Starting phenix.real_space_refine on Thu Jun 12 16:06:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fig_31596/06_2025/7fig_31596_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fig_31596/06_2025/7fig_31596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fig_31596/06_2025/7fig_31596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fig_31596/06_2025/7fig_31596.map" model { file = "/net/cci-nas-00/data/ceres_data/7fig_31596/06_2025/7fig_31596_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fig_31596/06_2025/7fig_31596_neut.cif" } resolution = 3.9 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= 0.000 sd= 0.003 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 1474 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: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 8122 2.51 5 N 2214 2.21 5 O 2404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12839 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2932 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 350} Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 4334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4334 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 527} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "X" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 678 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain: "Y" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 97} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.18, per 1000 atoms: 0.64 Number of scatterers: 12839 At special positions: 0 Unit cell: (93.005, 97.185, 182.875, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 2404 8.00 N 2214 7.00 C 8122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.06 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 156 " distance=2.03 Simple disulfide: pdb=" SG CYS R 279 " - pdb=" SG CYS R 343 " distance=2.03 Simple disulfide: pdb=" SG CYS R 280 " - pdb=" SG CYS R 353 " distance=2.02 Simple disulfide: pdb=" SG CYS R 439 " - pdb=" SG CYS R 514 " distance=2.02 Simple disulfide: pdb=" SG CYS X 7 " - pdb=" SG CYS X 31 " distance=2.03 Simple disulfide: pdb=" SG CYS X 10 " - pdb=" SG CYS X 60 " distance=2.03 Simple disulfide: pdb=" SG CYS X 28 " - pdb=" SG CYS X 82 " distance=2.03 Simple disulfide: pdb=" SG CYS X 32 " - pdb=" SG CYS X 84 " distance=2.03 Simple disulfide: pdb=" SG CYS X 59 " - pdb=" SG CYS X 87 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 9 " - pdb=" SG CYS Y 57 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 72 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 26 " - pdb=" SG CYS Y 110 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 34 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 38 " - pdb=" SG CYS Y 90 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 93 " - pdb=" SG CYS Y 100 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG R2000 " - " ASN R 174 " " NAG R2001 " - " ASN R 195 " " NAG X 101 " - " ASN X 52 " " NAG X 102 " - " ASN X 78 " " NAG Y1000 " - " ASN Y 13 " Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.7 seconds 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3082 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 21 sheets defined 36.0% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.514A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 62 through 91 Processing helix chain 'A' and resid 99 through 113 removed outlier: 4.087A pdb=" N ASP A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.826A pdb=" N ALA A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG A 129 " --> pdb=" O GLY A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.691A pdb=" N GLN A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.613A pdb=" N TYR A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ARG A 161 " --> pdb=" O ASN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 179 removed outlier: 3.690A pdb=" N VAL A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 removed outlier: 4.471A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 247 through 250 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 298 through 319 removed outlier: 4.115A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 removed outlier: 4.152A pdb=" N ARG A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 357 " --> pdb=" O MET A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.575A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 25 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 141 through 145 removed outlier: 3.589A pdb=" N PHE R 145 " --> pdb=" O THR R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 219 Processing helix chain 'R' and resid 241 through 245 Processing helix chain 'R' and resid 261 through 266 removed outlier: 3.747A pdb=" N VAL R 266 " --> pdb=" O GLU R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 277 No H-bonds generated for 'chain 'R' and resid 275 through 277' Processing helix chain 'R' and resid 278 through 283 removed outlier: 3.882A pdb=" N PHE R 282 " --> pdb=" O HIS R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 337 removed outlier: 3.918A pdb=" N LEU R 337 " --> pdb=" O GLY R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 359 through 387 removed outlier: 3.595A pdb=" N TRP R 367 " --> pdb=" O ARG R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 423 Processing helix chain 'R' and resid 425 through 436 removed outlier: 3.815A pdb=" N HIS R 429 " --> pdb=" O GLN R 425 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE R 431 " --> pdb=" O TYR R 427 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ASP R 432 " --> pdb=" O ASN R 428 " (cutoff:3.500A) Processing helix chain 'R' and resid 436 through 470 Processing helix chain 'R' and resid 479 through 500 Processing helix chain 'R' and resid 507 through 511 removed outlier: 3.953A pdb=" N VAL R 511 " --> pdb=" O TYR R 508 " (cutoff:3.500A) Processing helix chain 'R' and resid 521 through 554 Processing helix chain 'R' and resid 560 through 594 removed outlier: 3.988A pdb=" N ALA R 568 " --> pdb=" O ASP R 564 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE R 573 " --> pdb=" O LYS R 569 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU R 574 " --> pdb=" O LYS R 570 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP R 578 " --> pdb=" O LEU R 574 " (cutoff:3.500A) Proline residue: R 584 - end of helix removed outlier: 3.590A pdb=" N SER R 591 " --> pdb=" O PHE R 587 " (cutoff:3.500A) Processing helix chain 'R' and resid 603 through 623 removed outlier: 3.777A pdb=" N LEU R 607 " --> pdb=" O ASN R 603 " (cutoff:3.500A) Proline residue: R 613 - end of helix removed outlier: 4.600A pdb=" N SER R 616 " --> pdb=" O TYR R 612 " (cutoff:3.500A) Proline residue: R 620 - end of helix Processing helix chain 'R' and resid 627 through 641 removed outlier: 3.749A pdb=" N ASP R 633 " --> pdb=" O THR R 629 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 45 Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.956A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 191 Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 50 removed outlier: 3.566A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.781A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.826A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 153 removed outlier: 6.405A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.911A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.660A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.803A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.745A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 53 through 56 removed outlier: 6.002A pdb=" N LEU R 54 " --> pdb=" O GLU R 79 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE R 103 " --> pdb=" O SER R 