D 16 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8756 (ttm) REVERT: D 69 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8775 (mm-30) outliers start: 15 outliers final: 4 residues processed: 81 average time/residue: 0.2775 time to fit residues: 32.1556 Evaluate side-chains 65 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 133 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 21 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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** B 117 ASN A 40 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.025518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.018329 restraints weight = 114653.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.019072 restraints weight = 70408.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.019626 restraints weight = 49270.169| |-----------------------------------------------------------------------------| r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9305 Z= 0.339 Angle : 0.739 8.797 12635 Z= 0.392 Chirality : 0.045 0.309 1415 Planarity : 0.005 0.072 1627 Dihedral : 6.943 88.924 1345 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.77 % Allowed : 8.42 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.24), residues: 1144 helix: 0.18 (0.24), residues: 432 sheet: -0.12 (0.38), residues: 163 loop : 0.26 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 149 HIS 0.011 0.002 HIS B 248 PHE 0.019 0.002 PHE B 225 TYR 0.020 0.002 TYR D 32 ARG 0.006 0.001 ARG E 143 *********************** 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 75 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 44 MET cc_start: 0.8743 (tpp) cc_final: 0.8160 (tpp) REVERT: E 81 TYR cc_start: 0.9020 (m-10) cc_final: 0.8807 (m-80) REVERT: E 84 LEU cc_start: 0.9458 (mp) cc_final: 0.8951 (tp) REVERT: E 127 GLU cc_start: 0.9444 (tt0) cc_final: 0.9025 (mm-30) REVERT: E 130 PHE cc_start: 0.9629 (m-80) cc_final: 0.9270 (m-80) REVERT: A 119 MET cc_start: 0.9187 (mtp) cc_final: 0.8967 (mtp) REVERT: A 123 MET cc_start: 0.9729 (mmm) cc_final: 0.9288 (tpp) REVERT: A 154 ASP cc_start: 0.9598 (t0) cc_final: 0.9168 (p0) REVERT: A 305 MET cc_start: 0.9577 (mmt) cc_final: 0.9189 (mmm) REVERT: A 313 MET cc_start: 0.9625 (mmm) cc_final: 0.9233 (mmm) REVERT: D 16 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8887 (ttm) outliers start: 17 outliers final: 7 residues processed: 71 average time/residue: 0.1977 time to fit residues: 20.8750 Evaluate side-chains 63 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain A residue 152 VAL 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 D residue 173 CYS 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 79 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 35 optimal weight: 0.0370 chunk 28 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 overall best weight: 4.8066 ------------------------------------------------------------------------------- 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 D 155 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.024382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.017439 restraints weight = 116672.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.018165 restraints weight = 71750.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.018680 restraints weight = 50357.249| |-----------------------------------------------------------------------------| r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9305 Z= 0.262 Angle : 0.625 9.056 12635 Z= 0.328 Chirality : 0.042 0.152 1415 Planarity : 0.004 0.068 1627 Dihedral : 6.789 86.361 1345 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.56 % Allowed : 10.81 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1144 helix: 0.27 (0.24), residues: 452 sheet: 0.03 (0.40), residues: 156 loop : 0.27 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 582 HIS 0.010 0.002 HIS A 40 PHE 0.016 0.002 PHE B 225 TYR 0.017 0.002 TYR D 32 ARG 0.003 0.001 ARG E 143 *********************** 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 71 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 44 MET cc_start: 0.8795 (tpp) cc_final: 0.8435 (tpp) REVERT: E 81 TYR cc_start: 0.9072 (m-10) cc_final: 0.8804 (m-80) REVERT: E 84 LEU cc_start: 0.9482 (mp) cc_final: 0.9062 (mp) REVERT: E 127 GLU cc_start: 0.9453 (tt0) cc_final: 0.9026 (mm-30) REVERT: E 130 PHE cc_start: 0.9591 (m-80) cc_final: 0.9183 (m-80) REVERT: A 123 MET cc_start: 0.9562 (mmm) cc_final: 0.9208 (tpp) REVERT: A 132 MET cc_start: 0.9329 (tmm) cc_final: 0.9095 (tmm) REVERT: A 154 ASP cc_start: 0.9566 (t0) cc_final: 0.9093 (p0) REVERT: A 299 MET cc_start: 0.9171 (mmm) cc_final: 0.8881 (mmm) REVERT: A 305 MET cc_start: 0.9581 (OUTLIER) cc_final: 0.9235 (mmm) REVERT: A 313 MET cc_start: 0.9622 (mmm) cc_final: 0.9200 (mmm) outliers start: 15 outliers final: 7 residues processed: 67 average time/residue: 0.2116 time to fit residues: 20.8338 Evaluate side-chains 61 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 133 LEU 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 13 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 104 optimal weight: 0.0270 chunk 55 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 overall best weight: 4.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.023734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2387 r_free = 0.2387 target = 0.016886 restraints weight = 119261.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.017615 restraints weight = 72026.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.018146 restraints weight = 50053.724| |-----------------------------------------------------------------------------| r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.5427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9305 Z= 0.248 Angle : 0.614 9.858 12635 Z= 0.319 Chirality : 0.042 0.156 1415 Planarity : 0.004 0.066 1627 Dihedral : 6.649 82.956 1345 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.77 % Allowed : 11.43 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1144 helix: 0.47 (0.24), residues: 455 sheet: -0.17 (0.41), residues: 157 loop : 0.38 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 582 HIS 0.010 0.002 HIS A 40 PHE 0.014 0.002 PHE B 225 TYR 0.017 0.002 TYR D 32 ARG 0.005 0.001 ARG E 132 *********************** 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 70 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 44 MET cc_start: 0.8800 (tpp) cc_final: 0.8386 (tpp) REVERT: E 81 TYR cc_start: 0.9236 (m-10) cc_final: 0.8928 (m-80) REVERT: E 84 LEU cc_start: 0.9483 (mp) cc_final: 0.9053 (mp) REVERT: E 127 GLU cc_start: 0.9470 (OUTLIER) cc_final: 0.9262 (pp20) REVERT: E 130 PHE cc_start: 0.9580 (m-80) cc_final: 0.9292 (m-80) REVERT: A 44 MET cc_start: 0.8617 (tpp) cc_final: 0.8199 (tpp) REVERT: A 119 MET cc_start: 0.9524 (tmm) cc_final: 0.9262 (ppp) REVERT: A 154 ASP cc_start: 0.9600 (t0) cc_final: 0.9158 (p0) REVERT: A 176 MET cc_start: 0.7855 (tmm) cc_final: 0.7526 (tmm) REVERT: A 299 MET cc_start: 0.9303 (mmm) cc_final: 0.8753 (mmm) REVERT: A 305 MET cc_start: 0.9565 (mmt) cc_final: 0.9258 (mmm) REVERT: A 313 MET cc_start: 0.9654 (mmm) cc_final: 0.9245 (mmm) REVERT: A 325 MET cc_start: 0.8870 (tpp) cc_final: 0.8627 (tpp) REVERT: D 16 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.8869 (ttt) outliers start: 17 outliers final: 7 residues processed: 65 average time/residue: 0.3113 time to fit residues: 29.0388 Evaluate side-chains 61 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 91 VAL 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 96 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 23 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 overall best weight: 2.9784 ------------------------------------------------------------------------------- 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 = 0.2743 r_free = 0.2743 target = 0.023675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.016866 restraints weight = 119122.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.017597 restraints weight = 70876.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.018137 restraints weight = 48877.445| |-----------------------------------------------------------------------------| r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9305 Z= 0.197 Angle : 0.597 13.613 12635 Z= 0.301 Chirality : 0.043 0.343 1415 Planarity : 0.004 0.063 1627 Dihedral : 6.429 80.449 1345 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.56 % Allowed : 12.27 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1144 helix: 0.66 (0.25), residues: 462 sheet: -0.14 (0.41), residues: 157 loop : 0.43 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 582 HIS 0.011 0.001 HIS A 40 PHE 0.015 0.001 PHE B 225 TYR 0.012 0.001 TYR D 32 ARG 0.003 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 