Starting phenix.real_space_refine on Sun Jun 8 23:57:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyy_26199/06_2025/7tyy_26199.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyy_26199/06_2025/7tyy_26199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tyy_26199/06_2025/7tyy_26199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyy_26199/06_2025/7tyy_26199.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyy_26199/06_2025/7tyy_26199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyy_26199/06_2025/7tyy_26199.cif" } resolution = 3.0 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 6265 2.51 5 N 1676 2.21 5 O 1793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9802 Number of models: 1 Model: "" Number of chains: 12 Chain: "E" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 568 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 92} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 362 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 150 Chain: "P" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 238 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2941 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 17, 'TRANS': 351} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 74 Chain: "A" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1895 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2598 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 413 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 174 Unusual residues: {'NAG': 1, 'PLM': 5, 'Y01': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.80, per 1000 atoms: 0.80 Number of scatterers: 9802 At special positions: 0 Unit cell: (82.82, 99.22, 156.62, 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 68 16.00 O 1793 8.00 N 1676 7.00 C 6265 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS E 68 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS P 1 " - pdb=" SG CYS P 7 " distance=2.02 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied NAG-ASN " NAG R 501 " - " ASN R 130 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.3 seconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2360 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 14 sheets defined 44.0% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'E' and resid 60 through 77 removed outlier: 3.513A pdb=" N PHE E 67 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN E 70 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN E 75 " --> pdb=" O HIS E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 5.238A pdb=" N LYS E 81 " --> pdb=" O PRO E 78 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP E 83 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 107 removed outlier: 3.805A pdb=" N SER E 94 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU E 96 " --> pdb=" O PRO E 92 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG E 97 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N CYS E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 100 " --> pdb=" O LEU E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 127 removed outlier: 3.678A pdb=" N ARG E 118 " --> pdb=" O PRO E 114 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ILE E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN E 125 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS E 127 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 149 removed outlier: 3.944A pdb=" N LEU E 147 " --> pdb=" O GLU E 143 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET E 149 " --> pdb=" O VAL E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 165 removed outlier: 3.765A pdb=" N ILE E 157 " --> pdb=" O PRO E 153 " (cutoff:3.500A) Proline residue: E 158 - end of helix removed outlier: 3.522A pdb=" N VAL E 165 " --> pdb=" O ILE E 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 21 Processing helix chain 'R' and resid 38 through 62 removed outlier: 3.707A pdb=" N GLN R 60 " --> pdb=" O TYR R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 136 removed outlier: 4.332A pdb=" N ASN R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.544A pdb=" N ILE R 160 " --> pdb=" O HIS R 156 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU R 163 " --> pdb=" O SER R 159 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER R 166 " --> pdb=" O THR R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.552A pdb=" N ASN R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.581A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG R 214 " --> pdb=" O GLU R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 249 removed outlier: 3.794A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 284 Processing helix chain 'R' and resid 287 through 291 removed outlier: 3.519A pdb=" N TRP R 290 " --> pdb=" O ASP R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 329 Proline residue: R 304 - end of helix removed outlier: 3.555A pdb=" N ASN R 318 " --> pdb=" O PHE R 314 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG R 321 " --> pdb=" O LEU R 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 