129 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N CYS R 131 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE R 105 " --> pdb=" O CYS R 131 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR R 133 " --> pdb=" O ILE R 105 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASN R 107 " --> pdb=" O THR R 133 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU R 128 " --> pdb=" O GLU R 154 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N CYS R 156 " --> pdb=" O LEU R 128 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE R 130 " --> pdb=" O CYS R 156 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE R 151 " --> pdb=" O THR R 178 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LYS R 180 " --> pdb=" O PHE R 151 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU R 153 " --> pdb=" O LYS R 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL R 177 " --> pdb=" O LEU R 199 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER R 201 " --> pdb=" O VAL R 177 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN R 195 " --> pdb=" O GLY R 220 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR R 222 " --> pdb=" O ASN R 195 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N THR R 197 " --> pdb=" O THR R 222 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 53 through 56 removed outlier: 6.002A pdb=" N LEU R 54 " --> pdb=" O GLU R 79 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE R 103 " --> pdb=" O SER R 129 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N CYS R 131 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE R 105 " --> pdb=" O CYS R 131 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR R 133 " --> pdb=" O ILE R 105 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASN R 107 " --> pdb=" O THR R 133 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU R 128 " --> pdb=" O GLU R 154 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N CYS R 156 " --> pdb=" O LEU R 128 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE R 130 " --> pdb=" O CYS R 156 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE R 151 " --> pdb=" O THR R 178 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LYS R 180 " --> pdb=" O PHE R 151 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU R 153 " --> pdb=" O LYS R 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL R 177 " --> pdb=" O LEU R 199 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER R 201 " --> pdb=" O VAL R 177 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N THR R 226 " --> pdb=" O THR R 198 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR R 200 " --> pdb=" O THR R 226 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASP R 228 " --> pdb=" O THR R 200 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU R 202 " --> pdb=" O ASP R 228 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU R 227 " --> pdb=" O ILE R 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 63 through 64 Processing sheet with id=AB6, first strand: chain 'R' and resid 94 through 95 removed outlier: 6.348A pdb=" N PHE R 94 " --> pdb=" O ILE R 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'R' and resid 163 through 164 removed outlier: 3.502A pdb=" N VAL R 189 " --> pdb=" O LYS R 212 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'X' and resid 11 through 14 removed outlier: 10.790A pdb=" N THR Y 32 " --> pdb=" O PRO X 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'X' and resid 11 through 14 Processing sheet with id=AC1, first strand: chain 'X' and resid 59 through 69 removed outlier: 5.956A pdb=" N CYS X 60 " --> pdb=" O CYS X 84 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N CYS X 84 " --> pdb=" O CYS X 60 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA X 62 " --> pdb=" O CYS X 82 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N CYS X 82 " --> pdb=" O ALA X 62 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N SER X 64 " --> pdb=" O THR X 80 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'X' and resid 91 through 92 Processing sheet with id=AC3, first strand: chain 'Y' and resid 56 through 68 removed outlier: 6.544A pdb=" N SER Y 87 " --> pdb=" O ARG Y 60 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL Y 62 " --> pdb=" O ALA Y 85 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ALA Y 85 " --> pdb=" O VAL Y 62 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE Y 64 " --> pdb=" O ALA Y 83 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA Y 83 " --> pdb=" O PHE Y 64 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER Y 66 " --> pdb=" O SER Y 81 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N SER Y 81 " --> pdb=" O SER Y 66 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ARG Y 68 " --> pdb=" O VAL Y 79 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL Y 79 " --> pdb=" O ARG Y 68 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1599 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: 4.11 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2509 1.33 - 1.45: 3171 1.45 - 1.57: 7282 1.57 - 1.70: 0 1.70 - 1.82: 134 Bond restraints: 13096 Sorted by residual: bond pdb=" CZ ARG A 205 " pdb=" NH2 ARG A 205 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.30e-02 5.92e+03 1.36e+01 bond pdb=" CZ ARG A 90 " pdb=" NH2 ARG A 90 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.30e-02 5.92e+03 1.36e+01 bond pdb=" CZ ARG A 144 " pdb=" NH2 ARG A 144 " ideal model delta sigma weight residual 1.330 1.285 0.045 1.30e-02 5.92e+03 1.18e+01 bond pdb=" CZ ARG A 142 " pdb=" NH2 ARG A 142 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.16e+01 bond pdb=" CZ ARG N 98 " pdb=" NH2 ARG N 98 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.10e+01 ... (remaining 13091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 15965 1.74 - 3.48: 1423 3.48 - 5.23: 312 5.23 - 6.97: 44 6.97 - 8.71: 7 Bond angle restraints: 17751 Sorted by residual: angle pdb=" CA ASP N 50 " pdb=" CB ASP N 50 " pdb=" CG ASP N 50 " ideal model delta sigma weight residual 112.60 119.49 -6.89 1.00e+00 1.00e+00 4.74e+01 angle pdb=" C ARG N 105 " pdb=" N ASP N 106 " pdb=" CA ASP N 106 " ideal model delta sigma weight residual 120.65 129.03 -8.38 1.32e+00 5.74e-01 4.03e+01 angle pdb=" CA PHE N 68 " pdb=" CB PHE N 68 " pdb=" CG PHE N 68 " ideal model delta sigma weight residual 113.80 119.65 -5.85 1.00e+00 1.00e+00 3.42e+01 angle pdb=" CA ASP N 106 " pdb=" CB ASP N 106 " pdb=" CG ASP N 106 " ideal model delta sigma weight residual 112.60 118.39 -5.79 1.00e+00 1.00e+00 3.36e+01 angle pdb=" C GLN B 176 " pdb=" N THR B 177 " pdb=" CA THR B 177 " ideal model delta sigma weight residual 120.63 129.34 -8.71 1.61e+00 3.86e-01 2.93e+01 ... (remaining 17746 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 7327 17.46 - 34.93: 556 34.93 - 52.39: 76 52.39 - 69.85: 28 69.85 - 87.31: 16 Dihedral angle restraints: 8003 sinusoidal: 3238 harmonic: 4765 Sorted by residual: dihedral pdb=" CA CYS B 204 " pdb=" C CYS B 204 " pdb=" N ASP B 205 " pdb=" CA ASP B 205 " ideal model delta harmonic sigma weight residual 180.00 150.53 29.47 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 150.99 29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 151.15 28.85 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 8000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1723 0.076 - 0.152: 250 0.152 - 0.228: 51 0.228 - 0.305: 10 0.305 - 0.381: 4 Chirality restraints: 2038 Sorted by residual: chirality pdb=" CA TYR A 69 " pdb=" N TYR A 69 " pdb=" C TYR A 69 " pdb=" CB TYR A 69 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA THR N 114 " pdb=" N THR N 114 " pdb=" C THR N 114 " pdb=" CB THR N 114 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA CYS N 107 " pdb=" N CYS N 107 " pdb=" C CYS N 107 " pdb=" CB CYS N 107 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 2035 not shown) Planarity restraints: 2275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 95 " 0.146 2.00e-02 2.50e+03 8.22e-02 1.35e+02 pdb=" CG TYR N 95 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR N 95 " -0.062 2.00e-02 2.50e+03 pdb=" CD2 TYR N 95 " -0.068 2.00e-02 2.50e+03 pdb=" CE1 TYR N 95 " -0.056 2.00e-02 2.50e+03 pdb=" CE2 TYR N 95 " -0.048 2.00e-02 2.50e+03 pdb=" CZ TYR N 95 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR N 95 " 0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 167 " 0.116 2.00e-02 2.50e+03 6.53e-02 8.52e+01 pdb=" CG TYR A 167 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 167 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR A 167 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR A 167 " -0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR A 167 " -0.034 2.00e-02 2.50e+03 pdb=" CZ TYR A 167 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 167 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 154 " -0.121 2.00e-02 2.50e+03 6.31e-02 7.96e+01 pdb=" CG TYR A 154 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR A 154 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR A 154 " 0.055 2.00e-02 2.50e+03 pdb=" CE1 TYR A 154 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR A 154 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR A 154 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 154 " -0.085 2.00e-02 2.50e+03 ... (remaining 2272 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 116 2.59 - 3.17: 11968 3.17 - 3.74: 20140 3.74 - 4.32: 28900 4.32 - 4.90: 47044 Nonbonded interactions: 108168 Sorted by model distance: nonbonded pdb=" O CYS B 204 " pdb=" OD1 ASP B 228 " model vdw 2.011 3.040 nonbonded pdb=" NZ LYS B 57 " pdb=" OE1 GLN B 75 " model vdw 2.028 3.120 nonbonded pdb=" O3 NAG Y1000 " pdb=" O7 NAG Y1000 " model vdw 2.166 3.040 nonbonded pdb=" NE2 GLN R 170 " pdb=" O6 NAG R2001 " model vdw 2.266 3.120 nonbonded pdb=" NH1 ARG B 48 " pdb=" OD1 ASN B 340 " model vdw 2.267 3.120 ... (remaining 108163 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.250 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 13118 Z= 0.415 Angle : 1.111 8.711 17800 Z= 0.721 Chirality : 0.061 0.381 2038 Planarity : 0.012 0.172 2270 Dihedral : 13.423 87.313 4870 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.19), residues: 1616 helix: -1.57 (0.18), residues: 513 sheet: -1.25 (0.28), residues: 327 loop : -1.12 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.013 TRP N 47 HIS 0.010 0.003 HIS A 197 PHE 0.076 0.006 PHE N 27 TYR 0.146 0.013 TYR N 95 ARG 0.023 0.003 ARG X 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00068 ( 5) link_NAG-ASN : angle 2.60344 ( 15) hydrogen bonds : bond 0.19436 ( 566) hydrogen bonds : angle 8.53522 ( 1599) SS BOND : bond 0.00802 ( 17) SS BOND : angle 1.87328 ( 34) covalent geometry : bond 0.00698 (13096) covalent geometry : angle 1.10647 (17751) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 494 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TRP cc_start: 0.6015 (t-100) cc_final: 0.5462 (t-100) REVERT: A 206 ASP cc_start: 0.7431 (t0) cc_final: 0.7021 (t0) REVERT: A 207 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7948 (mt-10) REVERT: A 258 LEU cc_start: 0.8830 (mp) cc_final: 0.8577 (mp) REVERT: A 267 LYS cc_start: 0.8914 (mttt) cc_final: 0.8641 (mtmm) REVERT: A 359 GLU cc_start: 0.8085 (tp30) cc_final: 0.7761 (tp30) REVERT: B 6 GLN cc_start: 0.8245 (pp30) cc_final: 0.7790 (pp30) REVERT: B 7 LEU cc_start: 0.9286 (mt) cc_final: 0.8683 (mt) REVERT: B 78 LYS cc_start: 0.9048 (mmtt) cc_final: 0.8767 (mmmt) REVERT: B 93 ILE cc_start: 0.9363 (mt) cc_final: 0.8947 (mm) REVERT: B 99 TRP cc_start: 0.8333 (m100) cc_final: 0.7849 (m100) REVERT: B 111 TYR cc_start: 0.8582 (m-80) cc_final: 0.7728 (m-80) REVERT: B 118 ASP cc_start: 0.8319 (t0) cc_final: 0.7943 (p0) REVERT: B 120 ILE cc_start: 0.9012 (mt) cc_final: 0.8778 (mt) REVERT: B 191 SER cc_start: 0.8722 (t) cc_final: 0.8490 (p) REVERT: B 243 THR cc_start: 0.8658 (p) cc_final: 0.8429 (p) REVERT: B 250 CYS cc_start: 0.9088 (t) cc_final: 0.8760 (t) REVERT: B 280 LYS cc_start: 0.9049 (ttpp) cc_final: 0.8650 (ttpt) REVERT: B 292 PHE cc_start: 0.8601 (m-10) cc_final: 0.8113 (m-10) REVERT: B 308 LEU cc_start: 0.8794 (mt) cc_final: 0.8446 (mp) REVERT: B 316 SER cc_start: 0.8545 (t) cc_final: 0.8247 (t) REVERT: B 339 TRP cc_start: 0.8094 (m100) cc_final: 0.7489 (m100) REVERT: G 17 GLU cc_start: 0.8887 (tp30) cc_final: 0.7572 (tp30) REVERT: G 19 LEU cc_start: 0.9328 (mt) cc_final: 0.9101 (mp) REVERT: G 36 ASP cc_start: 0.9164 (t0) cc_final: 0.8933 (t0) REVERT: G 40 TYR cc_start: 0.9248 (t80) cc_final: 0.8907 (t80) REVERT: G 55 PRO cc_start: 0.8736 (Cg_exo) cc_final: 0.8183 (Cg_endo) REVERT: N 29 PHE cc_start: 0.8246 (t80) cc_final: 0.7721 (t80) REVERT: N 34 MET cc_start: 0.8522 (mmm) cc_final: 0.8189 (mmm) REVERT: N 36 TRP cc_start: 0.8519 (m100) cc_final: 0.8100 (m100) REVERT: N 46 GLU cc_start: 0.8287 (tt0) cc_final: 0.7897 (tt0) REVERT: N 47 TRP cc_start: 0.8323 (t60) cc_final: 0.7907 (t60) REVERT: N 50 ASP cc_start: 0.8479 (p0) cc_final: 0.8000 (p0) REVERT: N 95 TYR cc_start: 0.8202 (m-80) cc_final: 0.7982 (m-80) REVERT: N 111 THR cc_start: 0.9278 (p) cc_final: 0.9014 (m) REVERT: N 112 SER cc_start: 0.8609 (m) cc_final: 0.7882 (p) REVERT: R 54 LEU cc_start: 0.9295 (mt) cc_final: 0.8867 (mm) REVERT: R 56 LEU cc_start: 0.9556 (mt) cc_final: 0.9334 (mt) REVERT: R 79 GLU cc_start: 0.8479 (pt0) cc_final: 0.8169 (pm20) REVERT: R 104 LEU cc_start: 0.8786 (tp) cc_final: 0.8551 (tt) REVERT: R 154 GLU cc_start: 0.8137 (tt0) cc_final: 0.7817 (tt0) REVERT: R 186 PHE cc_start: 0.8961 (m-80) cc_final: 0.8684 (m-80) REVERT: R 200 THR cc_start: 0.8939 (m) cc_final: 0.8738 (p) REVERT: R 377 ASN cc_start: 0.8031 (m-40) cc_final: 0.7737 (m-40) REVERT: R 399 CYS cc_start: 0.8963 (m) cc_final: 0.8455 (t) REVERT: R 402 SER cc_start: 0.8756 (m) cc_final: 0.8467 (t) REVERT: R 405 ASP cc_start: 0.8360 (m-30) cc_final: 0.8117 (m-30) REVERT: R 574 LEU cc_start: 0.8881 (mt) cc_final: 0.8488 (mp) REVERT: R 578 ASP cc_start: 0.8760 (t0) cc_final: 0.8536 (t70) REVERT: X 15 ASN cc_start: 0.9369 (t0) cc_final: 0.9162 (t0) REVERT: X 18 PHE cc_start: 0.8497 (m-80) cc_final: 0.7851 (m-80) REVERT: X 27 GLN cc_start: 0.8720 (tt0) cc_final: 0.7966 (tm-30) REVERT: X 29 MET cc_start: 0.7800 (ptm) cc_final: 0.6917 (ptp) REVERT: X 51 LYS cc_start: 0.9327 (mmtt) cc_final: 0.8888 (mmtp) REVERT: Y 10 ARG cc_start: 0.8045 (pmt170) cc_final: 0.7826 (pmt170) REVERT: Y 41 MET cc_start: 0.8332 (ptm) cc_final: 0.7692 (pmm) REVERT: Y 42 THR cc_start: 0.9305 (t) cc_final: 0.9007 (t) REVERT: Y 43 ARG cc_start: 0.9278 (ttm110) cc_final: 0.9041 (ttp-110) outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 0.2758 time to fit residues: 194.1500 Evaluate side-chains 324 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN ** R 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 GLN Y 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.128651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.093437 restraints weight = 26559.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.096303 restraints weight = 12196.