44 MET cc_start: 0.8846 (tpp) cc_final: 0.8452 (tpp) REVERT: E 81 TYR cc_start: 0.9222 (m-10) cc_final: 0.8897 (m-80) REVERT: E 84 LEU cc_start: 0.9501 (mp) cc_final: 0.9086 (mp) REVERT: E 130 PHE cc_start: 0.9545 (m-80) cc_final: 0.9224 (m-80) REVERT: B 283 MET cc_start: 0.8835 (tpp) cc_final: 0.8338 (tpp) REVERT: A 49 GLN cc_start: 0.9317 (OUTLIER) cc_final: 0.8969 (tm-30) REVERT: A 154 ASP cc_start: 0.9621 (t0) cc_final: 0.9155 (p0) REVERT: A 176 MET cc_start: 0.7826 (tmm) cc_final: 0.7422 (tmm) REVERT: A 190 MET cc_start: 0.9484 (ptm) cc_final: 0.9198 (ppp) REVERT: A 299 MET cc_start: 0.9321 (mmm) cc_final: 0.8786 (mmm) REVERT: A 305 MET cc_start: 0.9585 (mmt) cc_final: 0.9250 (mmm) REVERT: A 313 MET cc_start: 0.9678 (mmm) cc_final: 0.9261 (mmm) REVERT: D 91 VAL cc_start: 0.9362 (OUTLIER) cc_final: 0.9124 (t) outliers start: 15 outliers final: 9 residues processed: 65 average time/residue: 0.2374 time to fit residues: 22.7721 Evaluate side-chains 62 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain D residue 91 VAL 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 15 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 109 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.2676 r_free = 0.2676 target = 0.022025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2328 r_free = 0.2328 target = 0.015697 restraints weight = 131521.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2366 r_free = 0.2366 target = 0.016383 restraints weight = 76397.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2393 r_free = 0.2393 target = 0.016886 restraints weight = 52110.275| |-----------------------------------------------------------------------------| r_work (final): 0.2373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.6595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 9305 Z= 0.394 Angle : 0.774 11.965 12635 Z= 0.402 Chirality : 0.044 0.205 1415 Planarity : 0.005 0.063 1627 Dihedral : 7.184 88.215 1345 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.77 % Allowed : 12.89 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.24), residues: 1144 helix: -0.01 (0.23), residues: 458 sheet: -0.88 (0.36), residues: 182 loop : 0.29 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 149 HIS 0.013 0.003 HIS A 40 PHE 0.018 0.002 PHE B 152 TYR 0.027 0.002 TYR D 32 ARG 0.008 0.001 ARG E 143 *********************** 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 65 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 44 MET cc_start: 0.8822 (tpp) cc_final: 0.8472 (tpp) REVERT: E 81 TYR cc_start: 0.9401 (m-10) cc_final: 0.9039 (m-80) REVERT: E 84 LEU cc_start: 0.9539 (mp) cc_final: 0.9106 (mp) REVERT: E 130 PHE cc_start: 0.9609 (m-80) cc_final: 0.9297 (m-80) REVERT: B 117 ASN cc_start: 0.9207 (OUTLIER) cc_final: 0.7667 (t0) REVERT: B 283 MET cc_start: 0.8903 (tpp) cc_final: 0.8449 (tpp) REVERT: A 47 MET cc_start: 0.9587 (pmm) cc_final: 0.9380 (pmm) REVERT: A 49 GLN cc_start: 0.9281 (OUTLIER) cc_final: 0.8732 (tm-30) REVERT: A 123 MET cc_start: 0.9468 (tpp) cc_final: 0.9196 (tmm) REVERT: A 124 PHE cc_start: 0.9416 (OUTLIER) cc_final: 0.8724 (m-80) REVERT: A 154 ASP cc_start: 0.9574 (t0) cc_final: 0.9283 (p0) REVERT: A 176 MET cc_start: 0.8154 (tmm) cc_final: 0.7791 (tmm) REVERT: A 299 MET cc_start: 0.9105 (mmm) cc_final: 0.8592 (mmm) REVERT: A 305 MET cc_start: 0.9559 (mmt) cc_final: 0.9247 (mmm) REVERT: D 245 MET cc_start: 0.9807 (mpp) cc_final: 0.9585 (ppp) outliers start: 17 outliers final: 10 residues processed: 61 average time/residue: 0.2350 time to fit residues: 22.1503 Evaluate side-chains 59 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 152 PHE 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 49 GLN Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 297 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 93 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 109 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 177 ASN B 271 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.022291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2338 r_free = 0.2338 target = 0.015783 restraints weight = 124721.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2376 r_free = 0.2376 target = 0.016481 restraints weight = 73438.