353 removed outlier: 3.803A pdb=" N LEU R 339 " --> pdb=" O SER R 335 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS R 343 " --> pdb=" O LEU R 339 " (cutoff:3.500A) Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 381 removed outlier: 3.556A pdb=" N TYR R 374 " --> pdb=" O LYS R 370 " (cutoff:3.500A) Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 405 Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.687A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.660A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 52 through 58' Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.550A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.869A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 350 removed outlier: 4.116A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.527A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 removed outlier: 4.389A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 10 through 24 removed outlier: 4.156A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.865A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing sheet with id=AA1, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AA2, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AA3, first strand: chain 'R' and resid 91 through 94 removed outlier: 3.532A pdb=" N SER R 91 " --> pdb=" O LYS R 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 120 through 121 removed outlier: 3.777A pdb=" N ARG R 126 " --> pdb=" O HIS R 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.962A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.949A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.513A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.520A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.734A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.717A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.701A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.552A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.106A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1320 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: 6.31 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1597 1.32 - 1.44: 2765 1.44 - 1.57: 5558 1.57 - 1.69: 0 1.69 - 1.82: 94 Bond restraints: 10014 Sorted by residual: bond pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" N HIS R 302 " pdb=" CA HIS R 302 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.26e-02 6.30e+03 8.23e+00 bond pdb=" N ILE R 301 " pdb=" CA ILE R 301 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.23e-02 6.61e+03 7.38e+00 bond pdb=" N VAL R 305 " pdb=" CA VAL R 305 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.21e-02 6.83e+03 7.09e+00 bond pdb=" N THR P 27 " pdb=" CA THR P 27 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.08e-02 8.57e+03 6.68e+00 ... (remaining 10009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 13558 3.84 - 7.68: 24 7.68 - 11.51: 0 11.51 - 15.35: 0 15.35 - 19.19: 2 Bond angle restraints: 13584 Sorted by residual: angle pdb=" CA PRO P 32 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 112.00 95.31 16.69 1.40e+00 5.10e-01 1.42e+02 angle pdb=" C THR P 31 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 125.00 144.19 -19.19 4.10e+00 5.95e-02 2.19e+01 angle pdb=" N LEU R 298 " pdb=" CA LEU R 298 " pdb=" C LEU R 298 " ideal model delta sigma weight residual 113.18 107.94 5.24 1.21e+00 6.83e-01 1.88e+01 angle pdb=" O THR P 31 " pdb=" C THR P 31 " pdb=" N PRO P 32 " ideal model delta sigma weight residual 121.66 125.45 -3.79 9.40e-01 1.13e+00 1.62e+01 angle pdb=" N THR P 27 " pdb=" CA THR P 27 " pdb=" C THR P 27 " ideal model delta sigma weight residual 112.30 107.07 5.23 1.36e+00 5.41e-01 1.48e+01 ... (remaining 13579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5576 17.72 - 35.44: 356 35.44 - 53.16: 98 53.16 - 70.88: 20 70.88 - 88.60: 12 Dihedral angle restraints: 6062 sinusoidal: 2413 harmonic: 3649 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 173.02 -80.02 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" CB CYS P 1 " pdb=" SG CYS P 1 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual -86.00 -128.76 42.76 1 1.00e+01 1.00e-02 2.55e+01 dihedral pdb=" CB CYS E 68 " pdb=" SG CYS E 68 " pdb=" SG CYS E 99 " pdb=" CB CYS E 99 " ideal model delta sinusoidal sigma weight residual -86.00 -47.08 -38.92 1 1.00e+01 1.00e-02 2.13e+01 ... (remaining 6059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1174 0.043 - 0.087: 259 0.087 - 0.130: 75 0.130 - 0.174: 6 0.174 - 0.217: 4 Chirality restraints: 1518 Sorted by residual: chirality pdb=" CB VAL P 8 " pdb=" CA VAL P 8 " pdb=" CG1 VAL P 8 " pdb=" CG2 VAL P 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA PHE R 359 " pdb=" N PHE R 359 " pdb=" C PHE R 359 " pdb=" CB PHE R 359 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.21 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ALA R 307 " pdb=" N ALA R 307 " pdb=" C ALA R 307 " pdb=" CB ALA R 307 " both_signs ideal model delta sigma weight residual False 2.48 2.69 