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.098774 restraints weight = 7811.627| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13118 Z= 0.195 Angle : 0.768 7.862 17800 Z= 0.403 Chirality : 0.047 0.194 2038 Planarity : 0.005 0.038 2270 Dihedral : 7.063 56.867 1884 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.78 % Allowed : 14.26 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1616 helix: 0.15 (0.22), residues: 512 sheet: -1.43 (0.27), residues: 342 loop : -0.42 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 82 HIS 0.007 0.001 HIS A 324 PHE 0.028 0.002 PHE B 241 TYR 0.026 0.002 TYR A 69 ARG 0.010 0.001 ARG Y 60 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 5) link_NAG-ASN : angle 2.30186 ( 15) hydrogen bonds : bond 0.05293 ( 566) hydrogen bonds : angle 5.93728 ( 1599) SS BOND : bond 0.00865 ( 17) SS BOND : angle 2.24634 ( 34) covalent geometry : bond 0.00428 (13096) covalent geometry : angle 0.75957 (17751) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 377 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4443 (ptt) cc_final: 0.2733 (mtt) REVERT: A 206 ASP cc_start: 0.7881 (t0) cc_final: 0.7522 (t0) REVERT: A 258 LEU cc_start: 0.8815 (mp) cc_final: 0.8562 (mp) REVERT: B 111 TYR cc_start: 0.8413 (m-80) cc_final: 0.7901 (m-80) REVERT: B 118 ASP cc_start: 0.8312 (t0) cc_final: 0.8033 (p0) REVERT: B 145 TYR cc_start: 0.9234 (p90) cc_final: 0.8833 (p90) REVERT: B 243 THR cc_start: 0.9093 (p) cc_final: 0.8697 (p) REVERT: B 246 ASP cc_start: 0.8876 (OUTLIER) cc_final: 0.8128 (t70) REVERT: B 280 LYS cc_start: 0.8904 (ttpp) cc_final: 0.8535 (ttpt) REVERT: B 292 PHE cc_start: 0.8663 (m-10) cc_final: 0.8225 (m-10) REVERT: B 297 TRP cc_start: 0.9177 (m100) cc_final: 0.8931 (m100) REVERT: B 308 LEU cc_start: 0.9133 (mt) cc_final: 0.8343 (mp) REVERT: B 339 TRP cc_start: 0.8195 (m100) cc_final: 0.7559 (m100) REVERT: G 17 GLU cc_start: 0.8918 (tp30) cc_final: 0.8383 (tp30) REVERT: G 28 ILE cc_start: 0.9133 (mm) cc_final: 0.8596 (tt) REVERT: G 32 LYS cc_start: 0.9216 (mtmt) cc_final: 0.8855 (ptmt) REVERT: G 40 TYR cc_start: 0.8962 (t80) cc_final: 0.8523 (t80) REVERT: N 38 ARG cc_start: 0.7524 (ptm-80) cc_final: 0.6831 (ptp90) REVERT: N 47 TRP cc_start: 0.8149 (t60) cc_final: 0.7749 (t60) REVERT: N 85 SER cc_start: 0.8483 (m) cc_final: 0.7936 (p) REVERT: N 109 ASP cc_start: 0.6455 (m-30) cc_final: 0.6020 (m-30) REVERT: N 112 SER cc_start: 0.8369 (m) cc_final: 0.7954 (p) REVERT: R 102 GLU cc_start: 0.8053 (mp0) cc_final: 0.7768 (mp0) REVERT: R 104 LEU cc_start: 0.9064 (tp) cc_final: 0.8823 (tt) REVERT: R 106 GLN cc_start: 0.9006 (tt0) cc_final: 0.8706 (tt0) REVERT: R 230 SER cc_start: 0.9294 (m) cc_final: 0.9023 (t) REVERT: R 233 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8796 (ttpt) REVERT: R 240 TYR cc_start: 0.8615 (t80) cc_final: 0.8364 (t80) REVERT: R 377 ASN cc_start: 0.8150 (m-40) cc_final: 0.7892 (m-40) REVERT: R 384 LEU cc_start: 0.9226 (mt) cc_final: 0.8972 (mt) REVERT: R 399 CYS cc_start: 0.8709 (m) cc_final: 0.8290 (t) REVERT: R 433 TRP cc_start: 0.8219 (t-100) cc_final: 0.7029 (t-100) REVERT: R 562 ASN cc_start: 0.8624 (p0) cc_final: 0.7954 (p0) REVERT: R 574 LEU cc_start: 0.9093 (mt) cc_final: 0.8826 (mp) REVERT: X 18 PHE cc_start: 0.8555 (m-80) cc_final: 0.8074 (m-80) REVERT: X 20 GLN cc_start: 0.7647 (tp40) cc_final: 0.7289 (tp40) REVERT: X 27 GLN cc_start: 0.8193 (tt0) cc_final: 0.7625 (tm-30) REVERT: X 29 MET cc_start: 0.7460 (ptm) cc_final: 0.6852 (ptm) REVERT: X 37 TYR cc_start: 0.8678 (p90) cc_final: 0.7961 (p90) REVERT: X 42 ARG cc_start: 0.8636 (mmp-170) cc_final: 0.7977 (mmm160) REVERT: X 45 LYS cc_start: 0.9334 (mtmm) cc_final: 0.8674 (mtmm) REVERT: X 51 LYS cc_start: 0.9569 (mmtt) cc_final: 0.9325 (mttm) REVERT: Y 41 MET cc_start: 0.8370 (ptm) cc_final: 0.7816 (pmm) REVERT: Y 42 THR cc_start: 0.9345 (t) cc_final: 0.9070 (t) REVERT: Y 43 ARG cc_start: 0.9289 (ttm110) cc_final: 0.8736 (ttp-110) REVERT: Y 95 ARG cc_start: 0.8402 (tmm160) cc_final: 0.8002 (tmm160) REVERT: Y 98 THR cc_start: 0.9363 (m) cc_final: 0.8948 (t) outliers start: 53 outliers final: 30 residues processed: 400 average time/residue: 0.2705 time to fit residues: 154.4815 Evaluate side-chains 345 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 313 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 233 LYS Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 536 VAL Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 547 ILE Chi-restraints excluded: chain R residue 553 VAL Chi-restraints excluded: chain R residue 602 THR Chi-restraints excluded: chain R residue 605 LYS Chi-restraints excluded: chain R residue 606 VAL Chi-restraints excluded: chain R residue 610 LEU Chi-restraints excluded: chain R residue 637 LEU Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 97 THR Chi-restraints excluded: chain Y residue 105 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 129 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 141 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 141 ASN ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 207 ASN R 377 ASN ** R 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 83 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.125020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.088377 restraints weight = 27293.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.091268 restraints weight = 14994.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.092863 restraints weight = 9747.262| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 13118 Z= 0.262 Angle : 0.756 8.504 17800 Z= 0.397 Chirality : 0.047 0.170 2038 Planarity : 0.005 0.041 2270 Dihedral : 6.613 56.784 1884 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.56 % Allowed : 16.75 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.21), residues: 1616 helix: 0.36 (0.22), residues: 511 sheet: -1.33 (0.27), residues: 324 loop : -0.40 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 82 HIS 0.006 0.002 HIS A 57 PHE 0.039 0.002 PHE R 186 TYR 0.026 0.002 TYR A 69 ARG 0.008 0.001 ARG N 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00109 ( 5) link_NAG-ASN : angle 2.08557 ( 15) hydrogen bonds : bond 0.04746 ( 566) hydrogen bonds : angle 5.76174 ( 1599) SS BOND : bond 0.00746 ( 17) SS BOND : angle 1.53913 ( 34) covalent geometry : bond 0.00575 (13096) covalent geometry : angle 0.75138 (17751) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 301 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4260 (ptt) cc_final: 0.2706 (mtt) REVERT: A 206 ASP cc_start: 0.7927 (t0) cc_final: 0.7686 (t0) REVERT: A 258 LEU cc_start: 0.8571 (mp) cc_final: 0.8323 (mp) REVERT: A 359 GLU cc_start: 0.8263 (mp0) cc_final: 0.7984 (mp0) REVERT: B 10 GLU cc_start: 0.9491 (mt-10) cc_final: 0.9006 (mp0) REVERT: B 12 GLU cc_start: 0.9245 (tp30) cc_final: 0.8166 (tp30) REVERT: B 15 LYS cc_start: 0.9250 (ttpt) cc_final: 0.9004 (tmmt) REVERT: B 99 TRP cc_start: 0.8619 (m100) cc_final: 0.7974 (m100) REVERT: B 111 TYR cc_start: 0.8378 (m-80) cc_final: 0.7892 (m-80) REVERT: B 118 ASP cc_start: 0.8340 (t0) cc_final: 0.8126 (p0) REVERT: B 130 GLU cc_start: 0.8568 (mt-10) cc_final: 0.7979 (pm20) REVERT: B 145 TYR cc_start: 0.9234 (p90) cc_final: 0.8964 (p90) REVERT: B 226 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7475 (mt-10) REVERT: B 243 THR cc_start: 0.9229 (p) cc_final: 0.8979 (p) REVERT: B 246 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8088 (t70) REVERT: B 280 LYS cc_start: 0.8946 (ttpp) cc_final: 0.8643 (ttpt) REVERT: B 325 MET cc_start: 0.8930 (mmt) cc_final: 0.8611 (mmm) REVERT: G 17 GLU cc_start: 0.8990 (tp30) cc_final: 0.8487 (tp30) REVERT: G 18 GLN cc_start: 0.8480 (tp40) cc_final: 0.7793 (tp40) REVERT: G 28 ILE cc_start: 0.9133 (mm) cc_final: 0.8523 (tt) REVERT: G 32 LYS cc_start: 0.9229 (mtmt) cc_final: 0.8828 (mtmt) REVERT: G 40 TYR cc_start: 0.8876 (t80) cc_final: 0.8616 (t80) REVERT: N 5 GLN cc_start: 0.7805 (mp10) cc_final: 0.7603 (mp10) REVERT: N 32 TYR cc_start: 0.7799 (m-10) cc_final: 0.7329 (m-10) REVERT: N 34 MET cc_start: 0.8738 (mmm) cc_final: 0.7998 (mmm) REVERT: N 36 TRP cc_start: 0.8676 (m100) cc_final: 0.7066 (m100) REVERT: N 85 SER cc_start: 0.8582 (m) cc_final: 0.8051 (p) REVERT: N 112 SER cc_start: 0.8456 (m) cc_final: 0.8097 (p) REVERT: N 117 TYR cc_start: 0.8058 (m-10) cc_final: 0.7839 (m-80) REVERT: R 88 ARG cc_start: 0.9182 (ptp-170) cc_final: 0.8867 (mtt-85) REVERT: R 102 GLU cc_start: 0.8040 (mp0) cc_final: 0.7829 (mp0) REVERT: R 104 LEU cc_start: 0.8990 (tp) cc_final: 0.8684 (tt) REVERT: R 106 GLN cc_start: 0.8987 (tt0) cc_final: 0.8560 (tt0) REVERT: R 108 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8529 (p) REVERT: R 200 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8610 (t) REVERT: R 230 SER cc_start: 0.9246 (m) cc_final: 0.9010 (t) REVERT: R 240 TYR cc_start: 0.8585 (t80) cc_final: 0.8278 (t80) REVERT: R 384 LEU cc_start: 0.9287 (mt) cc_final: 0.8984 (mt) REVERT: R 399 CYS cc_start: 0.8514 (m) cc_final: 0.8232 (t) REVERT: R 433 TRP cc_start: 0.8248 (t-100) cc_final: 0.7148 (t-100) REVERT: X 18 PHE cc_start: 0.8530 (m-80) cc_final: 0.8045 (m-80) REVERT: X 20 GLN cc_start: 0.7675 (tp40) cc_final: 0.7465 (tp40) REVERT: X 27 GLN cc_start: 0.8259 (tt0) cc_final: 0.7685 (tm-30) REVERT: X 29 MET cc_start: 0.7510 (ptm) cc_final: 0.7074 (ptt) REVERT: X 42 ARG cc_start: 0.8584 (mmp-170) cc_final: 0.7960 (mmm160) REVERT: X 45 LYS cc_start: 0.9349 (mtmm) cc_final: 0.8798 (mtmm) REVERT: X 51 LYS cc_start: 0.9615 (mmtt) cc_final: 0.9384 (mttm) REVERT: Y 41 MET cc_start: 0.8496 (ptm) cc_final: 0.8010 (pmm) REVERT: Y 42 THR cc_start: 0.9431 (t) cc_final: 0.9208 (t) REVERT: Y 98 THR cc_start: 0.9388 (m) cc_final: 0.9069 (p) outliers start: 78 outliers final: 56 residues processed: 346 average time/residue: 0.2457 time to fit residues: 123.5088 Evaluate side-chains 329 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 270 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 114 ILE Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 431 ILE Chi-restraints excluded: chain R residue 502 LEU Chi-restraints excluded: chain R residue 530 THR Chi-restraints excluded: chain R residue 536 VAL Chi-restraints excluded: chain R residue 547 ILE Chi-restraints excluded: chain R residue 553 VAL Chi-restraints excluded: chain R residue 575 ILE Chi-restraints excluded: chain R residue 606 VAL Chi-restraints excluded: chain R residue 610 LEU Chi-restraints excluded: chain R residue 637 LEU Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain Y residue 38 CYS Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 62 VAL Chi-restraints excluded: chain Y residue 66 SER Chi-restraints excluded: chain Y residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 79 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 chunk 114 optimal weight: 0.0770 chunk 35 optimal weight: 4.9990 overall best weight: 3.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 238 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 619 ASN ** 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 = 0.3932 r_free = 0.3932 target = 0.123968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.089190 restraints weight = 27549.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.091423 restraints weight = 13271.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.092700 restraints weight = 9156.632| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13118 Z= 0.260 Angle : 0.742 8.981 17800 Z= 0.387 Chirality : 0.046 0.168 2038 Planarity : 0.005 0.039 2270 Dihedral : 6.396 56.777 1884 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.70 % Allowed : 17.32 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.21), residues: 1616 helix: 0.47 (0.23), residues: 508 sheet: -1.33 (0.27), residues: 331 loop : -0.39 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.005 0.001 HIS B 225 PHE 0.027 0.002 PHE R 186 TYR 0.026 0.002 TYR A 69 ARG 0.005 0.000 ARG Y 8 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 5) link_NAG-ASN : angle 2.01297 ( 15) hydrogen bonds : bond 0.04562 ( 566) hydrogen bonds : angle 5.67743 ( 1599) SS BOND : bond 0.00587 ( 17) SS BOND : angle 1.45725 ( 34) covalent geometry : bond 0.00566 (13096) covalent geometry : angle 0.73771 (17751) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 289 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4174 (ptt) cc_final: 0.2638 (mtt) REVERT: A 172 GLN cc_start: 0.8370 (pm20) cc_final: 0.7978 (pp30) REVERT: A 206 ASP cc_start: 0.8030 (t0) cc_final: 0.7773 (t0) REVERT: A 241 LYS cc_start: 0.9303 (tttt) cc_final: 0.9075 (ttpt) REVERT: B 99 TRP cc_start: 0.8629 (m100) cc_final: 0.7998 (m100) REVERT: B 111 TYR cc_start: 0.8500 (m-80) cc_final: 0.7952 (m-80) REVERT: B 118 ASP cc_start: 0.8336 (t0) cc_final: 0.8099 (p0) REVERT: B 130 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8067 (pm20) REVERT: B 138 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7589 (tm-30) REVERT: B 145 TYR cc_start: 0.9256 (p90) cc_final: 0.8936 (p90) REVERT: B 226 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7304 (mt-10) REVERT: B 243 THR cc_start: 0.9194 (p) cc_final: 0.8951 (p) REVERT: B 246 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8121 (t70) REVERT: B 280 LYS cc_start: 0.8940 (ttpp) cc_final: 0.8654 (ttpt) REVERT: B 308 LEU cc_start: 0.9063 (mp) cc_final: 0.8104 (mp) REVERT: B 315 VAL cc_start: 0.9244 (t) cc_final: 0.9022 (p) REVERT: B 325 MET cc_start: 0.8929 (mmt) cc_final: 0.8622 (mmm) REVERT: B 339 TRP cc_start: 0.8253 (m100) cc_final: 0.7636 (m100) REVERT: G 15 LEU cc_start: 0.9523 (tp) cc_final: 0.9265 (mt) REVERT: G 17 GLU cc_start: 0.9027 (tp30) cc_final: 0.8573 (tp30) REVERT: G 21 MET cc_start: 0.8560 (mmm) cc_final: 0.8342 (mmm) REVERT: G 28 ILE cc_start: 0.9120 (mm) cc_final: 0.8486 (tt) REVERT: G 32 LYS cc_start: 0.9231 (mtmt) cc_final: 0.8996 (mtmt) REVERT: G 40 TYR cc_start: 0.8915 (t80) cc_final: 0.8540 (t80) REVERT: G 44 HIS cc_start: 0.8997 (m-70) cc_final: 0.8368 (m90) REVERT: N 5 GLN cc_start: 0.7876 (mp10) cc_final: 0.7657 (mp10) REVERT: N 32 TYR cc_start: 0.7973 (m-10) cc_final: 0.7233 (m-10) REVERT: N 34 MET cc_start: 0.8830 (mmm) cc_final: 0.8234 (mmm) REVERT: N 36 TRP cc_start: 0.8578 (m100) cc_final: 0.7024 (m100) REVERT: N 47 TRP cc_start: 0.7813 (t60) cc_final: 0.7559 (t60) REVERT: N 85 SER cc_start: 0.8650 (m) cc_final: 0.8112 (p) REVERT: N 108 PHE cc_start: 0.7325 (OUTLIER) cc_final: 0.7072 (m-80) REVERT: N 117 TYR cc_start: 0.7961 (m-10) cc_final: 0.7749 (m-80) REVERT: R 88 ARG cc_start: 0.9189 (ptp-170) cc_final: 0.8871 (mtm110) REVERT: R 102 GLU cc_start: 0.8071 (mp0) cc_final: 0.7810 (mp0) REVERT: R 106 GLN cc_start: 0.8973 (tt0) cc_final: 0.8508 (tt0) REVERT: R 108 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8535 (p) REVERT: R 200 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8603 (t) REVERT: R 230 SER cc_start: 0.9303 (m) cc_final: 0.8891 (t) REVERT: R 240 TYR cc_start: 0.8509 (t80) cc_final: 0.8270 (t80) REVERT: R 374 ILE cc_start: 0.8983 (mm) cc_final: 0.8060 (mm) REVERT: R 377 ASN cc_start: 0.8232 (m-40) cc_final: 0.8017 (m-40) REVERT: R 384 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9025 (mt) REVERT: R 399 CYS cc_start: 0.8595 (m) cc_final: 0.8255 (t) REVERT: R 405 ASP cc_start: 0.8752 (m-30) cc_final: 0.8449 (t0) REVERT: R 433 TRP cc_start: 0.8287 (t-100) cc_final: 0.7187 (t-100) REVERT: R 534 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8543 (mp) REVERT: R 582 MET cc_start: 0.8062 (tmm) cc_final: 0.7855 (tmm) REVERT: X 18 PHE cc_start: 0.8580 (m-80) cc_final: 0.8041 (m-80) REVERT: X 20 GLN cc_start: 0.7704 (tp40) cc_final: 0.7474 (tp40) REVERT: X 27 GLN cc_start: 0.8165 (tt0) cc_final: 0.7577 (tm-30) REVERT: X 29 MET cc_start: 0.7546 (ptm) cc_final: 0.7178 (ptt) REVERT: Y 41 MET cc_start: 0.8608 (ptm) cc_final: 0.7982 (pmm) REVERT: Y 42 THR cc_start: 0.9437 (t) cc_final: 0.9219 (t) outliers start: 80 outliers final: 59 residues