Starting phenix.real_space_refine on Wed Jan 22 10:33:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uqo_42476/01_2025/8uqo_42476.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uqo_42476/01_2025/8uqo_42476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uqo_42476/01_2025/8uqo_42476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uqo_42476/01_2025/8uqo_42476.map" model { file = "/net/cci-nas-00/data/ceres_data/8uqo_42476/01_2025/8uqo_42476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uqo_42476/01_2025/8uqo_42476.cif" } resolution = 3.37 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= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5422 atoms to isotropic. 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: 10 Type Number sf(0) Gaussians Ca 1 9.91 5 Al 1 5.89 5 P 2 5.49 5 Mg 1 5.21 5 S 86 5.16 5 C 8836 2.51 5 N 2371 2.21 5 O 2657 1.98 5 F 4 1.80 5 H 2 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 13961 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2418 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 11, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 80 Chain: "C" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2399 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 12, 'ASN:plan1': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 111 Chain: "D" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 311 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 42} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 385 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2484 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 11, 'TRANS': 303} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 92 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 100 Chain: "Q" Number of atoms: 5926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5926 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 48, 'TRANS': 702} Chain breaks: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 91 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 2, 'TYR:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 8.51, per 1000 atoms: 0.61 Number of scatterers: 13961 At special positions: 0 Unit cell: (89.773, 137.596, 147.664, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Ca 1 19.99 S 86 16.00 P 2 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 2657 8.00 N 2371 7.00 C 8836 6.00 H 2 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Atom "HETATM13959 O HOH A 501 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 1.7 seconds 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3446 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 28 sheets defined 25.2% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.932A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 12 Processing helix chain 'C' and resid 12 through 24 removed outlier: 3.891A pdb=" N ARG C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP C 20 " --> pdb=" O ASN C 16 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG C 22 " --> pdb=" O ILE C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 9 through 19 removed outlier: 3.920A pdb=" N LEU D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 32 Processing helix chain 'D' and resid 33 through 43 removed outlier: 3.576A pdb=" N ALA D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 20 removed outlier: 3.983A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 23 No H-bonds generated for 'chain 'G' and resid 21 through 23' Processing helix chain 'G' and resid 29 through 42 removed outlier: 3.613A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.849A pdb=" N ARG A 73 " --> pdb=" O ASP A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 98 removed outlier: 4.049A pdb=" N TYR A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 109 through 115 removed outlier: 3.992A pdb=" N VAL A 113 " --> pdb=" O HIS A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 removed outlier: 3.613A pdb=" N VAL A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP A 130 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 131 " --> pdb=" O PRO A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 146 removed outlier: 3.859A pdb=" N ASP A 146 " --> pdb=" O GLN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.687A pdb=" N TYR A 151 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 215 through 220 removed outlier: 3.628A pdb=" N HIS A 218 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE A 220 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 259 removed outlier: 3.545A pdb=" N GLU A 250 " --> pdb=" O ASN A 246 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 259 " --> pdb=" O PHE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 261 No H-bonds generated for 'chain 'A' and resid 260 through 261' Processing helix chain 'A' and resid 262 through 266 removed outlier: 3.835A pdb=" N GLN A 265 " --> pdb=" O PRO A 262 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASN A 266 " --> pdb=" O TRP A 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 262 through 266' Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 301 through 315 removed outlier: 3.517A pdb=" N ALA A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 310 " --> pdb=" O ARG A 306 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP A 315 " --> pdb=" O LYS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 349 removed outlier: 4.131A pdb=" N PHE A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 340 " --> pdb=" O ASN A 336 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 78 No H-bonds generated for 'chain 'Q' and resid 76 through 78' Processing helix chain 'Q' and resid 83 through 91 removed outlier: 3.808A pdb=" N GLU Q 88 " --> pdb=" O PRO Q 84 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL Q 89 " --> pdb=" O LYS Q 85 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU Q 90 " --> pdb=" O ILE Q 86 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY Q 91 " --> pdb=" O ARG Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 132 Processing helix chain 'Q' and resid 135 through 140 Processing helix chain 'Q' and resid 141 through 146 removed outlier: 3.686A pdb=" N ASN Q 146 " --> pdb=" O ILE Q 142 " (cutoff:3.500A) Processing helix chain 'Q' and resid 157 through 163 removed outlier: 3.681A pdb=" N GLN Q 163 " --> pdb=" O LYS Q 159 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 176 Processing helix chain 'Q' and resid 185 through 193 removed outlier: 4.217A pdb=" N GLU Q 191 " --> pdb=" O GLU Q 187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 204 through 208 removed outlier: 3.627A pdb=" N PHE Q 208 " --> pdb=" O PRO Q 205 " (cutoff:3.500A) Processing helix chain 'Q' and resid 209 through 217 removed outlier: 3.872A pdb=" N ARG Q 215 " --> pdb=" O GLU Q 211 " (cutoff:3.500A) Processing helix chain 'Q' and resid 243 through 