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2403 r_free = 0.2403 target = 0.016986 restraints weight = 50533.046| |-----------------------------------------------------------------------------| r_work (final): 0.2381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.6649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9305 Z= 0.233 Angle : 0.637 11.678 12635 Z= 0.324 Chirality : 0.043 0.259 1415 Planarity : 0.004 0.061 1627 Dihedral : 6.774 82.601 1345 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.14 % Allowed : 13.72 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1144 helix: 0.48 (0.24), residues: 457 sheet: -0.53 (0.40), residues: 159 loop : 0.34 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 582 HIS 0.011 0.002 HIS A 40 PHE 0.013 0.001 PHE B 225 TYR 0.016 0.001 TYR D 32 ARG 0.004 0.001 ARG E 181 *********************** 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 61 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 44 MET cc_start: 0.8897 (tpp) cc_final: 0.8579 (tpp) REVERT: E 81 TYR cc_start: 0.9342 (m-10) cc_final: 0.8957 (m-80) REVERT: E 84 LEU cc_start: 0.9563 (mp) cc_final: 0.9161 (mp) REVERT: E 130 PHE cc_start: 0.9565 (m-80) cc_final: 0.9236 (m-80) REVERT: B 117 ASN cc_start: 0.9181 (OUTLIER) cc_final: 0.7780 (t0) REVERT: B 283 MET cc_start: 0.8896 (tpp) cc_final: 0.8475 (tpp) REVERT: A 49 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8807 (tm-30) REVERT: A 123 MET cc_start: 0.9492 (tpp) cc_final: 0.9202 (tmm) REVERT: A 154 ASP cc_start: 0.9598 (t0) cc_final: 0.9273 (p0) REVERT: A 176 MET cc_start: 0.7980 (tmm) cc_final: 0.7568 (tmm) REVERT: A 299 MET cc_start: 0.9195 (mmm) cc_final: 0.8713 (mmm) REVERT: A 305 MET cc_start: 0.9580 (mmt) cc_final: 0.9245 (mmm) REVERT: A 313 MET cc_start: 0.9717 (mmm) cc_final: 0.9200 (mmm) REVERT: D 16 MET cc_start: 0.9017 (ptm) cc_final: 0.8778 (ppp) REVERT: D 245 MET cc_start: 0.9815 (mpp) cc_final: 0.9608 (ppp) outliers start: 11 outliers final: 8 residues processed: 59 average time/residue: 0.2402 time to fit residues: 22.0626 Evaluate side-chains 59 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 124 LYS 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 86 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 39 optimal weight: 50.0000 chunk 17 optimal weight: 20.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 HIS ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 HIS ** 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 = 0.021665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2318 r_free = 0.2318 target = 0.015419 restraints weight = 125401.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2355 r_free = 0.2355 target = 0.016087 restraints weight = 73732.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2382 r_free = 0.2382 target = 0.016579 restraints weight = 50675.707| |-----------------------------------------------------------------------------| r_work (final): 0.2361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.7095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9305 Z= 0.295 Angle : 0.694 10.842 12635 Z= 0.354 Chirality : 0.042 0.236 1415 Planarity : 0.005 0.060 1627 Dihedral : 6.948 88.125 1345 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.35 % Allowed : 13.83 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.25), residues: 1144 helix: 0.33 (0.24), residues: 457 sheet: -0.63 (0.41), residues: 161 loop : 0.31 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 582 HIS 0.010 0.002 HIS A 40 PHE 0.014 0.002 PHE B 225 TYR 0.020 0.002 TYR D 32 ARG 0.006 0.001 ARG B 246 *********************** 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 61 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 44 MET cc_start: 0.8875 (tpp) cc_final: 0.8585 (tpp) REVERT: E 81 TYR cc_start: 0.9397 (m-10) cc_final: 0.8983 (m-80) REVERT: E 84 LEU cc_start: 0.9563 (mp) cc_final: 0.9156 (mp) REVERT: E 130 PHE cc_start: 0.9572 (m-80) cc_final: 0.9241 (m-80) REVERT: B 117 ASN cc_start: 0.9151 (OUTLIER) cc_final: 0.7695 (t0) REVERT: B 283 MET cc_start: 0.8920 (tpp) cc_final: 0.8511 (tpp) REVERT: A 49 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8723 (tm-30) REVERT: A 119 MET cc_start: 0.9612 (tmm) cc_final: 0.9372 (ppp) REVERT: A 123 MET cc_start: 0.9569 (tpp) cc_final: 0.9290 (tmm) REVERT: A 154 ASP cc_start: 0.9568 (t0) cc_final: 0.9299 (p0) REVERT: A 176 MET cc_start: 0.8101 (tmm) cc_final: 0.7676 (tmm) REVERT: A 299 MET cc_start: 0.9131 (mmm) cc_final: 0.8638 (mmm) REVERT: A 305 MET cc_start: 0.9585 (mmt) cc_final: 0.9245 (mmm) REVERT: A 325 MET cc_start: 0.8836 (tpp) cc_final: 0.8633 (tpp) REVERT: D 245 MET cc_start: 0.9825 (mpp) cc_final: 0.9601 (ppp) outliers start: 13 outliers final: 10 residues processed: 58 average time/residue: 0.2053 time to fit residues: 18.0335 Evaluate side-chains 60 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 124 LYS 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 61 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 37 optimal weight: 0.2980 chunk 60 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.022379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2346 r_free = 0.2346 target = 0.015830 restraints weight = 120804.