processed: 336 average time/residue: 0.2352 time to fit residues: 115.4257 Evaluate side-chains 320 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 255 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 114 ILE Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 384 LEU Chi-restraints excluded: chain R residue 431 ILE Chi-restraints excluded: chain R residue 454 VAL Chi-restraints excluded: chain R residue 502 LEU Chi-restraints excluded: chain R residue 530 THR Chi-restraints excluded: chain R residue 534 LEU Chi-restraints excluded: chain R residue 536 VAL Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 547 ILE Chi-restraints excluded: chain R residue 549 ILE Chi-restraints excluded: chain R residue 553 VAL Chi-restraints excluded: chain R residue 606 VAL Chi-restraints excluded: chain R residue 610 LEU Chi-restraints excluded: chain R residue 614 ILE Chi-restraints excluded: chain R residue 637 LEU Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain Y residue 38 CYS Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 62 VAL Chi-restraints excluded: chain Y residue 66 SER Chi-restraints excluded: chain Y residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 85 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 158 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 160 HIS ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 425 GLN R 619 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.125750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.090421 restraints weight = 26831.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.094666 restraints weight = 12926.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.095175 restraints weight = 7941.704| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 13118 Z= 0.178 Angle : 0.699 10.443 17800 Z= 0.361 Chirality : 0.045 0.270 2038 Planarity : 0.004 0.039 2270 Dihedral : 6.035 57.278 1884 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.56 % Allowed : 19.53 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.21), residues: 1616 helix: 0.64 (0.23), residues: 508 sheet: -1.26 (0.27), residues: 345 loop : -0.21 (0.24), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 297 HIS 0.006 0.001 HIS X 83 PHE 0.015 0.001 PHE R 493 TYR 0.025 0.001 TYR A 69 ARG 0.004 0.000 ARG Y 8 Details of bonding type rmsd link_NAG-ASN : bond 0.00102 ( 5) link_NAG-ASN : angle 1.84474 ( 15) hydrogen bonds : bond 0.04281 ( 566) hydrogen bonds : angle 5.46316 ( 1599) SS BOND : bond 0.00514 ( 17) SS BOND : angle 2.18114 ( 34) covalent geometry : bond 0.00402 (13096) covalent geometry : angle 0.69090 (17751) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 308 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4061 (ptt) cc_final: 0.2558 (mtt) REVERT: A 206 ASP cc_start: 0.8093 (t0) cc_final: 0.7791 (t0) REVERT: A 241 LYS cc_start: 0.9297 (tttt) cc_final: 0.9047 (ttpt) REVERT: A 359 GLU cc_start: 0.8104 (mp0) cc_final: 0.7736 (mp0) REVERT: B 12 GLU cc_start: 0.9278 (tp30) cc_final: 0.8366 (tp30) REVERT: B 99 TRP cc_start: 0.8564 (m100) cc_final: 0.7967 (m100) REVERT: B 111 TYR cc_start: 0.8433 (m-80) cc_final: 0.7976 (m-80) REVERT: B 130 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8056 (pm20) REVERT: B 138 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7681 (tm-30) REVERT: B 226 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7250 (mt-10) REVERT: B 243 THR cc_start: 0.9159 (p) cc_final: 0.8937 (p) REVERT: B 246 ASP cc_start: 0.8774 (OUTLIER) cc_final: 0.8102 (t70) REVERT: B 280 LYS cc_start: 0.8890 (ttpp) cc_final: 0.8366 (ttpt) REVERT: B 292 PHE cc_start: 0.8641 (m-10) cc_final: 0.8273 (m-10) REVERT: B 325 MET cc_start: 0.8838 (mmt) cc_final: 0.8542 (mmm) REVERT: B 339 TRP cc_start: 0.8117 (m100) cc_final: 0.7577 (m100) REVERT: G 17 GLU cc_start: 0.9054 (tp30) cc_final: 0.8516 (tp30) REVERT: G 18 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8803 (tp-100) REVERT: G 22 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7889 (mt-10) REVERT: G 28 ILE cc_start: 0.9148 (mm) cc_final: 0.8613 (tt) REVERT: G 40 TYR cc_start: 0.8816 (t80) cc_final: 0.8483 (t80) REVERT: G 44 HIS cc_start: 0.8936 (m-70) cc_final: 0.8405 (m90) REVERT: N 32 TYR cc_start: 0.7962 (m-10) cc_final: 0.7598 (m-10) REVERT: N 34 MET cc_start: 0.8748 (mmm) cc_final: 0.8232 (mmm) REVERT: N 36 TRP cc_start: 0.8478 (m100) cc_final: 0.7010 (m100) REVERT: N 38 ARG cc_start: 0.7705 (ptp90) cc_final: 0.6956 (ptm-80) REVERT: N 47 TRP cc_start: 0.7647 (t60) cc_final: 0.7260 (t60) REVERT: N 85 SER cc_start: 0.8622 (m) cc_final: 0.8122 (p) REVERT: N 117 TYR cc_start: 0.7906 (m-10) cc_final: 0.7677 (m-80) REVERT: R 88 ARG cc_start: 0.9154 (ptp-170) cc_final: 0.8869 (mtm110) REVERT: R 102 GLU cc_start: 0.8000 (mp0) cc_final: 0.7698 (mp0) REVERT: R 108 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8401 (p) REVERT: R 200 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8459 (t) REVERT: R 228 ASP cc_start: 0.8286 (t70) cc_final: 0.7997 (t0) REVERT: R 230 SER cc_start: 0.9321 (m) cc_final: 0.8968 (t) REVERT: R 240 TYR cc_start: 0.8462 (t80) cc_final: 0.8242 (t80) REVERT: R 270 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: R 359 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.8069 (m-80) REVERT: R 384 LEU cc_start: 0.9273 (mt) cc_final: 0.8955 (mt) REVERT: R 398 MET cc_start: 0.8572 (tpp) cc_final: 0.8342 (tpp) REVERT: R 399 CYS cc_start: 0.8577 (m) cc_final: 0.8217 (t) REVERT: R 433 TRP cc_start: 0.8287 (t-100) cc_final: 0.7311 (t-100) REVERT: R 534 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8518 (mp) REVERT: R 559 MET cc_start: 0.4559 (mpp) cc_final: 0.3431 (mpp) REVERT: R 571 MET cc_start: 0.8682 (ttp) cc_final: 0.8254 (ttt) REVERT: X 20 GLN cc_start: 0.7603 (tp40) cc_final: 0.7343 (tp40) REVERT: X 27 GLN cc_start: 0.8050 (tt0) cc_final: 0.7460 (tm-30) REVERT: X 29 MET cc_start: 0.7715 (ptm) cc_final: 0.7258 (ptt) REVERT: X 35 ARG cc_start: 0.8753 (ttt180) cc_final: 0.8382 (ttp80) REVERT: X 45 LYS cc_start: 0.9387 (ptpp) cc_final: 0.9057 (mtmm) REVERT: Y 41 MET cc_start: 0.8576 (ptm) cc_final: 0.7976 (pmm) outliers start: 78 outliers final: 46 residues processed: 353 average time/residue: 0.3071 time to fit residues: 159.0103 Evaluate side-chains 336 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 282 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 114 ILE Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 270 GLU Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 359 TYR Chi-restraints excluded: chain R residue 385 LEU Chi-restraints excluded: chain R residue 454 VAL Chi-restraints excluded: chain R residue 502 LEU Chi-restraints excluded: chain R residue 530 THR Chi-restraints excluded: chain R residue 534 LEU Chi-restraints excluded: chain R residue 536 VAL Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 547 ILE Chi-restraints excluded: chain R residue 549 ILE Chi-restraints excluded: chain R residue 575 ILE Chi-restraints excluded: chain R residue 602 THR Chi-restraints excluded: chain R residue 606 VAL Chi-restraints excluded: chain R residue 610 LEU Chi-restraints excluded: chain R residue 614 ILE Chi-restraints excluded: chain R residue 637 LEU Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain Y residue 38 CYS Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 55 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 140 optimal weight: 40.0000 chunk 79 optimal weight: 10.0000 chunk 109 optimal weight: 0.0270 chunk 143 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 overall best weight: 1.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 ASN ** R 377 ASN ** 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 = 0.3958 r_free = 0.3958 target = 0.125876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.090418 restraints weight = 27500.