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1515 not shown) Planarity restraints: 1725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN P 26 " 0.014 2.00e-02 2.50e+03 2.69e-02 7.24e+00 pdb=" C ASN P 26 " -0.047 2.00e-02 2.50e+03 pdb=" O ASN P 26 " 0.017 2.00e-02 2.50e+03 pdb=" N THR P 27 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 299 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C TYR R 299 " 0.033 2.00e-02 2.50e+03 pdb=" O TYR R 299 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE R 300 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR P 31 " -0.033 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO P 32 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO P 32 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO P 32 " -0.026 5.00e-02 4.00e+02 ... (remaining 1722 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 330 2.72 - 3.26: 9996 3.26 - 3.81: 16541 3.81 - 4.35: 22015 4.35 - 4.90: 35463 Nonbonded interactions: 84345 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.174 3.040 nonbonded pdb=" O TYR R 374 " pdb=" OG SER R 378 " model vdw 2.229 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.252 3.040 nonbonded pdb=" OH TYR B 289 " pdb=" NE1 TRP B 297 " model vdw 2.265 3.120 ... (remaining 84340 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 71.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 32.560 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:49.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 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 : 0.003 0.108 10025 Z= 0.222 Angle : 0.576 19.189 13605 Z= 0.350 Chirality : 0.041 0.217 1518 Planarity : 0.003 0.045 1724 Dihedral : 13.400 88.597 3675 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.03 % Allowed : 14.04 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.20), residues: 1230 helix: -2.79 (0.17), residues: 473 sheet: -2.22 (0.30), residues: 215 loop : -1.51 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 76 HIS 0.003 0.000 HIS R 302 PHE 0.008 0.001 PHE E 128 TYR 0.009 0.001 TYR N 60 ARG 0.002 0.000 ARG N 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00192 ( 1) link_NAG-ASN : angle 1.32165 ( 3) hydrogen bonds : bond 0.26749 ( 468) hydrogen bonds : angle 9.63821 ( 1320) SS BOND : bond 0.00462 ( 9) SS BOND : angle 1.04397 ( 18) covalent geometry : bond 0.00319 (10014) covalent geometry : angle 0.57466 (13584) Misc. bond : bond 0.10769 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 222 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: E 103 PHE cc_start: 0.6332 (m-10) cc_final: 0.5854 (m-80) REVERT: R 48 MET cc_start: 0.6999 (ttm) cc_final: 0.6506 (ttt) REVERT: R 49 MET cc_start: 0.7668 (mmm) cc_final: 0.6923 (mpp) REVERT: R 99 PHE cc_start: 0.7522 (m-80) cc_final: 0.7304 (m-80) REVERT: R 143 LYS cc_start: 0.7028 (tttt) cc_final: 0.6359 (mtmt) REVERT: R 213 ARG cc_start: 0.5391 (mtt90) cc_final: 0.4915 (mtp-110) REVERT: R 230 MET cc_start: 0.7091 (mtm) cc_final: 0.6770 (ttp) REVERT: R 346 MET cc_start: 0.6678 (mmp) cc_final: 0.6055 (ptp) REVERT: A 221 MET cc_start: 0.7775 (ttm) cc_final: 0.7419 (ttp) REVERT: A 265 ARG cc_start: 0.6230 (mmt180) cc_final: 0.5878 (mtt90) REVERT: B 19 ARG cc_start: 0.6639 (mtm180) cc_final: 0.6247 (mtm180) REVERT: G 17 GLU cc_start: 0.6131 (mm-30) cc_final: 0.5790 (pt0) REVERT: G 21 MET cc_start: 0.6199 (mmm) cc_final: 0.5976 (ttt) REVERT: N 106 ASP cc_start: 0.6811 (p0) cc_final: 0.6401 (p0) outliers start: 20 outliers final: 9 residues processed: 239 average time/residue: 1.3265 time to fit residues: 338.5188 Evaluate side-chains 170 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 161 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 CYS Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 305 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 57 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 70 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 186 ASN R 286 ASN R 399 GLN A 12 GLN ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 264 ASN A 278 ASN A 294 GLN A 357 HIS A 371 ASN B 156 GLN B 175 GLN B 266 HIS B 268 ASN N 31 ASN N 77 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.182861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.148484 restraints weight = 11064.661| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.39 r_work: 0.3503 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10025 Z= 0.137 Angle : 0.546 7.642 13605 Z= 0.290 Chirality : 0.041 0.175 1518 Planarity : 0.004 0.041 1724 Dihedral : 6.833 59.552 1596 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.26 % Allowed : 17.90 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.23), residues: 1230 helix: -0.58 (0.22), residues: 489 sheet: -1.58 (0.31), residues: 221 loop : -1.04 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 169 HIS 0.007 0.001 HIS R 277 PHE 0.018 0.001 PHE R 359 TYR 0.020 0.001 TYR A 358 ARG 0.010 0.001 ARG A 380 Details of bonding type rmsd link_NAG-ASN : bond 0.00035 ( 1) link_NAG-ASN : angle 1.08939 ( 3) hydrogen bonds : bond 0.04348 ( 468) hydrogen bonds : angle 5.66748 ( 1320) SS BOND : bond 0.00427 ( 9) SS BOND : angle 1.44173 ( 18) covalent geometry : bond 0.00299 (10014) covalent geometry : angle 0.54331 (13584) Misc. bond : bond 0.00045 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 1.074 Fit side-chains REVERT: E 103 PHE cc_start: 0.6664 (m-10) cc_final: 0.6134 (m-80) REVERT: R 49 MET cc_start: 0.7822 (mmm) cc_final: 0.6313 (mpp) REVERT: R 52 GLN cc_start: 0.7435 (tt0) cc_final: 0.7094 (tm-30) REVERT: R 99 PHE cc_start: 0.7563 (m-80) cc_final: 0.7330 (m-80) REVERT: R 143 LYS cc_start: 0.6953 (tttt) cc_final: 0.6204 (mtmt) REVERT: R 230 MET cc_start: 0.7543 (mtm) cc_final: 0.7135 (ttp) REVERT: R 240 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7386 (mm-30) REVERT: R 306 MET cc_start: 0.8338 (mmm) cc_final: 0.7988 (mmt) REVERT: R 346 MET cc_start: 0.7492 (mmp) cc_final: 0.6452 (tmt) REVERT: A 31 GLN cc_start: 0.7732 (tp40) cc_final: 0.7012 (tt0) REVERT: A 221 MET cc_start: 0.8350 (ttm) cc_final: 0.8062 (ttp) REVERT: A 299 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6022 (tt0) REVERT: A 392 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7030 (mt-10) REVERT: B 217 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.6955 (ppp) REVERT: N 5 GLN cc_start: 0.6799 (mm-40) cc_final: 0.6177 (mm-40) REVERT: N 87 LYS cc_start: 0.8468 (mtpt) cc_final: 0.8202 (mttt) REVERT: N 106 ASP cc_start: 0.7173 (p0) cc_final: 0.6739 (p0) outliers start: 32 outliers final: 13 residues processed: 187 average time/residue: 1.0123 time to fit residues: 205.6183 Evaluate side-chains 152 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 92 TYR Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 323 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 17 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 76 optimal weight: 0.1980 chunk 60 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 336 HIS A 12 GLN ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 357 HIS B 268 ASN N 31 ASN N 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.174623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.141174 restraints weight = 11469.793| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.73 r_work: 0.3508 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10025 Z= 0.122 Angle : 0.509 6.532 13605 Z= 0.267 Chirality : 0.041 0.180 1518 Planarity : 0.003 0.043 1724 Dihedral : 6.539 59.561 1588 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.46 % Allowed : 18.41 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.76 (0.24), residues: 1230 helix: 0.28 (0.24), residues: 491 sheet: -1.23 (0.32), residues: 220 loop : -0.78 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.005 0.001 HIS R 381 PHE 0.020 0.001 PHE R 119 TYR 0.017 0.001 TYR R 372 ARG 0.009 0.001 ARG N 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00125 ( 1) link_NAG-ASN : angle 1.11596 ( 3) hydrogen bonds : bond 0.03818 ( 468) hydrogen bonds : angle 5.12820 ( 1320) SS BOND : bond 0.00387 ( 9) SS BOND : angle 1.29321 ( 18) covalent geometry : bond 0.00268 (10014) covalent geometry : angle 0.50658 (13584) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 1.122 Fit side-chains REVERT: E 103 PHE cc_start: 0.6559 (m-10) cc_final: 0.6044 (m-80) REVERT: R 49 MET cc_start: 0.7877 (mmm) cc_final: 0.7056 (mpp) REVERT: R 110 LYS cc_start: 0.4322 (tttp) cc_final: 0.4006 (ttmm) REVERT: R 143 LYS cc_start: 0.7009 (tttt) cc_final: 0.6277 (mtmt) REVERT: R 230 MET cc_start: 0.7500 (mtm) cc_final: 0.7127 (ttp) REVERT: R 240 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7496 (mm-30) REVERT: R 306 MET cc_start: 0.8517 (mmm) cc_final: 0.8314 (mmt) REVERT: R 321 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6698 (ttm170) REVERT: R 346 MET cc_start: 0.7559 (mmp) cc_final: 0.6574 (tmt) REVERT: A 31 GLN cc_start: 0.7645 (tp40) cc_final: 0.6913 (tt0) REVERT: A 221 MET cc_start: 0.8250 (ttm) cc_final: 0.7971 (ttp) REVERT: B 130 GLU cc_start: 0.5137 (OUTLIER) cc_final: 0.4784 (mp0) REVERT: B 217 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7147 (ppp) REVERT: N 5 GLN cc_start: 0.6793 (OUTLIER) cc_final: 0.6317 (mm-40) REVERT: N 87 LYS cc_start: 0.8580 (mtpt) cc_final: 0.8343 (mttt) REVERT: N 106 ASP cc_start: 0.7452 (p0) cc_final: 0.7055 (p0) outliers start: 34 outliers final: 12 residues processed: 170 average time/residue: 1.0580 time to fit residues: 195.0457 Evaluate side-chains 151 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 chunk 31 optimal weight: 0.0020 chunk 108 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 22 optimal weight: 0.0040 chunk 66 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 overall best weight: 0.