253 Processing helix chain 'Q' and resid 275 through 280 Processing helix chain 'Q' and resid 282 through 287 removed outlier: 3.533A pdb=" N LEU Q 286 " --> pdb=" O ASN Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 293 through 298 Processing helix chain 'Q' and resid 322 through 324 No H-bonds generated for 'chain 'Q' and resid 322 through 324' Processing helix chain 'Q' and resid 347 through 355 removed outlier: 3.745A pdb=" N ARG Q 351 " --> pdb=" O VAL Q 347 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA Q 353 " --> pdb=" O MET Q 349 " (cutoff:3.500A) Processing helix chain 'Q' and resid 389 through 400 Processing helix chain 'Q' and resid 418 through 433 removed outlier: 4.105A pdb=" N ALA Q 423 " --> pdb=" O ALA Q 419 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS Q 424 " --> pdb=" O LYS Q 420 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE Q 433 " --> pdb=" O CYS Q 429 " (cutoff:3.500A) Processing helix chain 'Q' and resid 434 through 437 removed outlier: 3.913A pdb=" N LEU Q 437 " --> pdb=" O GLY Q 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 434 through 437' Processing helix chain 'Q' and resid 590 through 594 Processing helix chain 'Q' and resid 605 through 610 Processing helix chain 'Q' and resid 622 through 626 Processing helix chain 'Q' and resid 634 through 640 removed outlier: 3.835A pdb=" N GLU Q 638 " --> pdb=" O MET Q 634 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN Q 640 " --> pdb=" O PHE Q 636 " (cutoff:3.500A) Processing helix chain 'Q' and resid 660 through 664 Processing helix chain 'Q' and resid 680 through 686 Processing helix chain 'Q' and resid 691 through 696 removed outlier: 4.362A pdb=" N SER Q 696 " --> pdb=" O TYR Q 692 " (cutoff:3.500A) Processing helix chain 'Q' and resid 702 through 706 removed outlier: 3.666A pdb=" N ARG Q 706 " --> pdb=" O GLU Q 703 " (cutoff:3.500A) Processing helix chain 'Q' and resid 861 through 872 removed outlier: 3.549A pdb=" N GLN Q 871 " --> pdb=" O SER Q 867 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.811A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.993A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 104 through 105 removed outlier: 6.189A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 156 through 157 Processing sheet with id=AA5, first strand: chain 'B' and resid 190 through 191 removed outlier: 3.730A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.912A pdb=" N ALA B 242 " --> pdb=" O CYS B 233 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 250 through 252 removed outlier: 3.647A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.880A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 47 through 48 removed outlier: 3.782A pdb=" N LYS C 337 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 69 through 72 removed outlier: 3.803A pdb=" N ILE C 80 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 123 through 124 removed outlier: 3.531A pdb=" N ILE C 123 " --> pdb=" O ARG C 137 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.908A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.747A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 232 through 234 Processing sheet with id=AB6, first strand: chain 'C' and resid 252 through 253 removed outlier: 6.645A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 276 through 277 removed outlier: 3.527A pdb=" N SER C 277 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 189 through 195 removed outlier: 7.049A pdb=" N LEU A 40 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N VAL A 204 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU A 42 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL A 206 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU A 44 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 9.701A pdb=" N SER A 225 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS A 41 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N MET A 227 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU A 43 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU A 229 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU A 45 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ALA A 231 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Q' and resid 26 through 30 removed outlier: 5.623A pdb=" N THR Q 42 " --> pdb=" O THR Q 55 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR Q 55 " --> pdb=" O THR Q 42 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Q' and resid 69 through 74 removed outlier: 3.726A pdb=" N MET Q 104 " --> pdb=" O PHE Q 120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Q' and resid 170 through 171 Processing sheet with id=AC3, first strand: chain 'Q' and resid 241 through 242 Processing sheet with id=AC4, first strand: chain 'Q' and resid 326 through 328 Processing sheet with id=AC5, first strand: chain 'Q' and resid 360 through 363 removed outlier: 6.864A pdb=" N VAL Q 361 " --> pdb=" O SER Q 411 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Q' and resid 365 through 366 removed outlier: 3.568A pdb=" N VAL Q 387 " --> pdb=" O ILE Q 377 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Q' and resid 598 through 599 removed outlier: 6.321A pdb=" N GLU Q 598 " --> pdb=" O MET Q 617 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N SER Q 619 " --> pdb=" O GLU Q 598 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU Q 644 " --> pdb=" O GLU Q 616 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER Q 618 " --> pdb=" O LEU Q 644 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG Q 646 " --> pdb=" O SER Q 618 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Q' and resid 781 through 786 removed outlier: 4.130A pdb=" N LYS Q 785 " --> pdb=" O ASN Q 726 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASN Q 726 " --> pdb=" O LYS Q 785 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL Q 732 " --> pdb=" O TYR Q 841 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR Q 841 " --> pdb=" O VAL Q 732 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER Q 734 " --> pdb=" O LEU Q 839 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR Q 842 " --> pdb=" O GLY Q 819 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Q' and resid 781 through 786 removed outlier: 4.130A pdb=" N LYS Q 785 " --> pdb=" O ASN Q 726 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASN Q 726 " --> pdb=" O LYS Q 785 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER Q 845 " --> pdb=" O ALA Q 727 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 761 through 763 349 hydrogen bonds defined for protein. 