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2384 r_free = 0.2384 target = 0.016557 restraints weight = 70791.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.017068 restraints weight = 48416.800| |-----------------------------------------------------------------------------| r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.6961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9305 Z= 0.164 Angle : 0.627 11.444 12635 Z= 0.310 Chirality : 0.043 0.154 1415 Planarity : 0.003 0.059 1627 Dihedral : 6.465 80.784 1345 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.14 % Allowed : 14.14 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.26), residues: 1144 helix: 0.81 (0.25), residues: 459 sheet: -0.41 (0.42), residues: 157 loop : 0.33 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 582 HIS 0.010 0.001 HIS A 40 PHE 0.011 0.001 PHE B 225 TYR 0.015 0.001 TYR A 306 ARG 0.004 0.000 ARG D 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 44 MET cc_start: 0.8861 (tpp) cc_final: 0.8566 (tpp) REVERT: E 81 TYR cc_start: 0.9301 (m-10) cc_final: 0.8987 (m-80) REVERT: E 84 LEU cc_start: 0.9554 (mp) cc_final: 0.9159 (mp) REVERT: E 130 PHE cc_start: 0.9505 (m-80) cc_final: 0.9150 (m-80) REVERT: B 117 ASN cc_start: 0.9094 (OUTLIER) cc_final: 0.7669 (t0) REVERT: B 282 MET cc_start: 0.8376 (tmm) cc_final: 0.7400 (tmm) REVERT: B 283 MET cc_start: 0.8888 (tpp) cc_final: 0.8400 (tpp) REVERT: A 154 ASP cc_start: 0.9596 (t0) cc_final: 0.9214 (p0) REVERT: A 176 MET cc_start: 0.7972 (tmm) cc_final: 0.7489 (tmm) REVERT: A 190 MET cc_start: 0.9487 (ptm) cc_final: 0.9239 (ppp) REVERT: A 299 MET cc_start: 0.9198 (mmm) cc_final: 0.8731 (mmm) REVERT: A 305 MET cc_start: 0.9593 (mmt) cc_final: 0.9242 (mmm) REVERT: A 313 MET cc_start: 0.9633 (mmm) cc_final: 0.9158 (mmm) REVERT: A 325 MET cc_start: 0.8939 (tpp) cc_final: 0.8727 (tpp) REVERT: D 124 LYS cc_start: 0.9563 (OUTLIER) cc_final: 0.8636 (pttp) outliers start: 11 outliers final: 8 residues processed: 60 average time/residue: 0.1940 time to fit residues: 17.6639 Evaluate side-chains 59 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 124 LYS 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 99 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 80 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 69 optimal weight: 0.0670 chunk 79 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 overall best weight: 1.2322 ------------------------------------------------------------------------------- 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 = 0.2709 r_free = 0.2709 target = 0.022620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2357 r_free = 0.2357 target = 0.015970 restraints weight = 118004.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2395 r_free = 0.2395 target = 0.016689 restraints weight = 69761.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.017219 restraints weight = 48218.424| |-----------------------------------------------------------------------------| r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.6977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 9305 Z= 0.166 Angle : 0.627 10.741 12635 Z= 0.308 Chirality : 0.042 0.147 1415 Planarity : 0.003 0.060 1627 Dihedral : 6.087 78.500 1345 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.94 % Allowed : 14.55 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.26), residues: 1144 helix: 0.85 (0.25), residues: 462 sheet: -0.20 (0.41), residues: 164 loop : 0.34 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 582 HIS 0.007 0.001 HIS B 173 PHE 0.011 0.001 PHE A 223 TYR 0.014 0.001 TYR A 306 ARG 0.004 0.000 ARG D 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2948.43 seconds wall clock time: 54 minutes 18.28 seconds (3258.28 seconds total)