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 336 HIS A 12 GLN A 357 HIS N 31 ASN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.175402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.142590 restraints weight = 11438.972| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.65 r_work: 0.3527 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10025 Z= 0.107 Angle : 0.487 6.498 13605 Z= 0.257 Chirality : 0.040 0.181 1518 Planarity : 0.003 0.047 1724 Dihedral : 6.321 59.323 1587 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.26 % Allowed : 19.94 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.39 (0.24), residues: 1230 helix: 0.66 (0.24), residues: 499 sheet: -1.15 (0.32), residues: 226 loop : -0.62 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS R 381 PHE 0.010 0.001 PHE R 137 TYR 0.019 0.001 TYR R 372 ARG 0.008 0.000 ARG N 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00153 ( 1) link_NAG-ASN : angle 1.25032 ( 3) hydrogen bonds : bond 0.03443 ( 468) hydrogen bonds : angle 4.84024 ( 1320) SS BOND : bond 0.00358 ( 9) SS BOND : angle 1.14334 ( 18) covalent geometry : bond 0.00234 (10014) covalent geometry : angle 0.48481 (13584) Misc. bond : bond 0.00032 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 1.092 Fit side-chains REVERT: E 103 PHE cc_start: 0.6508 (m-80) cc_final: 0.5953 (m-80) REVERT: R 49 MET cc_start: 0.7849 (mmm) cc_final: 0.6395 (mpp) REVERT: R 77 ASP cc_start: 0.7757 (p0) cc_final: 0.7531 (p0) REVERT: R 110 LYS cc_start: 0.4254 (tttp) cc_final: 0.3977 (ttmm) REVERT: R 143 LYS cc_start: 0.7001 (tttt) cc_final: 0.6292 (mtmt) REVERT: R 230 MET cc_start: 0.7518 (mtm) cc_final: 0.7224 (ttp) REVERT: R 240 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7500 (mm-30) REVERT: R 346 MET cc_start: 0.7476 (mmp) cc_final: 0.6560 (tmt) REVERT: A 24 LYS cc_start: 0.7427 (mmtm) cc_final: 0.7213 (pttt) REVERT: A 31 GLN cc_start: 0.7587 (tp40) cc_final: 0.6983 (tt0) REVERT: A 221 MET cc_start: 0.8244 (ttm) cc_final: 0.7985 (ttp) REVERT: A 299 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6167 (tt0) REVERT: B 217 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7218 (ppp) REVERT: N 1 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.7090 (tt0) REVERT: N 5 GLN cc_start: 0.6880 (OUTLIER) cc_final: 0.6522 (mm-40) outliers start: 32 outliers final: 14 residues processed: 167 average time/residue: 1.0358 time to fit residues: 187.8841 Evaluate side-chains 152 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 118 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 GLN A 357 HIS A 371 ASN N 31 ASN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.170390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.136851 restraints weight = 11340.829| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.77 r_work: 0.3440 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10025 Z= 0.173 Angle : 0.540 6.677 13605 Z= 0.283 Chirality : 0.042 0.204 1518 Planarity : 0.004 0.047 1724 Dihedral : 6.614 56.346 1587 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.07 % Allowed : 19.63 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.41 (0.24), residues: 1230 helix: 0.63 (0.24), residues: 500 sheet: -1.20 (0.32), residues: 235 loop : -0.56 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.003 0.001 HIS R 381 PHE 0.019 0.002 PHE R 359 TYR 0.019 0.001 TYR R 284 ARG 0.007 0.001 ARG N 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00061 ( 1) link_NAG-ASN : angle 1.47878 ( 3) hydrogen bonds : bond 0.03690 ( 468) hydrogen bonds : angle 4.93213 ( 1320) SS BOND : bond 0.00473 ( 9) SS BOND : angle 1.61063 ( 18) covalent geometry : bond 0.00392 (10014) covalent geometry : angle 0.53700 (13584) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 1.141 Fit side-chains REVERT: E 103 PHE cc_start: 0.6498 (m-80) cc_final: 0.6007 (m-80) REVERT: R 49 MET cc_start: 0.7806 (mmm) cc_final: 0.6827 (mpp) REVERT: R 52 GLN cc_start: 0.7650 (tt0) cc_final: 0.7027 (tm-30) REVERT: R 77 ASP cc_start: 0.7854 (p0) cc_final: 0.7544 (p0) REVERT: R 110 LYS cc_start: 0.4274 (tttp) cc_final: 0.3981 (ttmm) REVERT: R 143 LYS cc_start: 0.7059 (tttt) cc_final: 0.6313 (mtmt) REVERT: R 240 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7462 (mm-30) REVERT: R 321 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6875 (ttm170) REVERT: R 373 ASP cc_start: 0.7845 (m-30) cc_final: 0.7581 (m-30) REVERT: R 405 GLN cc_start: 0.6286 (mp10) cc_final: 0.6069 (mp10) REVERT: A 31 GLN cc_start: 0.7549 (tp40) cc_final: 0.6854 (tt0) REVERT: A 221 MET cc_start: 0.8320 (ttm) cc_final: 0.7945 (ttp) REVERT: A 299 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6228 (tt0) REVERT: B 130 GLU cc_start: 0.5147 (OUTLIER) cc_final: 0.4801 (mp0) REVERT: B 217 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7246 (ppp) REVERT: N 1 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.7040 (tt0) REVERT: N 5 GLN cc_start: 0.7106 (OUTLIER) cc_final: 0.6835 (mm-40) REVERT: N 106 ASP cc_start: 0.7430 (p0) cc_final: 0.7184 (p0) outliers start: 40 outliers final: 20 residues processed: 166 average time/residue: 1.0341 time to fit residues: 186.9223 Evaluate side-chains 160 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 77 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 84 optimal weight: 0.0040 chunk 74 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 110 optimal weight: 0.0040 chunk 57 optimal weight: 0.6980 