957 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: 5.36 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.14: 2 1.14 - 1.31: 2357 1.31 - 1.48: 5845 1.48 - 1.65: 5906 1.65 - 1.82: 134 Bond restraints: 14244 Sorted by residual: bond pdb=" O HOH A 501 " pdb=" H1 HOH A 501 " ideal model delta sigma weight residual 0.850 0.967 -0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" O HOH A 501 " pdb=" H2 HOH A 501 " ideal model delta sigma weight residual 0.850 0.966 -0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" CA SER B 189 " pdb=" CB SER B 189 " ideal model delta sigma weight residual 1.535 1.453 0.082 1.58e-02 4.01e+03 2.70e+01 bond pdb=" F2 ALF A 402 " pdb="AL ALF A 402 " ideal model delta sigma weight residual 1.685 1.782 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" F4 ALF A 402 " pdb="AL ALF A 402 " ideal model delta sigma weight residual 1.686 1.779 -0.093 2.00e-02 2.50e+03 2.17e+01 ... (remaining 14239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.15: 19371 14.15 - 28.31: 4 28.31 - 42.46: 0 42.46 - 56.62: 0 56.62 - 70.77: 2 Bond angle restraints: 19377 Sorted by residual: angle pdb=" F1 ALF A 402 " pdb="AL ALF A 402 " pdb=" F2 ALF A 402 " ideal model delta sigma weight residual 108.68 179.45 -70.77 3.00e+00 1.11e-01 5.57e+02 angle pdb=" F3 ALF A 402 " pdb="AL ALF A 402 " pdb=" F4 ALF A 402 " ideal model delta sigma weight residual 109.63 178.48 -68.85 3.00e+00 1.11e-01 5.27e+02 angle pdb=" N ASN B 268 " pdb=" CA ASN B 268 " pdb=" C ASN B 268 " ideal model delta sigma weight residual 114.39 103.74 10.65 1.45e+00 4.76e-01 5.40e+01 angle pdb=" F2 ALF A 402 " pdb="AL ALF A 402 " pdb=" F4 ALF A 402 " ideal model delta sigma weight residual 110.21 89.46 20.75 3.00e+00 1.11e-01 4.79e+01 angle pdb=" F1 ALF A 402 " pdb="AL ALF A 402 " pdb=" F3 ALF A 402 " ideal model delta sigma weight residual 109.69 88.97 20.72 3.00e+00 1.11e-01 4.77e+01 ... (remaining 19372 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.36: 7712 20.36 - 40.72: 686 40.72 - 61.07: 86 61.07 - 81.43: 22 81.43 - 101.79: 6 Dihedral angle restraints: 8512 sinusoidal: 3194 harmonic: 5318 Sorted by residual: dihedral pdb=" CA TYR Q 406 " pdb=" C TYR Q 406 " pdb=" N PRO Q 407 " pdb=" CA PRO Q 407 " ideal model delta harmonic sigma weight residual -180.00 -153.01 -26.99 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" O2B GDP A 401 " pdb=" O3A GDP A 401 " pdb=" PB GDP A 401 " pdb=" PA GDP A 401 " ideal model delta sinusoidal sigma weight residual -180.00 -78.21 -101.79 1 2.00e+01 2.50e-03 2.89e+01 dihedral pdb=" CA LEU B 139 " pdb=" C LEU B 139 " pdb=" N ALA B 140 " pdb=" CA ALA B 140 " ideal model delta harmonic sigma weight residual -180.00 -157.50 -22.50 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 8509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1535 0.058 - 0.117: 534 0.117 - 0.175: 120 0.175 - 0.234: 27 0.234 - 0.292: 8 Chirality restraints: 2224 Sorted by residual: chirality pdb=" CB VAL Q 756 " pdb=" CA VAL Q 756 " pdb=" CG1 VAL Q 756 " pdb=" CG2 VAL Q 756 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB VAL Q 61 " pdb=" CA VAL Q 61 " pdb=" CG1 VAL Q 61 " pdb=" CG2 VAL Q 61 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA TYR A 101 " pdb=" N TYR A 101 " pdb=" C TYR A 101 " pdb=" CB TYR A 101 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 2221 not shown) Planarity restraints: 2500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU Q 354 " -0.022 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C LEU Q 354 " 0.077 2.00e-02 2.50e+03 pdb=" O LEU Q 354 " -0.029 2.00e-02 2.50e+03 pdb=" N LEU Q 355 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE Q 285 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C PHE Q 285 " 0.064 2.00e-02 2.50e+03 pdb=" O PHE Q 285 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU Q 286 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER Q 455 " -0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO Q 456 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO Q 456 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO Q 456 " -0.050 5.00e-02 4.00e+02 ... (remaining 2497 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.62: 222 2.62 - 3.11: 9302 3.11 - 3.61: 16003 3.61 - 4.10: 22438 4.10 - 4.60: 33873 Nonbonded interactions: 81838 Sorted by model distance: nonbonded pdb=" OG1 THR A 186 " pdb="MG MG A 403 " model vdw 2.121 2.050 nonbonded pdb=" OG SER A 53 " pdb="MG MG A 403 " model vdw 2.136 2.050 nonbonded pdb=" O3B GDP A 401 " pdb=" F3 ALF A 402 " model vdw 2.197 2.870 nonbonded pdb=" O1B GDP A 401 " pdb=" F4 ALF A 402 " model vdw 2.209 2.870 nonbonded pdb=" O SER Q 656 " pdb=" OG1 THR Q 678 " model vdw 2.233 2.800 ... (remaining 81833 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 6 through 26 or (resid 27 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 36 and (name N or name CA or name C or name O or name CB )) or resi \ d 37 through 67 or (resid 68 and (name N or name CA or name C or name O or name \ CB )) or resid 69 through 87 or (resid 88 through 89 and (name N or name CA or n \ ame C or name O or name CB )) or resid 90 through 152 or (resid 153 through 154 \ and (name N or name CA or name C or name O or name CB )) or resid 155 through 17 \ 1 or (resid 172 and (name N or name CA or name C or name O or name CB )) or resi \ d 173 through 174 or (resid 175 and (name N or name CA or name C or name O or na \ me CB )) or resid 176 through 196 or (resid 197 and (name N or name CA or name C \ or name O or name CB )) or resid 198 through 216 or (resid 217 and (name N or n \ ame CA or name C or name O or name CB )) or resid 218 through 250 or (resid 251 \ and (name N or name CA or name C or name O or name CB )) or resid 252 through 25 \ 5 or (resid 256 through 259 and (name N or name CA or name C or name O or name C \ B )) or resid 260 through 300 or (resid 301 through 302 and (name N or name CA o \ r name C or name O or name CB )) or resid 303 through 321 or (resid 322 and (nam \ e N or name CA or name C or name O or name CB )) or resid 323 through 336 or (re \ sid 337 and (name N or name CA or name C or name O or name CB )) or resid 338 th \ rough 340)) selection = (chain 'C' and (resid 6 through 7 or (resid 8 through 9 and (name N or name CA o \ r name C or name O or name CB )) or resid 10 through 14 or (resid 15 and (name N \ or name CA or name C or name O or name CB )) or resid 16 through 19 or (resid 2 \ 0 through 24 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 5 through 88 or (resid 89 and (name N or name CA or name C or name O or name CB \ )) or resid 90 through 225 or (resid 226 and (name N or name CA or name C or nam \ e O or name CB )) or resid 227 through 282 or (resid 283 and (name N or name CA \ or name C or name O or name CB )) or resid 284 through 340)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.380 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.870 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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 : 0.011 0.122 14242 Z= 0.723 Angle : 1.343 70.773 19376 Z= 0.681 Chirality : 0.064 0.292 2224 