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.094254 restraints weight = 13137.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.095306 restraints weight = 8317.044| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13118 Z= 0.167 Angle : 0.744 16.454 17800 Z= 0.374 Chirality : 0.045 0.246 2038 Planarity : 0.004 0.038 2270 Dihedral : 5.878 56.956 1884 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.70 % Allowed : 21.67 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1616 helix: 0.64 (0.23), residues: 502 sheet: -1.29 (0.26), residues: 344 loop : -0.11 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS X 90 PHE 0.037 0.002 PHE B 241 TYR 0.024 0.001 TYR A 69 ARG 0.005 0.000 ARG A 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 5) link_NAG-ASN : angle 1.65375 ( 15) hydrogen bonds : bond 0.04166 ( 566) hydrogen bonds : angle 5.35400 ( 1599) SS BOND : bond 0.00457 ( 17) SS BOND : angle 2.35762 ( 34) covalent geometry : bond 0.00378 (13096) covalent geometry : angle 0.73656 (17751) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 297 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4266 (ptt) cc_final: 0.2678 (mtt) REVERT: A 172 GLN cc_start: 0.8436 (pm20) cc_final: 0.8078 (pp30) REVERT: A 176 ARG cc_start: 0.7101 (ptt90) cc_final: 0.6797 (ppt170) REVERT: A 206 ASP cc_start: 0.8180 (t0) cc_final: 0.7863 (t0) REVERT: A 241 LYS cc_start: 0.9301 (tttt) cc_final: 0.9068 (ttpt) REVERT: A 244 TRP cc_start: 0.9422 (t-100) cc_final: 0.8884 (t-100) REVERT: B 12 GLU cc_start: 0.8946 (tp30) cc_final: 0.8744 (tp30) REVERT: B 15 LYS cc_start: 0.9021 (tmmt) cc_final: 0.8733 (pptt) REVERT: B 82 TRP cc_start: 0.9135 (OUTLIER) cc_final: 0.8753 (m-10) REVERT: B 111 TYR cc_start: 0.8384 (m-80) cc_final: 0.7986 (m-80) REVERT: B 130 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8070 (pm20) REVERT: B 138 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7733 (tm-30) REVERT: B 226 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7081 (mt-10) REVERT: B 243 THR cc_start: 0.9139 (p) cc_final: 0.8920 (p) REVERT: B 246 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8064 (t70) REVERT: B 292 PHE cc_start: 0.8627 (m-10) cc_final: 0.8281 (m-10) REVERT: B 325 MET cc_start: 0.8737 (mmt) cc_final: 0.8446 (mmm) REVERT: B 339 TRP cc_start: 0.8097 (m100) cc_final: 0.7611 (m100) REVERT: G 17 GLU cc_start: 0.9069 (tp30) cc_final: 0.8668 (tp30) REVERT: G 18 GLN cc_start: 0.9223 (tp40) cc_final: 0.8854 (tp-100) REVERT: G 22 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7982 (mt-10) REVERT: G 28 ILE cc_start: 0.9037 (mm) cc_final: 0.8532 (tt) REVERT: G 40 TYR cc_start: 0.8809 (t80) cc_final: 0.8388 (t80) REVERT: G 44 HIS cc_start: 0.8946 (m-70) cc_final: 0.8413 (m90) REVERT: N 29 PHE cc_start: 0.7961 (t80) cc_final: 0.7748 (t80) REVERT: N 32 TYR cc_start: 0.8035 (m-10) cc_final: 0.7710 (m-10) REVERT: N 34 MET cc_start: 0.8756 (mmm) cc_final: 0.8187 (mmm) REVERT: N 36 TRP cc_start: 0.8491 (m100) cc_final: 0.6908 (m100) REVERT: N 38 ARG cc_start: 0.7669 (ptp90) cc_final: 0.7062 (ptm-80) REVERT: N 46 GLU cc_start: 0.7985 (mp0) cc_final: 0.7741 (mp0) REVERT: N 85 SER cc_start: 0.8658 (m) cc_final: 0.8154 (p) REVERT: N 87 LYS cc_start: 0.9245 (ttmt) cc_final: 0.9043 (ttmt) REVERT: N 117 TYR cc_start: 0.7982 (m-10) cc_final: 0.7728 (m-80) REVERT: R 88 ARG cc_start: 0.9148 (ptp-170) cc_final: 0.8837 (mtm110) REVERT: R 102 GLU cc_start: 0.7988 (mp0) cc_final: 0.7688 (mp0) REVERT: R 106 GLN cc_start: 0.8775 (tt0) cc_final: 0.8237 (tt0) REVERT: R 108 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8317 (p) REVERT: R 170 GLN cc_start: 0.6836 (tp40) cc_final: 0.6504 (tp40) REVERT: R 200 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8419 (t) REVERT: R 230 SER cc_start: 0.9286 (m) cc_final: 0.8936 (t) REVERT: R 240 TYR cc_start: 0.8436 (t80) cc_final: 0.8225 (t80) REVERT: R 270 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: R 359 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.8091 (m-80) REVERT: R 372 LEU cc_start: 0.9475 (tt) cc_final: 0.9195 (tp) REVERT: R 377 ASN cc_start: 0.7689 (m-40) cc_final: 0.7337 (t0) REVERT: R 384 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8967 (mt) REVERT: R 399 CYS cc_start: 0.8585 (m) cc_final: 0.8209 (t) REVERT: R 433 TRP cc_start: 0.8264 (t-100) cc_final: 0.7307 (t-100) REVERT: R 534 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8508 (mp) REVERT: R 559 MET cc_start: 0.4486 (mpp) cc_final: 0.3402 (mpp) REVERT: R 571 MET cc_start: 0.8587 (ttp) cc_final: 0.8288 (ttt) REVERT: X 15 ASN cc_start: 0.8981 (OUTLIER) cc_final: 0.8368 (p0) REVERT: X 18 PHE cc_start: 0.8526 (m-80) cc_final: 0.8181 (m-80) REVERT: X 20 GLN cc_start: 0.7660 (tp40) cc_final: 0.7431 (tp40) REVERT: X 27 GLN cc_start: 0.7992 (tt0) cc_final: 0.7362 (tm-30) REVERT: X 29 MET cc_start: 0.7848 (ptm) cc_final: 0.7217 (ptt) REVERT: X 35 ARG cc_start: 0.8896 (ttt180) cc_final: 0.8597 (ttp-170) REVERT: X 45 LYS cc_start: 0.9319 (ptpp) cc_final: 0.8976 (mtmm) REVERT: Y 41 MET cc_start: 0.8538 (ptm) cc_final: 0.7961 (pmm) REVERT: Y 99 ASP cc_start: 0.8147 (t0) cc_final: 0.7858 (t0) outliers start: 80 outliers final: 53 residues processed: 344 average time/residue: 0.2863 time to fit residues: 145.1037 Evaluate side-chains 341 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 278 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 114 ILE Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain R residue 156 CYS Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 270 GLU Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 359 TYR Chi-restraints excluded: chain R residue 384 LEU Chi-restraints excluded: chain R residue 431 ILE Chi-restraints excluded: chain R residue 454 VAL Chi-restraints excluded: chain R residue 496 LEU Chi-restraints excluded: chain R residue 502 LEU Chi-restraints excluded: chain R residue 519 VAL Chi-restraints excluded: chain R residue 530 THR Chi-restraints excluded: chain R residue 534 LEU Chi-restraints excluded: chain R residue 536 VAL Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 547 ILE Chi-restraints excluded: chain R residue 575 ILE Chi-restraints excluded: chain R residue 602 THR Chi-restraints excluded: chain R residue 606 VAL Chi-restraints excluded: chain R residue 610 LEU Chi-restraints excluded: chain R residue 614 ILE Chi-restraints excluded: chain R residue 637 LEU Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 38 CYS Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 55 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 34 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS G 18 GLN ** N 35 ASN ** 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 = 0.3943 r_free = 0.3943 target = 0.124849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.090597 restraints weight = 27565.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.092513 restraints weight = 12902.