chunk 68 optimal weight: 0.0010 overall best weight: 0.2810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 GLN A 357 HIS ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.174980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.142564 restraints weight = 11476.210| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.70 r_work: 0.3518 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10025 Z= 0.098 Angle : 0.487 7.006 13605 Z= 0.253 Chirality : 0.040 0.191 1518 Planarity : 0.003 0.052 1724 Dihedral : 6.183 57.455 1587 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.26 % Allowed : 21.16 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.17 (0.24), residues: 1230 helix: 0.93 (0.24), residues: 502 sheet: -1.16 (0.32), residues: 235 loop : -0.52 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.006 0.001 HIS R 302 PHE 0.025 0.001 PHE R 359 TYR 0.011 0.001 TYR N 60 ARG 0.009 0.000 ARG N 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 1) link_NAG-ASN : angle 1.42302 ( 3) hydrogen bonds : bond 0.03283 ( 468) hydrogen bonds : angle 4.60098 ( 1320) SS BOND : bond 0.00365 ( 9) SS BOND : angle 0.83880 ( 18) covalent geometry : bond 0.00212 (10014) covalent geometry : angle 0.48554 (13584) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 1.062 Fit side-chains REVERT: E 103 PHE cc_start: 0.6387 (m-80) cc_final: 0.5857 (m-80) REVERT: R 49 MET cc_start: 0.7771 (mmm) cc_final: 0.6450 (mpp) REVERT: R 77 ASP cc_start: 0.7789 (p0) cc_final: 0.7507 (p0) REVERT: R 110 LYS cc_start: 0.4235 (tttp) cc_final: 0.3985 (ttmm) REVERT: R 143 LYS cc_start: 0.6976 (tttt) cc_final: 0.6272 (mtmt) REVERT: R 230 MET cc_start: 0.7446 (mtm) cc_final: 0.7230 (ttp) REVERT: R 240 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7526 (mm-30) REVERT: R 321 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6592 (ttm170) REVERT: R 346 MET cc_start: 0.7413 (mmp) cc_final: 0.6372 (ptp) REVERT: R 373 ASP cc_start: 0.7784 (m-30) cc_final: 0.7522 (m-30) REVERT: R 405 GLN cc_start: 0.6263 (mp10) cc_final: 0.6055 (mp10) REVERT: A 12 GLN cc_start: 0.4831 (OUTLIER) cc_final: 0.3497 (tm130) REVERT: A 24 LYS cc_start: 0.7398 (mmtm) cc_final: 0.7140 (pttt) REVERT: A 31 GLN cc_start: 0.7502 (tp40) cc_final: 0.6846 (tt0) REVERT: A 221 MET cc_start: 0.8228 (ttm) cc_final: 0.7925 (ttp) REVERT: A 299 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6236 (tt0) REVERT: A 334 VAL cc_start: 0.7655 (t) cc_final: 0.7352 (p) REVERT: B 217 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7245 (ppp) REVERT: N 106 ASP cc_start: 0.7511 (p0) cc_final: 0.7286 (p0) outliers start: 32 outliers final: 17 residues processed: 165 average time/residue: 0.9366 time to fit residues: 169.0072 Evaluate side-chains 160 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.0870 chunk 98 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 119 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 GLN A 357 HIS A 387 HIS N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.174238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.141828 restraints weight = 11493.512| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.71 r_work: 0.3509 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10025 Z= 0.113 Angle : 0.493 6.435 13605 Z= 0.258 Chirality : 0.041 0.190 1518 Planarity : 0.004 0.053 1724 Dihedral : 6.184 57.659 1587 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.15 % Allowed : 21.77 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.04 (0.24), residues: 1230 helix: 1.06 (0.24), residues: 502 sheet: -1.18 (0.32), residues: 240 loop : -0.42 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.007 0.001 HIS R 302 PHE 0.018 0.001 PHE R 119 TYR 0.019 0.001 TYR R 284 ARG 0.006 0.000 ARG N 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00114 ( 1) link_NAG-ASN : angle 1.45636 ( 3) hydrogen bonds : bond 0.03300 ( 468) hydrogen bonds : angle 4.51791 ( 1320) SS BOND : bond 0.00348 ( 9) SS BOND : angle 1.05993 ( 18) covalent geometry : bond 0.00252 (10014) covalent geometry : angle 0.49161 (13584) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.205 Fit side-chains REVERT: E 103 PHE cc_start: 0.6375 (m-80) cc_final: 0.5841 (m-80) REVERT: R 49 MET cc_start: 0.7733 (mmm) cc_final: 0.6889 (mpp) REVERT: R 77 ASP cc_start: 0.7851 (p0) cc_final: 0.7548 (p0) REVERT: R 110 LYS cc_start: 0.4363 (tttp) cc_final: 0.4103 (ttmm) REVERT: R 143 LYS cc_start: 0.7000 (tttt) cc_final: 0.6285 (mtmt) REVERT: R 230 MET cc_start: 0.7492 (mtm) cc_final: 0.7264 (ttp) REVERT: R 240 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7492 (mm-30) REVERT: R 346 MET cc_start: 0.7413 (mmp) cc_final: 0.6353 (ptp) REVERT: R 373 ASP cc_start: 0.7694 (m-30) cc_final: 0.7480 (m-30) REVERT: R 405 GLN cc_start: 0.6394 (mp10) cc_final: 0.6189 (mp10) REVERT: A 24 LYS cc_start: 0.7402 (mmtm) cc_final: 0.7150 (pttt) REVERT: A 31 GLN cc_start: 0.7535 (tp40) cc_final: 0.6888 (tt0) REVERT: A 221 MET cc_start: 0.8170 (ttm) cc_final: 0.7837 (ttp) REVERT: A 299 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6251 (tt0) REVERT: A 334 VAL cc_start: 0.7663 (t) cc_final: 0.7357 (p) REVERT: B 217 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7328 (pp-130) outliers start: 31 outliers final: 19 residues processed: 157 average time/residue: 1.0397 time to fit residues: 178.2824 Evaluate side-chains 152 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 69 optimal weight: 0.0980 chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 30.