Planarity : 0.007 0.091 2500 Dihedral : 15.568 101.788 5066 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.43 % Favored : 91.51 % Rotamer: Outliers : 0.82 % Allowed : 12.18 % Favored : 87.00 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % 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: -5.05 (0.15), residues: 1803 helix: -4.37 (0.12), residues: 477 sheet: -3.36 (0.22), residues: 387 loop : -2.73 (0.17), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 169 HIS 0.013 0.002 HIS Q 808 PHE 0.051 0.004 PHE Q 636 TYR 0.030 0.003 TYR Q 746 ARG 0.009 0.001 ARG Q 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 258 time to evaluate : 1.440 Fit side-chains REVERT: B 6 GLN cc_start: 0.7424 (mt0) cc_final: 0.7124 (tt0) REVERT: B 67 SER cc_start: 0.8675 (m) cc_final: 0.8102 (p) REVERT: B 101 MET cc_start: 0.8210 (mmm) cc_final: 0.7618 (mmt) REVERT: A 311 LYS cc_start: 0.8008 (mmtm) cc_final: 0.7590 (tttt) REVERT: Q 283 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7613 (tm-30) REVERT: Q 742 LYS cc_start: 0.8001 (mttt) cc_final: 0.7643 (tptt) outliers start: 12 outliers final: 8 residues processed: 269 average time/residue: 0.3253 time to fit residues: 122.1900 Evaluate side-chains 202 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 194 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 100 PRO Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain Q residue 35 THR Chi-restraints excluded: chain Q residue 169 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 6.9990 chunk 136 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 141 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 91 HIS B 155 ASN B 237 ASN B 293 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 119 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 GLN A 152 GLN A 218 HIS A 222 ASN A 317 ASN A 336 ASN Q 114 ASN Q 321 GLN Q 332 HIS Q 415 HIS ** Q 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 467 ASN Q 770 ASN ** Q 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 831 GLN ** Q 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.198485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.164452 restraints weight = 16241.496| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.38 r_work: 0.3658 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14242 Z= 0.176 Angle : 0.499 6.602 19376 Z= 0.265 Chirality : 0.041 0.147 2224 Planarity : 0.004 0.070 2500 Dihedral : 6.471 68.549 1989 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.81 % Allowed : 14.92 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.05 (0.17), residues: 1803 helix: -2.99 (0.19), residues: 481 sheet: -3.01 (0.23), residues: 374 loop : -2.33 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS A 287 PHE 0.017 0.001 PHE B 199 TYR 0.014 0.001 TYR Q 648 ARG 0.006 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 239 time to evaluate : 1.593 Fit side-chains REVERT: B 6 GLN cc_start: 0.7693 (mt0) cc_final: 0.6806 (tt0) REVERT: B 67 SER cc_start: 0.8912 (m) cc_final: 0.8253 (p) REVERT: C 13 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.6989 (pp30) REVERT: C 234 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.6969 (m-80) REVERT: A 42 LEU cc_start: 0.8432 (mp) cc_final: 0.8190 (mt) REVERT: A 97 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7750 (mp) REVERT: A 133 LYS cc_start: 0.7914 (tttt) cc_final: 0.7279 (tptt) REVERT: A 236 ASP cc_start: 0.8476 (t0) cc_final: 0.8266 (t70) REVERT: A 291 TYR cc_start: 0.7623 (m-80) cc_final: 0.7192 (m-80) REVERT: A 311 LYS cc_start: 0.7851 (mmtm) cc_final: 0.7496 (tttt) REVERT: Q 76 ARG cc_start: 0.7671 (ptm-80) cc_final: 0.7180 (ttp-110) REVERT: Q 101 GLU cc_start: 0.8336 (tp30) cc_final: 0.8123 (tp30) REVERT: Q 178 MET cc_start: 0.8737 (ttm) cc_final: 0.8519 (ttm) REVERT: Q 199 ARG cc_start: 0.8192 (ttp-170) cc_final: 0.7429 (tpp-160) REVERT: Q 610 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8220 (tmtt) REVERT: Q 742 LYS cc_start: 0.8389 (mttt) cc_final: 0.7648 (tptt) REVERT: Q 782 ASP cc_start: 0.8263 (p0) cc_final: 0.8054 (p0) outliers start: 41 outliers final: 27 residues processed: 266 average time/residue: 0.2809 time to fit residues: 107.2131 Evaluate side-chains 244 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain Q residue 35 THR Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 125 ASP Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 385 THR Chi-restraints excluded: chain Q residue 592 THR Chi-restraints excluded: chain Q residue 610 LYS Chi-restraints excluded: chain Q residue 757 ASP Chi-restraints excluded: chain Q residue 808 HIS Chi-restraints excluded: chain Q residue 842 THR Chi-restraints excluded: chain Q residue 845 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 4 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 169 optimal weight: 0.0000 chunk 157 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 155 optimal weight: 0.0170 chunk 127 optimal weight: 0.6980 overall best weight: 1.0824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 ASN ** Q 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.196104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.162118 restraints weight = 16328.593| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.40 r_work: 0.3627 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14242 Z= 0.206 Angle : 0.480 6.677 19376 Z= 0.249 Chirality : 0.041 0.150 2224 Planarity : 0.003 0.058 2500 Dihedral : 5.245 67.866 1971 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 23.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.70 % Allowed : 17.04 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.48 (0.18), residues: 1803 helix: -2.20 (0.22), residues: 485 sheet: -2.87 (0.24), residues: 376 loop : -2.06 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 169 HIS 0.003 0.001 HIS Q 852 PHE 0.016 0.001 PHE B 199 TYR 0.014 0.001 TYR Q 428 ARG 0.002 0.000 ARG Q 741 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 221 time to evaluate : 1.546 Fit side-chains REVERT: B 6 GLN cc_start: 0.7756 (mt0) cc_final: 0.6881 (tt0) REVERT: B 188 MET cc_start: 0.8224 (mmm) cc_final: 0.7755 (mmt) REVERT: C 13 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6857 (pp30) REVERT: C 83 ASP cc_start: 0.7364 (t0) cc_final: 0.7072 (t0) REVERT: C 139 LEU cc_start: 0.7027 (mt) cc_final: 0.6752 (mt) REVERT: C 234 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7191 (m-80) REVERT: C 283 ARG cc_start: 0.7609 (tpt-90) cc_final: 0.7201 (tpt-90) REVERT: A 42 LEU cc_start: 0.8451 (mp) cc_final: 0.8227 (mt) REVERT: A 311 LYS cc_start: 0.7862 (mmtm) cc_final: 0.7504 (tttt) REVERT: Q 76 ARG cc_start: 0.7817 (ptm-80) cc_final: 0.7348 (ttp-110) REVERT: Q 101 GLU cc_start: 0.8361 (tp30) cc_final: 0.8014 (tp30) REVERT: Q 178 MET cc_start: 0.8766 (ttm) cc_final: 0.8512 (ttm) REVERT: Q 199 ARG cc_start: 0.8043 (ttp-170) cc_final: 