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.095082 restraints weight = 9069.980| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13118 Z= 0.218 Angle : 0.760 15.307 17800 Z= 0.386 Chirality : 0.046 0.240 2038 Planarity : 0.004 0.038 2270 Dihedral : 5.943 64.160 1884 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 5.70 % Allowed : 22.10 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1616 helix: 0.58 (0.23), residues: 508 sheet: -1.38 (0.26), residues: 346 loop : -0.09 (0.24), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS G 44 PHE 0.029 0.002 PHE X 18 TYR 0.024 0.002 TYR A 69 ARG 0.004 0.000 ARG A 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00125 ( 5) link_NAG-ASN : angle 1.71555 ( 15) hydrogen bonds : bond 0.04263 ( 566) hydrogen bonds : angle 5.35414 ( 1599) SS BOND : bond 0.00508 ( 17) SS BOND : angle 2.28948 ( 34) covalent geometry : bond 0.00483 (13096) covalent geometry : angle 0.75253 (17751) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 275 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4319 (ptt) cc_final: 0.2689 (mtt) REVERT: A 172 GLN cc_start: 0.8492 (pm20) cc_final: 0.8109 (pp30) REVERT: A 176 ARG cc_start: 0.7133 (ptt90) cc_final: 0.6787 (ppt170) REVERT: A 206 ASP cc_start: 0.8175 (t0) cc_final: 0.7888 (t0) REVERT: A 241 LYS cc_start: 0.9318 (tttt) cc_final: 0.9094 (ttpt) REVERT: B 12 GLU cc_start: 0.8903 (tp30) cc_final: 0.8571 (tp30) REVERT: B 15 LYS cc_start: 0.8991 (tmmt) cc_final: 0.8689 (pptt) REVERT: B 82 TRP cc_start: 0.9134 (OUTLIER) cc_final: 0.8751 (m-10) REVERT: B 99 TRP cc_start: 0.8551 (m100) cc_final: 0.8325 (m100) REVERT: B 105 TYR cc_start: 0.9220 (OUTLIER) cc_final: 0.8537 (t80) REVERT: B 111 TYR cc_start: 0.8405 (m-80) cc_final: 0.7859 (m-80) REVERT: B 130 GLU cc_start: 0.8554 (mt-10) cc_final: 0.7993 (pm20) REVERT: B 138 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7738 (tm-30) REVERT: B 226 GLU cc_start: 0.7445 (mt-10) cc_final: 0.6958 (mt-10) REVERT: B 243 THR cc_start: 0.9182 (p) cc_final: 0.8953 (p) REVERT: B 246 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8122 (t70) REVERT: B 292 PHE cc_start: 0.8686 (m-10) cc_final: 0.8322 (m-10) REVERT: B 325 MET cc_start: 0.8756 (mmt) cc_final: 0.8446 (mmm) REVERT: B 339 TRP cc_start: 0.8004 (m100) cc_final: 0.7583 (m100) REVERT: G 17 GLU cc_start: 0.8979 (tp30) cc_final: 0.8535 (tp30) REVERT: G 18 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8726 (tp-100) REVERT: G 21 MET cc_start: 0.8581 (mmm) cc_final: 0.8372 (mmm) REVERT: G 22 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7780 (mt-10) REVERT: G 28 ILE cc_start: 0.9005 (mm) cc_final: 0.8334 (tt) REVERT: G 40 TYR cc_start: 0.8837 (t80) cc_final: 0.8365 (t80) REVERT: G 44 HIS cc_start: 0.8867 (m-70) cc_final: 0.8309 (m90) REVERT: N 29 PHE cc_start: 0.8022 (t80) cc_final: 0.7786 (t80) REVERT: N 34 MET cc_start: 0.8658 (mmm) cc_final: 0.8163 (mmm) REVERT: N 36 TRP cc_start: 0.8510 (m100) cc_final: 0.6970 (m100) REVERT: N 38 ARG cc_start: 0.7881 (ptp90) cc_final: 0.7229 (ptm-80) REVERT: N 46 GLU cc_start: 0.7965 (mp0) cc_final: 0.7644 (mp0) REVERT: N 47 TRP cc_start: 0.7801 (t60) cc_final: 0.7477 (t60) REVERT: N 85 SER cc_start: 0.8679 (m) cc_final: 0.8166 (p) REVERT: R 88 ARG cc_start: 0.9124 (ptp-170) cc_final: 0.8841 (mtm110) REVERT: R 102 GLU cc_start: 0.7980 (mp0) cc_final: 0.7694 (mp0) REVERT: R 106 GLN cc_start: 0.8772 (tt0) cc_final: 0.8231 (tt0) REVERT: R 108 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8267 (p) REVERT: R 170 GLN cc_start: 0.6966 (tp40) cc_final: 0.6628 (tp40) REVERT: R 200 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8256 (t) REVERT: R 230 SER cc_start: 0.9350 (m) cc_final: 0.8982 (t) REVERT: R 240 TYR cc_start: 0.8450 (t80) cc_final: 0.8177 (t80) REVERT: R 270 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: R 372 LEU cc_start: 0.9420 (tt) cc_final: 0.9119 (tp) REVERT: R 377 ASN cc_start: 0.7749 (m-40) cc_final: 0.7363 (t0) REVERT: R 384 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9086 (mt) REVERT: R 399 CYS cc_start: 0.8631 (m) cc_final: 0.8307 (t) REVERT: R 410 LEU cc_start: 0.9260 (mt) cc_final: 0.8893 (tt) REVERT: R 433 TRP cc_start: 0.8363 (t-100) cc_final: 0.7434 (t-100) REVERT: R 534 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8519 (mp) REVERT: R 559 MET cc_start: 0.4574 (mpp) cc_final: 0.3465 (mpp) REVERT: R 571 MET cc_start: 0.8579 (ttp) cc_final: 0.8338 (ttt) REVERT: X 6 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8265 (p0) REVERT: X 20 GLN cc_start: 0.7575 (tp40) cc_final: 0.7347 (tp40) REVERT: X 27 GLN cc_start: 0.7911 (tt0) cc_final: 0.7461 (tm-30) REVERT: X 29 MET cc_start: 0.7849 (ptm) cc_final: 0.7340 (ptt) REVERT: X 35 ARG cc_start: 0.8876 (ttt180) cc_final: 0.8618 (ttp-170) REVERT: X 47 MET cc_start: 0.8262 (mmm) cc_final: 0.7916 (mmm) REVERT: Y 41 MET cc_start: 0.8494 (ptm) cc_final: 0.7960 (pmm) REVERT: Y 99 ASP cc_start: 0.8145 (t0) cc_final: 0.7790 (t0) outliers start: 80 outliers final: 55 residues processed: 322 average time/residue: 0.2502 time to fit residues: 119.4897 Evaluate side-chains 335 residues out of total 1414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 269 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 114 ILE Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain R residue 156 CYS Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 270 GLU Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 384 LEU Chi-restraints excluded: chain R residue 454 VAL Chi-restraints excluded: chain R residue 460 ILE Chi-restraints excluded: chain R residue 496 LEU Chi-restraints excluded: chain R residue 502 LEU Chi-restraints excluded: chain R residue 519 VAL Chi-restraints excluded: chain R residue 530 THR Chi-restraints excluded: chain R residue 534 LEU Chi-restraints excluded: chain R residue 536 VAL Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 547 ILE Chi-restraints excluded: chain R residue 549 ILE Chi-restraints excluded: chain R residue 575 ILE Chi-restraints excluded: chain R residue 602 THR Chi-restraints excluded: chain R residue 606 VAL Chi-restraints excluded: chain R residue 610 LEU Chi-restraints excluded: chain R residue 614 ILE Chi-restraints excluded: chain R residue 637 LEU Chi-restraints excluded: chain X residue 6 ASP Chi-restraints excluded: chain X residue 53 VAL Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 38 CYS Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 42 THR Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.6467 > 50: distance: 77 - 82: 26.151 distance: 82 - 83: 27.312 distance: 83 - 84: 8.803 distance: 83 - 86: 40.878 distance: 84 - 90: 52.529 distance: 86 - 87: 35.212 distance: 87 - 88: 7.920 distance: 88 - 89: 28.235 distance: 90 - 91: 18.486 distance: 91 - 92: 22.910 distance: 91 - 94: 56.879 distance: 92 - 93: 12.937 distance: 92 - 97: 5.116 distance: 94 - 95: 32.033 distance: 94 - 96: 8.038 distance: 98 - 99: 17.044 distance: 99 - 100: 26.210 distance: 99 - 108: 14.599 distance: 101 - 102: 51.316 distance: 102 - 103: 21.582 distance: 103 - 104: 48.938 distance: 104 - 105: 31.058 distance: 105 - 106: 21.256 distance: 105 - 107: 32.332 distance: 108 - 109: 19.527 distance: 109 - 110: 8.642 distance: 109 - 112: 23.512 distance: 110 - 111: 28.856 distance: 110 - 115: 32.274 distance: 112 - 113: 15.776 distance: 112 - 114: 14.553 distance: 115 - 116: 9.710 distance: 116 - 117: 32.638 distance: 116 - 119: 15.313 distance: 117 - 118: 8.938 distance: 117 - 123: 8.554 distance: 119 - 120: 37.344 distance: 120 - 121: 4.044 distance: 120 - 122: 6.133 distance: 123 - 124: 28.016 distance: 124 - 125: 36.978 distance: 124 - 127: 23.473 distance: 125 - 126: 18.053 distance: 125 - 132: 44.463 distance: 127 - 128: 26.162 distance: 128 - 129: 24.372 distance: 129 - 130: 18.629 distance: 129 - 131: 23.882 distance: 132 - 133: 22.722 distance: 133 - 134: 33.417 distance: 134 - 136: 56.010 distance: 136 - 137: 16.409 distance: 137 - 138: 34.030 distance: 137 - 140: 13.236 distance: 138 - 139: 10.234 distance: 138 - 143: 28.618 distance: 140 - 141: 12.441 distance: 140 - 142: 21.067 distance: 143 - 144: 7.821 distance: 144 - 145: 36.464 distance: 144 - 147: 27.685 distance: 145 - 146: 18.155 distance: 145 - 151: 36.700 distance: 147 - 148: 27.031 distance: 148 - 149: 18.302 distance: 148 - 150: 30.451 distance: 151 - 152: 10.539 distance: 151 - 157: 25.645 distance: 152 - 153: 14.508 distance: 152 - 155: 7.625 distance: 153 - 154: 22.779 distance: 153 - 158: 29.109 distance: 155 - 156: 17.565 distance: 156 - 157: 24.575