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN B 156 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.173619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.139228 restraints weight = 11503.052| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.43 r_work: 0.3514 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10025 Z= 0.114 Angle : 0.493 8.090 13605 Z= 0.257 Chirality : 0.041 0.204 1518 Planarity : 0.003 0.053 1724 Dihedral : 6.135 57.210 1587 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.05 % Allowed : 22.08 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.03 (0.24), residues: 1230 helix: 1.12 (0.24), residues: 506 sheet: -1.23 (0.31), residues: 249 loop : -0.30 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.006 0.001 HIS R 302 PHE 0.016 0.001 PHE R 119 TYR 0.016 0.001 TYR N 80 ARG 0.006 0.000 ARG N 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00103 ( 1) link_NAG-ASN : angle 1.52030 ( 3) hydrogen bonds : bond 0.03292 ( 468) hydrogen bonds : angle 4.48333 ( 1320) SS BOND : bond 0.00353 ( 9) SS BOND : angle 0.97472 ( 18) covalent geometry : bond 0.00253 (10014) covalent geometry : angle 0.49140 (13584) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 1.246 Fit side-chains REVERT: E 103 PHE cc_start: 0.6399 (m-80) cc_final: 0.5883 (m-80) REVERT: R 49 MET cc_start: 0.7685 (mmm) cc_final: 0.6926 (mpp) REVERT: R 77 ASP cc_start: 0.7846 (p0) cc_final: 0.7581 (p0) REVERT: R 110 LYS cc_start: 0.4375 (tttp) cc_final: 0.4124 (ttmm) REVERT: R 143 LYS cc_start: 0.7025 (tttt) cc_final: 0.6332 (mtmt) REVERT: R 240 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7498 (mm-30) REVERT: R 262 TYR cc_start: 0.8045 (m-80) cc_final: 0.7666 (m-80) REVERT: R 346 MET cc_start: 0.7407 (mmp) cc_final: 0.6343 (ptp) REVERT: R 373 ASP cc_start: 0.7763 (m-30) cc_final: 0.7492 (m-30) REVERT: R 405 GLN cc_start: 0.6399 (mp10) cc_final: 0.6192 (mp10) REVERT: A 24 LYS cc_start: 0.7364 (mmtm) cc_final: 0.7139 (pttt) REVERT: A 31 GLN cc_start: 0.7552 (tp40) cc_final: 0.6899 (tt0) REVERT: A 221 MET cc_start: 0.8136 (ttm) cc_final: 0.7757 (ttp) REVERT: A 299 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6252 (tt0) REVERT: A 334 VAL cc_start: 0.7662 (t) cc_final: 0.7355 (p) REVERT: B 130 GLU cc_start: 0.5203 (OUTLIER) cc_final: 0.4748 (mp0) REVERT: N 1 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.7089 (tt0) outliers start: 30 outliers final: 18 residues processed: 158 average time/residue: 1.0870 time to fit residues: 186.9841 Evaluate side-chains 156 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 39 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.173049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140751 restraints weight = 11437.449| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.71 r_work: 0.3487 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10025 Z= 0.123 Angle : 0.507 7.920 13605 Z= 0.265 Chirality : 0.041 0.191 1518 Planarity : 0.003 0.053 1724 Dihedral : 6.162 58.199 1587 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.54 % Allowed : 22.99 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.06 (0.24), residues: 1230 helix: 1.13 (0.23), residues: 507 sheet: -1.22 (0.32), residues: 249 loop : -0.27 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.006 0.001 HIS R 302 PHE 0.011 0.001 PHE R 285 TYR 0.020 0.001 TYR R 284 ARG 0.006 0.000 ARG N 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00087 ( 1) link_NAG-ASN : angle 1.57996 ( 3) hydrogen bonds : bond 0.03314 ( 468) hydrogen bonds : angle 4.49873 ( 1320) SS BOND : bond 0.00352 ( 9) SS BOND : angle 1.13261 ( 18) covalent geometry : bond 0.00277 (10014) covalent geometry : angle 0.50537 (13584) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.254 Fit side-chains REVERT: E 103 PHE cc_start: 0.6384 (m-80) cc_final: 0.5862 (m-80) REVERT: R 49 MET cc_start: 0.7662 (mmm) cc_final: 0.6914 (mpp) REVERT: R 77 ASP cc_start: 0.7824 (p0) cc_final: 0.7538 (p0) REVERT: R 106 GLU cc_start: 0.4112 (mp0) cc_final: 0.3769 (mm-30) REVERT: R 110 LYS cc_start: 0.4342 (tttp) cc_final: 0.4096 (ttmm) REVERT: R 143 LYS cc_start: 0.7017 (tttt) cc_final: 0.6335 (mtmt) REVERT: R 240 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7504 (mm-30) REVERT: R 262 TYR cc_start: 0.8067 (m-80) cc_final: 0.7688 (m-80) REVERT: R 346 MET cc_start: 0.7441 (mmp) cc_final: 0.6557 (tmt) REVERT: R 373 ASP cc_start: 0.7703 (m-30) cc_final: 0.7475 (m-30) REVERT: R 405 GLN cc_start: 0.6493 (mp10) cc_final: 0.6279 (mp10) REVERT: A 24 LYS cc_start: 0.7387 (mmtm) cc_final: 0.7136 (pttt) REVERT: A 31 GLN cc_start: 0.7533 (tp40) cc_final: 0.6895 (tt0) REVERT: A 221 MET cc_start: 0.8179 (ttm) cc_final: 0.7811 (ttp) REVERT: A 299 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6277 (tt0) REVERT: A 334 VAL cc_start: 0.7687 (t) cc_final: 0.7373 (p) REVERT: B 130 GLU cc_start: 0.5208 (OUTLIER) cc_final: 0.4752 (mp0) REVERT: B 217 MET cc_start: 0.7896 (mmm) cc_final: 0.7549 (ptm) REVERT: N 1 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.7092 (tt0) outliers start: 25 outliers final: 19 residues processed: 157 average time/residue: 1.1736 time to fit residues: 202.6147 Evaluate side-chains 158 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 18 optimal weight: 1.9990 chunk 73 optimal weight: 0.0270 chunk 79 optimal weight: 2.9990 chunk 57 optimal weight: 0.0980 chunk 34 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.173892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.141816 restraints weight = 11400.848| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.68 r_work: 0.3508 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10025 Z= 0.112 Angle : 0.502 7.954 13605 Z= 0.262 Chirality : 0.041 0.194 1518 Planarity : 0.003 0.054 1724 Dihedral : 6.083 59.614 1587 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.95 % Allowed : 22.58 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.15 (0.24), residues: 1230 helix: 1.25 (0.24), residues: 503 sheet: -1.18 (0.32), residues: 238 loop : -0.29 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS R 302 PHE 0.010 0.001 PHE R 137 TYR 0.019 0.001 TYR R 372 ARG 0.005 0.000 ARG N 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00136 ( 1) link_NAG-ASN : angle 1.59252 ( 3) hydrogen bonds : bond 0.03244 ( 468) hydrogen bonds : angle 4.41972 ( 1320) SS BOND : bond 0.00327 ( 9) SS BOND : angle 1.00425 ( 18) covalent geometry : bond 0.00250 (10014) covalent geometry : angle 0.50016 (13584) Misc. bond : bond 0.00010 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 2.522 Fit side-chains REVERT: E 103 PHE cc_start: 0.6362 (m-80) cc_final: 0.5838 (m-80) REVERT: R 49 MET cc_start: 0.7649 (mmm) cc_final: 0.6919 (mpp) REVERT: R 77 ASP cc_start: 0.7843 (p0) cc_final: 0.7533 (p0) REVERT: R 106 GLU cc_start: 0.4201 (mp0) cc_final: 0.3532 (mm-30) REVERT: R 110 LYS cc_start: 0.4339 (tttp) cc_final: 0.4098 (ttmm) REVERT: R 137 PHE cc_start: 0.7187 (m-80) cc_final: 0.6671 (p90) REVERT: R 143 LYS cc_start: 0.6971 (tttt) cc_final: 0.6309 (mtmt) REVERT: R 230 MET cc_start: 0.7488 (mtm) cc_final: 0.7247 (ttp) REVERT: R 240 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7522 (mm-30) REVERT: R 262 TYR cc_start: 0.8025 (m-80) cc_final: 0.7644 (m-80) REVERT: R 346 MET cc_start: 0.7409 (mmp) cc_final: 0.6333 (ptp) REVERT: R 373 ASP cc_start: 0.7722 (m-30) cc_final: 0.7441 (m-30) REVERT: R 405 GLN cc_start: 0.6502 (mp10) cc_final: 0.6294 (mp10) REVERT: A 24 LYS cc_start: 0.7376 (mmtm) cc_final: 0.7148 (pttt) REVERT: A 31 GLN cc_start: 0.7521 (tp40) cc_final: 0.6882 (tt0) REVERT: A 221 MET cc_start: 0.8157 (ttm) cc_final: 0.7800 (ttp) REVERT: A 299 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.6248 (tt0) REVERT: A 334 VAL cc_start: 0.7651 (t) cc_final: 0.7348 (p) REVERT: B 130 GLU cc_start: 0.5214 (OUTLIER) cc_final: 0.4757 (mp0) REVERT: B 217 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7544 (ptm) outliers start: 29 outliers final: 21 residues processed: 161 average time/residue: 1.0441 time to fit residues: 184.2017 Evaluate side-chains 162 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain R residue 81 CYS Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 146 TYR Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 91 optimal weight: 0.0980 chunk 8 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 38 optimal weight: 0.0970 chunk 107 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 357 HIS N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.174610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.142525 restraints weight = 11416.596| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.63 r_work: 0.3524 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10025 Z= 0.106 Angle : 0.502 7.889 13605 Z= 0.261 Chirality : 0.040 0.198 1518 Planarity : 0.003 0.054 1724 Dihedral : 6.023 58.889 1587 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.54 % Allowed : 23.40 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.23 (0.24), residues: 1230 helix: 1.29 (0.23), residues: 507 sheet: -1.14 (0.32), residues: 237 loop : -0.22 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS R 302 PHE 0.013 0.001 PHE A 222 TYR 0.020 0.001 TYR R 284 ARG 0.005 0.000 ARG N 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00145 ( 1) link_NAG-ASN : angle 1.57613 ( 3) hydrogen bonds : bond 0.03220 ( 468) hydrogen bonds : angle 4.35118 ( 1320) SS BOND : bond 0.00314 ( 9) SS BOND : angle 0.91021 ( 18) covalent geometry : bond 0.00234 (10014) covalent geometry : angle 0.50094 (13584) Misc. bond : bond 0.00008 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8031.67 seconds wall clock time: 141 minutes 17.42 seconds (8477.42 seconds total)