0.7324 (tpt170) REVERT: Q 254 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7803 (mm110) REVERT: Q 610 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8181 (tmtt) REVERT: Q 742 LYS cc_start: 0.8442 (mttt) cc_final: 0.7669 (tptt) REVERT: Q 782 ASP cc_start: 0.8432 (p0) cc_final: 0.8195 (p0) outliers start: 54 outliers final: 42 residues processed: 251 average time/residue: 0.3013 time to fit residues: 107.9736 Evaluate side-chains 253 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 207 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 125 ASP Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 254 GLN Chi-restraints excluded: chain Q residue 385 THR Chi-restraints excluded: chain Q residue 460 MET Chi-restraints excluded: chain Q residue 584 VAL Chi-restraints excluded: chain Q residue 592 THR Chi-restraints excluded: chain Q residue 610 LYS Chi-restraints excluded: chain Q residue 719 ILE Chi-restraints excluded: chain Q residue 757 ASP Chi-restraints excluded: chain Q residue 787 VAL Chi-restraints excluded: chain Q residue 808 HIS Chi-restraints excluded: chain Q residue 842 THR Chi-restraints excluded: chain Q residue 845 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 52 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 67 optimal weight: 0.0060 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 176 optimal weight: 0.0470 chunk 51 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 overall best weight: 1.4100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 75 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN Q 114 ASN Q 141 ASN ** Q 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 865 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.193682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.159712 restraints weight = 16441.908| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.41 r_work: 0.3605 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14242 Z= 0.251 Angle : 0.501 7.822 19376 Z= 0.257 Chirality : 0.042 0.134 2224 Planarity : 0.003 0.055 2500 Dihedral : 5.072 65.734 1968 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 26.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.93 % Allowed : 18.07 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.20 (0.19), residues: 1803 helix: -1.81 (0.23), residues: 483 sheet: -2.84 (0.24), residues: 378 loop : -1.91 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 169 HIS 0.003 0.001 HIS Q 808 PHE 0.022 0.002 PHE B 199 TYR 0.015 0.001 TYR A 291 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 213 time to evaluate : 1.542 Fit side-chains REVERT: B 6 GLN cc_start: 0.7730 (mt0) cc_final: 0.6929 (tt0) REVERT: B 188 MET cc_start: 0.8280 (mmm) cc_final: 0.7513 (mmt) REVERT: C 13 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6753 (pp30) REVERT: C 83 ASP cc_start: 0.7481 (t0) cc_final: 0.7208 (t0) REVERT: C 234 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: C 283 ARG cc_start: 0.7715 (tpt-90) cc_final: 0.7252 (tpt-90) REVERT: A 42 LEU cc_start: 0.8503 (mp) cc_final: 0.8286 (mt) REVERT: A 130 ASP cc_start: 0.6672 (m-30) cc_final: 0.6329 (m-30) REVERT: A 311 LYS cc_start: 0.8074 (mmtm) cc_final: 0.7658 (tttt) REVERT: Q 76 ARG cc_start: 0.7825 (ptm-80) cc_final: 0.7449 (ttp-110) REVERT: Q 101 GLU cc_start: 0.8333 (tp30) cc_final: 0.8001 (tp30) REVERT: Q 178 MET cc_start: 0.8761 (ttm) cc_final: 0.8531 (ttm) REVERT: Q 199 ARG cc_start: 0.7993 (ttp-170) cc_final: 0.7347 (tpt170) REVERT: Q 254 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.7698 (mm110) REVERT: Q 610 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8252 (tmtt) REVERT: Q 742 LYS cc_start: 0.8485 (mttt) cc_final: 0.7713 (tptt) REVERT: Q 782 ASP cc_start: 0.8395 (p0) cc_final: 0.8149 (p0) REVERT: Q 869 MET cc_start: 0.6883 (ttm) cc_final: 0.6612 (mtm) outliers start: 72 outliers final: 56 residues processed: 256 average time/residue: 0.2784 time to fit residues: 103.7683 Evaluate side-chains 265 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 205 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 113 VAL Chi-restraints excluded: chain Q residue 125 ASP Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 254 GLN Chi-restraints excluded: chain Q residue 378 THR Chi-restraints excluded: chain Q residue 385 THR Chi-restraints excluded: chain Q residue 398 GLU Chi-restraints excluded: chain Q residue 460 MET Chi-restraints excluded: chain Q residue 584 VAL Chi-restraints excluded: chain Q residue 592 THR Chi-restraints excluded: chain Q residue 610 LYS Chi-restraints excluded: chain Q residue 654 VAL Chi-restraints excluded: chain Q residue 678 THR Chi-restraints excluded: chain Q residue 683 MET Chi-restraints excluded: chain Q residue 719 ILE Chi-restraints excluded: chain Q residue 756 VAL Chi-restraints excluded: chain Q residue 757 ASP Chi-restraints excluded: chain Q residue 787 VAL Chi-restraints excluded: chain Q residue 808 HIS Chi-restraints excluded: chain Q residue 842 THR Chi-restraints excluded: chain Q residue 845 SER Chi-restraints excluded: chain Q residue 863 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 137 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 138 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 ASN ** Q 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.190570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.157206 restraints weight = 16667.709| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.44 r_work: 0.3579 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 14242 Z= 0.360 Angle : 0.564 7.984 19376 Z= 0.289 Chirality : 0.044 0.172 2224 Planarity : 0.004 0.074 2500 Dihedral : 5.370 69.329 1968 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 30.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 6.02 % Allowed : 19.44 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.17 (0.19), residues: 1803 helix: -1.71 (0.23), residues: 487 sheet: -2.86 (0.25), residues: 375 loop : -1.92 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 31 HIS 0.004 0.001 HIS Q 808 PHE 0.028 0.002 PHE B 199 TYR 0.019 0.002 TYR Q 746 ARG 0.003 0.000 ARG Q 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 206 time to evaluate : 1.590 Fit side-chains REVERT: B 6 GLN cc_start: 0.7830 (mt0) cc_final: 0.6895 (tt0) REVERT: B 101 MET cc_start: 0.8613 (mmt) cc_final: 0.8265 (mtt) REVERT: B 188 MET cc_start: 0.8341 (mmm) cc_final: 0.7612 (mmt) REVERT: C 83 ASP cc_start: 0.7510 (t0) cc_final: 0.7229 (t0) REVERT: C 234 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7623 (m-80) REVERT: C 283 ARG cc_start: 0.7681 (tpt-90) cc_final: 0.7247 (tpt-90) REVERT: A 42 LEU cc_start: 0.8567 (mp) cc_final: 0.8323 (mt) REVERT: A 130 ASP cc_start: 0.6859 (m-30) cc_final: 0.6500 (m-30) REVERT: A 311 LYS cc_start: 0.8087 (mmtm) cc_final: 0.7683 (tttt) REVERT: Q 76 ARG cc_start: 0.7890 (ptm-80) cc_final: 0.7538 (ttp-110) REVERT: Q 178 MET cc_start: 0.8822 (ttm) cc_final: 0.8543 (ttm) REVERT: Q 199 ARG cc_start: 0.7964 (ttp-170) cc_final: 0.7283 (tpt170) REVERT: Q 254 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.7765 (mm110) REVERT: Q 610 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8329 (tmtt) REVERT: Q 742 LYS cc_start: 0.8537 (mttt) cc_final: 0.7799 (tptt) REVERT: Q 750 ASP cc_start: 0.8091 (m-30) cc_final: 0.7780 (m-30) REVERT: Q 782 ASP cc_start: 0.8425 (p0) cc_final: 0.8223 (p0) outliers start: 88 outliers final: 72 residues processed: 259 average time/residue: 0.2955 time to fit residues: 110.2213 Evaluate side-chains 277 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 202 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 125 ASP Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain Q residue 202 SER Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 226 ILE Chi-restraints excluded: chain Q residue 254 GLN Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain Q residue 378 THR Chi-restraints excluded: chain Q residue 385 THR Chi-restraints excluded: chain Q residue 398 GLU Chi-restraints excluded: chain Q residue 457 GLN Chi-restraints excluded: chain Q residue 460 MET Chi-restraints excluded: chain Q residue 584 VAL Chi-restraints excluded: chain Q residue 592 THR Chi-restraints excluded: chain Q residue 610 LYS Chi-restraints excluded: chain Q residue 654 VAL Chi-restraints excluded: chain Q residue 678 THR Chi-restraints excluded: chain Q residue 683 MET Chi-restraints excluded: chain Q residue 699 LEU Chi-restraints excluded: chain Q residue 712 PHE Chi-restraints excluded: chain Q residue 719 ILE Chi-restraints excluded: chain Q residue 747 VAL Chi-restraints excluded: chain Q residue 756 VAL Chi-restraints excluded: chain Q residue 757 ASP Chi-restraints excluded: chain Q residue 787 VAL Chi-restraints excluded: chain Q residue 808 HIS Chi-restraints excluded: chain Q residue 842 THR Chi-restraints excluded: chain Q residue 845 SER Chi-restraints excluded: chain Q residue 863 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 85 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 179 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 111 optimal weight: 0.2980 chunk 178 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 20 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 0.0770 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 ASN ** Q 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.197245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.163586 restraints weight = 16460.436| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.41 r_work: 0.3645 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14242 Z= 0.114 Angle : 0.419 6.157 19376 Z= 0.218 Chirality : 0.040 0.131 2224 Planarity : 0.003 0.069 2500 Dihedral : 4.465 50.214 1968 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 29.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.08 % Allowed : 23.07 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.72 (0.19), residues: 1803 helix: -1.26 (0.24), residues: 493 sheet: -2.63 (0.25), residues: 372 loop : -1.68 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 63 HIS 0.003 0.000 HIS B 266 PHE 0.021 0.001 PHE C 292 TYR 0.009 0.001 TYR Q 53 ARG 0.002 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 1.607 Fit side-chains REVERT: B 6 GLN cc_start: 0.7772 (mt0) cc_final: 0.7098 (tt0) REVERT: B 188 MET cc_start: 0.8082 (mmm) cc_final: 0.7349 (mmt) REVERT: C 13 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.6919 (pp30) REVERT: C 83 ASP cc_start: 0.7257 (t0) cc_final: 0.7042 (t0) REVERT: C 169 TRP cc_start: 0.8170 (m-10) cc_final: 0.7847 (m-10) REVERT: C 207 SER cc_start: 0.8354 (m) cc_final: 0.8118 (p) REVERT: C 219 ARG cc_start: 0.6743 (mtp-110) cc_final: 0.6490 (mtp-110) REVERT: C 234 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7135 (m-80) REVERT: C 283 ARG cc_start: 0.7604 (tpt-90) cc_final: 0.7191 (tpt-90) REVERT: A 42 LEU cc_start: 0.8274 (mp) cc_final: 0.8054 (mt) REVERT: A 311 LYS cc_start: 0.8024 (mmtm) cc_final: 0.7614 (tttt) REVERT: Q 76 ARG cc_start: 0.7626 (ptm-80) cc_final: 0.7353 (ttp-110) REVERT: Q 101 GLU cc_start: 0.8248 (tp30) cc_final: 0.7941 (tp30) REVERT: Q 178 MET cc_start: 0.8670 (ttm) cc_final: 0.8308 (ttt) REVERT: Q 199 ARG cc_start: 0.7793 (ttp-170) cc_final: 0.7360 (tpt170) REVERT: Q 634 MET cc_start: 0.7684 (mmm) cc_final: 0.7310 (mmm) REVERT: Q 742 LYS cc_start: 0.8297 (mttt) cc_final: 0.7667 (tptt) REVERT: Q 782 ASP cc_start: 0.8219 (p0) cc_final: 0.7976 (p0) outliers start: 45 outliers final: 33 residues processed: 250 average time/residue: 0.3060 time to fit residues: 109.9221 Evaluate side-chains 246 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 211 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 114 ASN Chi-restraints excluded: chain Q residue 125 ASP Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 385 THR Chi-restraints excluded: chain Q residue 398 GLU Chi-restraints excluded: chain Q residue 584 VAL Chi-restraints excluded: chain Q residue 678 THR Chi-restraints excluded: chain Q residue 699 LEU Chi-restraints excluded: chain Q residue 771 SER Chi-restraints excluded: chain Q residue 787 VAL Chi-restraints excluded: chain Q residue 808 HIS Chi-restraints excluded: chain Q residue 845 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 130 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 29 optimal weight: 0.2980 chunk 12 optimal weight: 4.9990 chunk 153 optimal weight: 0.6980 chunk 142 optimal weight: 0.5980 chunk 117 optimal weight: 0.0770 chunk 55 optimal weight: 8.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 ASN ** Q 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.195246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.161388 restraints weight = 16540.689| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.29 r_work: 0.3634 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14242 Z= 0.179 Angle : 0.442 5.954 19376 Z= 0.227 Chirality : 0.041 0.132 2224 Planarity : 0.003 0.062 2500 Dihedral : 4.487 53.721 1968 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 29.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.31 % Allowed : 22.25 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.55 (0.20), residues: 1803 helix: -1.01 (0.25), residues: 486 sheet: -2.54 (0.25), residues: 383 loop : -1.61 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 297 HIS 0.002 0.000 HIS B 266 PHE 0.017 0.001 PHE C 292 TYR 0.011 0.001 TYR Q 648 ARG 0.002 0.000 ARG Q 185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 215 time to evaluate : 1.565 Fit side-chains REVERT: B 6 GLN cc_start: 0.7791 (mt0) cc_final: 0.7108 (tt0) REVERT: B 101 MET cc_start: 0.8563 (mmt) cc_final: 0.8219 (mtt) REVERT: B 188 MET cc_start: 0.8257 (mmm) cc_final: 0.7541 (mmt) REVERT: C 13 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7230 (pp30) REVERT: C 169 TRP cc_start: 0.8290 (m-10) cc_final: 0.7973 (m-10) REVERT: C 207 SER cc_start: 0.8368 (m) cc_final: 0.8122 (p) REVERT: C 219 ARG cc_start: 0.6882 (mtp-110) cc_final: 0.6609 (mtp-110) REVERT: C 234 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7293 (m-80) REVERT: C 283 ARG cc_start: 0.7626 (tpt-90) cc_final: 0.7151 (tpt-90) REVERT: A 42 LEU cc_start: 0.8462 (mp) cc_final: 0.8230 (mt) REVERT: A 200 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8072 (mt) REVERT: A 311 LYS cc_start: 0.7946 (mmtm) cc_final: 0.7561 (tttt) REVERT: Q 76 ARG cc_start: 0.7810 (ptm-80) cc_final: 0.7482 (ttp-110) REVERT: Q 101 GLU cc_start: 0.8458 (tp30) cc_final: 0.8057 (tp30) REVERT: Q 178 MET cc_start: 0.8759 (ttm) cc_final: 0.8341 (ttt) REVERT: Q 199 ARG cc_start: 0.7950 (ttp-170) cc_final: 0.7293 (tpt170) REVERT: Q 254 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.7632 (mm110) REVERT: Q 634 MET cc_start: 0.7773 (mmm) cc_final: 0.7438 (mmm) REVERT: Q 742 LYS cc_start: 0.8456 (mttt) cc_final: 0.7703 (tptt) REVERT: Q 782 ASP cc_start: 0.8400 (p0) cc_final: 0.8141 (p0) outliers start: 63 outliers final: 49 residues processed: 255 average time/residue: 0.3236 time to fit residues: 119.4752 Evaluate side-chains 265 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 212 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 114 ASN Chi-restraints excluded: chain Q residue 125 ASP Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 254 GLN Chi-restraints excluded: chain Q residue 290 GLN Chi-restraints excluded: chain Q residue 385 THR Chi-restraints excluded: chain Q residue 398 GLU Chi-restraints excluded: chain Q residue 584 VAL Chi-restraints excluded: chain Q residue 592 THR Chi-restraints excluded: chain Q residue 683 MET Chi-restraints excluded: chain Q residue 699 LEU Chi-restraints excluded: chain Q residue 771 SER Chi-restraints excluded: chain Q residue 787 VAL Chi-restraints excluded: chain Q residue 808 HIS Chi-restraints excluded: chain Q residue 845 SER Chi-restraints excluded: chain Q residue 863 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 112 optimal weight: 0.3980 chunk 157 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 87 optimal weight: 0.0060 chunk 31 optimal weight: 1.9990 chunk 134 optimal weight: 0.2980 chunk 17 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 158 optimal weight: 0.1980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN ** Q 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 666 ASN ** Q 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 852 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.198196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.164727 restraints weight = 16315.818| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.29 r_work: 0.3676 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14242 Z= 0.108 Angle : 0.403 5.799 19376 Z= 0.208 Chirality : 0.040 0.130 2224 Planarity : 0.002 0.057 2500 Dihedral : 4.140 45.482 1968 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 29.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.94 % Allowed : 23.82 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.22 (0.20), residues: 1803 helix: -0.80 (0.26), residues: 487 sheet: -2.29 (0.26), residues: 373 loop : -1.41 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 297 HIS 0.003 0.000 HIS B 266 PHE 0.015 0.001 PHE C 292 TYR 0.009 0.001 TYR Q 53 ARG 0.002 0.000 ARG Q 185 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 216 time to evaluate : 1.667 Fit side-chains REVERT: B 6 GLN cc_start: 0.7827 (mt0) cc_final: 0.7169 (tt0) REVERT: B 101 MET cc_start: 0.8487 (mmt) cc_final: 0.8124 (mtt) REVERT: B 188 MET cc_start: 0.8179 (mmm) cc_final: 0.7477 (mmt) REVERT: C 13 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7308 (pp30) REVERT: C 207 SER cc_start: 0.8361 (m) cc_final: 0.8145 (p) REVERT: C 219 ARG cc_start: 0.6818 (mtp-110) cc_final: 0.6548 (mtp-110) REVERT: C 234 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7093 (m-80) REVERT: C 283 ARG cc_start: 0.7642 (tpt-90) cc_final: 0.7188 (tpt-90) REVERT: A 42 LEU cc_start: 0.8414 (mp) cc_final: 0.8202 (mt) REVERT: A 299 GLN cc_start: 0.6121 (tp-100) cc_final: 0.5742 (tp-100) REVERT: A 311 LYS cc_start: 0.7919 (mmtm) cc_final: 0.7566 (tttt) REVERT: Q 76 ARG cc_start: 0.7750 (ptm-80) cc_final: 0.7443 (ttp-110) REVERT: Q 101 GLU cc_start: 0.8466 (tp30) cc_final: 0.8050 (tp30) REVERT: Q 178 MET cc_start: 0.8705 (ttm) cc_final: 0.8327 (ttt) REVERT: Q 199 ARG cc_start: 0.7926 (ttp-170) cc_final: 0.7391 (tpt170) REVERT: Q 254 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7625 (mm110) REVERT: Q 742 LYS cc_start: 0.8432 (mttt) cc_final: 0.7729 (tptt) REVERT: Q 782 ASP cc_start: 0.8353 (p0) cc_final: 0.8082 (p0) outliers start: 43 outliers final: 34 residues processed: 248 average time/residue: 0.3162 time to fit residues: 113.8101 Evaluate side-chains 247 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 210 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 116 VAL Chi-restraints excluded: chain Q residue 125 ASP Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 254 GLN Chi-restraints excluded: chain Q residue 290 GLN Chi-restraints excluded: chain Q residue 385 THR Chi-restraints excluded: chain Q residue 398 GLU Chi-restraints excluded: chain Q residue 584 VAL Chi-restraints excluded: chain Q residue 699 LEU Chi-restraints excluded: chain Q residue 766 THR Chi-restraints excluded: chain Q residue 771 SER Chi-restraints excluded: chain Q residue 808 HIS Chi-restraints excluded: chain Q residue 863 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 92 optimal weight: 4.9990 chunk 147 optimal weight: 0.0060 chunk 0 optimal weight: 20.0000 chunk 136 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 18 optimal weight: 0.1980 chunk 64 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 167 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.192805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.159020 restraints weight = 16492.118| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.39 r_work: 0.3603 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14242 Z= 0.257 Angle : 0.488 6.163 19376 Z= 0.249 Chirality : 0.042 0.137 2224 Planarity : 0.003 0.058 2500 Dihedral : 4.623 58.817 1968 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 31.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.83 % Allowed : 23.68 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.33 (0.20), residues: 1803 helix: -0.77 (0.26), residues: 487 sheet: -2.49 (0.25), residues: 390 loop : -1.46 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 297 HIS 0.003 0.001 HIS Q 808 PHE 0.023 0.001 PHE B 199 TYR 0.015 0.001 TYR Q 746 ARG 0.002 0.000 ARG Q 185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 210 time to evaluate : 1.503 Fit side-chains REVERT: B 6 GLN cc_start: 0.7790 (mt0) cc_final: 0.7143 (tt0) REVERT: B 101 MET cc_start: 0.8612 (mmt) cc_final: 0.8311 (mtt) REVERT: B 188 MET cc_start: 0.8314 (mmm) cc_final: 0.7658 (mmt) REVERT: C 13 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7252 (pp30) REVERT: C 207 SER cc_start: 0.8394 (m) cc_final: 0.8178 (p) REVERT: C 219 ARG cc_start: 0.6902 (mtp-110) cc_final: 0.6602 (mtp-110) REVERT: C 234 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7405 (m-80) REVERT: C 283 ARG cc_start: 0.7641 (tpt-90) cc_final: 0.7110 (tpt-90) REVERT: A 42 LEU cc_start: 0.8508 (mp) cc_final: 0.8275 (mt) REVERT: A 130 ASP cc_start: 0.6836 (m-30) cc_final: 0.6423 (m-30) REVERT: A 200 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8102 (mt) REVERT: A 299 GLN cc_start: 0.6129 (tp-100) cc_final: 0.5774 (tp-100) REVERT: A 311 LYS cc_start: 0.7955 (mmtm) cc_final: 0.7603 (tttt) REVERT: Q 76 ARG cc_start: 0.7807 (ptm-80) cc_final: 0.7489 (ttp-110) REVERT: Q 101 GLU cc_start: 0.8425 (tp30) cc_final: 0.8024 (tp30) REVERT: Q 254 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7494 (mm110) REVERT: Q 634 MET cc_start: 0.7678 (mmm) cc_final: 0.7400 (mmm) REVERT: Q 742 LYS cc_start: 0.8495 (mttt) cc_final: 0.7776 (tptt) REVERT: Q 782 ASP cc_start: 0.8394 (p0) cc_final: 0.8140 (p0) outliers start: 56 outliers final: 49 residues processed: 246 average time/residue: 0.3036 time to fit residues: 107.4147 Evaluate side-chains 260 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 207 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 125 ASP Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain Q residue 202 SER Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 254 GLN Chi-restraints excluded: chain Q residue 290 GLN Chi-restraints excluded: chain Q residue 385 THR Chi-restraints excluded: chain Q residue 398 GLU Chi-restraints excluded: chain Q residue 584 VAL Chi-restraints excluded: chain Q residue 592 THR Chi-restraints excluded: chain Q residue 654 VAL Chi-restraints excluded: chain Q residue 699 LEU Chi-restraints excluded: chain Q residue 766 THR Chi-restraints excluded: chain Q residue 771 SER Chi-restraints excluded: chain Q residue 787 VAL Chi-restraints excluded: chain Q residue 808 HIS Chi-restraints excluded: chain Q residue 842 THR Chi-restraints excluded: chain Q residue 863 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 69 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 170 optimal weight: 0.0040 chunk 51 optimal weight: 0.0070 chunk 63 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 148 optimal weight: 0.1980 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 overall best weight: 0.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 693 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.197827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.164295 restraints weight = 16318.549| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.29 r_work: 0.3668 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14242 Z= 0.113 Angle : 0.410 5.820 19376 Z= 0.211 Chirality : 0.040 0.130 2224 Planarity : 0.002 0.054 2500 Dihedral : 4.136 46.076 1968 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 29.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.15 % Allowed : 24.44 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.06 (0.20), residues: 1803 helix: -0.59 (0.26), residues: 488 sheet: -2.31 (0.26), residues: 384 loop : -1.27 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 297 HIS 0.003 0.000 HIS B 266 PHE 0.013 0.001 PHE A 339 TYR 0.008 0.001 TYR Q 53 ARG 0.002 0.000 ARG C 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 217 time to evaluate : 1.473 Fit side-chains REVERT: B 6 GLN cc_start: 0.7794 (mt0) cc_final: 0.7191 (tt0) REVERT: B 101 MET cc_start: 0.8503 (mmt) cc_final: 0.8154 (mtt) REVERT: B 188 MET cc_start: 0.8176 (mmm) cc_final: 0.7513 (mmt) REVERT: C 219 ARG cc_start: 0.6850 (mtp-110) cc_final: 0.6575 (mtp-110) REVERT: C 234 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7212 (m-80) REVERT: C 283 ARG cc_start: 0.7698 (tpt-90) cc_final: 0.7197 (tpt-90) REVERT: A 42 LEU cc_start: 0.8429 (mp) cc_final: 0.8213 (mt) REVERT: A 299 GLN cc_start: 0.6128 (tp-100) cc_final: 0.5758 (tp-100) REVERT: A 311 LYS cc_start: 0.7906 (mmtm) cc_final: 0.7587 (tttt) REVERT: Q 76 ARG cc_start: 0.7765 (ptm-80) cc_final: 0.7457 (ttp-110) REVERT: Q 101 GLU cc_start: 0.8415 (tp30) cc_final: 0.8020 (tp30) REVERT: Q 178 MET cc_start: 0.8705 (ttm) cc_final: 0.8316 (ttt) REVERT: Q 254 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.7540 (mm110) REVERT: Q 634 MET cc_start: 0.7682 (mmm) cc_final: 0.7395 (mmm) REVERT: Q 742 LYS cc_start: 0.8380 (mttt) cc_final: 0.7712 (tptt) REVERT: Q 782 ASP cc_start: 0.8355 (p0) cc_final: 0.8090 (p0) outliers start: 46 outliers final: 41 residues processed: 249 average time/residue: 0.3002 time to fit residues: 106.6153 Evaluate side-chains 256 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 125 ASP Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 254 GLN Chi-restraints excluded: chain Q residue 290 GLN Chi-restraints excluded: chain Q residue 385 THR Chi-restraints excluded: chain Q residue 398 GLU Chi-restraints excluded: chain Q residue 584 VAL Chi-restraints excluded: chain Q residue 592 THR Chi-restraints excluded: chain Q residue 654 VAL Chi-restraints excluded: chain Q residue 699 LEU Chi-restraints excluded: chain Q residue 766 THR Chi-restraints excluded: chain Q residue 771 SER Chi-restraints excluded: chain Q residue 808 HIS Chi-restraints excluded: chain Q residue 842 THR Chi-restraints excluded: chain Q residue 863 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 133 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 31 optimal weight: 0.0570 chunk 177 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 830 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.194181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.160566 restraints weight = 16569.845| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.40 r_work: 0.3613 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14242 Z= 0.216 Angle : 0.458 6.039 19376 Z= 0.234 Chirality : 0.041 0.134 2224 Planarity : 0.003 0.056 2500 Dihedral : 4.412 54.843 1968 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 31.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.11 % Allowed : 23.41 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.10 (0.20), residues: 1803 helix: -0.52 (0.26), residues: 490 sheet: -2.44 (0.25), residues: 390 loop : -1.30 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 297 HIS 0.003 0.001 HIS Q 852 PHE 0.019 0.001 PHE B 199 TYR 0.015 0.001 TYR Q 428 ARG 0.003 0.000 ARG Q 741 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7500.23 seconds wall clock time: 139 minutes 25.49 seconds (8365.49 seconds total)