Starting phenix.real_space_refine on Sun Jun 29 17:26:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t0w_25583/06_2025/7t0w_25583_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t0w_25583/06_2025/7t0w_25583.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/7t0w_25583/06_2025/7t0w_25583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t0w_25583/06_2025/7t0w_25583.map" model { file = "/net/cci-nas-00/data/ceres_data/7t0w_25583/06_2025/7t0w_25583_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t0w_25583/06_2025/7t0w_25583_trim.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= 0.003 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: 5 Type Number sf(0) Gaussians S 95 5.16 5 C 11221 2.51 5 N 2856 2.21 5 O 3255 1.98 5 H 16968 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34395 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5473 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 5454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5454 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "C" Number of atoms: 5473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5473 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 5454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5454 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "E" Number of atoms: 5443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5443 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "L2" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1582 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "H" Number of atoms: 1821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1821 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "H2" Number of atoms: 1821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1821 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "L" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1568 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 17.37, per 1000 atoms: 0.51 Number of scatterers: 34395 At special positions: 0 Unit cell: (144.586, 108.979, 143.507, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 95 16.00 O 3255 8.00 N 2856 7.00 C 11221 6.00 H 16968 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.04 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.04 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYSH2 22 " - pdb=" SG CYSH2 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN N 5 " - " MAN N 6 " " MAN N 8 " - " MAN N 9 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " MAN N 7 " - " MAN N 10 " ALPHA1-6 " BMA N 3 " - " MAN N 7 " " MAN N 7 " - " MAN N 8 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG F 1 " - " ASN A 80 " " NAG G 1 " - " ASN C 80 " " NAG I 1 " - " ASN C 149 " " NAG J 1 " - " ASN D 111 " " NAG K 1 " - " ASN E 208 " " NAG M 1 " - " ASN A 149 " " NAG N 1 " - " ASN B 111 " Time building additional restraints: 10.24 Conformation dependent library (CDL) restraints added in 2.9 seconds 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4024 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 21 sheets defined 34.0% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'A' and resid 7 through 21 Processing helix chain 'A' and resid 70 through 73 removed outlier: 3.518A pdb=" N SER A 73 " --> pdb=" O LYS A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 73' Processing helix chain 'A' and resid 84 through 90 removed outlier: 3.527A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 242 removed outlier: 4.675A pdb=" N MET A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix removed outlier: 4.009A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TRP A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 242 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 272 removed outlier: 3.509A pdb=" N ARG A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 306 Processing helix chain 'A' and resid 309 through 339 Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 11 through 22 removed outlier: 3.621A pdb=" N PHE B 15 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 76 removed outlier: 3.633A pdb=" N LYS B 76 " --> pdb=" O GLU B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 73 through 76' Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 223 through 244 removed outlier: 4.712A pdb=" N LEU B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 251 through 275 removed outlier: 3.501A pdb=" N ASN B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 311 Processing helix chain 'B' and resid 314 through 346 removed outlier: 3.775A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix removed outlier: 3.954A pdb=" N ILE B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN B 346 " --> pdb=" O ALA B 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 21 Processing helix chain 'C' and resid 70 through 73 removed outlier: 3.544A pdb=" N SER C 73 " --> pdb=" O LYS C 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 73' Processing helix chain 'C' and resid 84 through 90 removed outlier: 3.592A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 238 removed outlier: 4.672A pdb=" N MET C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 246 through 272 removed outlier: 4.160A pdb=" N GLU C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 307 removed outlier: 4.785A pdb=" N PHE C 307 " --> pdb=" O ASN C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 339 Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 12 through 23 removed outlier: 4.498A pdb=" N LEU D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 removed outlier: 3.550A pdb=" N LYS D 76 " --> pdb=" O GLU D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 73 through 76' Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 142 through 146 removed outlier: 4.614A pdb=" N ASP D 145 " --> pdb=" O HIS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 183 through 186 removed outlier: 4.466A pdb=" N SER D 186 " --> pdb=" O GLU D 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 183 through 186' Processing helix chain 'D' and resid 223 through 230 removed outlier: 3.639A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.581A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 251 through 277 Processing helix chain 'D' and resid 284 through 311 Processing helix chain 'D' and resid 314 through 347 Proline residue: D 330 - end of helix removed outlier: 4.191A pdb=" N ARG D 347 " --> pdb=" O THR D 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 85 through 88 removed outlier: 3.721A pdb=" N LYS E 88 " --> pdb=" O ARG E 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 85 through 88' Processing helix chain 'E' and resid 99 through 105 removed outlier: 4.026A pdb=" N MET E 102 " --> pdb=" O ASN E 99 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY E 104 " --> pdb=" O ASN E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 240 removed outlier: 4.227A pdb=" N ILE E 238 " --> pdb=" O GLY E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 252 Processing helix chain 'E' and resid 252 through 257 removed outlier: 4.026A pdb=" N TRP E 256 " --> pdb=" O TRP E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 286 removed outlier: 3.684A pdb=" N ILE E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG E 284 " --> pdb=" O SER E 280 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER E 286 " --> pdb=" O ILE E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 322 removed outlier: 4.252A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 356 removed outlier: 3.810A pdb=" N LYS E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET E 331 " --> pdb=" O ARG E 327 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP E 332 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE E 337 " --> pdb=" O SER E 333 " (cutoff:3.500A) Proline residue: E 340 - end of helix removed outlier: 3.529A pdb=" N LEU E 355 " --> pdb=" O TRP E 351 " (cutoff:3.500A) Processing helix chain 'L2' and resid 80 through 84 Processing helix chain 'H' and resid 61 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.747A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H2' and resid 61 through 65 removed outlier: 3.519A pdb=" N GLNH2 65 " --> pdb=" O GLNH2 62 " (cutoff:3.500A) Processing helix chain 'H2' and resid 87 through 91 removed outlier: 3.579A pdb=" N ASPH2 90 " --> pdb=" O ARGH2 87 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THRH2 91 " --> pdb=" O SERH2 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H2' and resid 87 through 91' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.536A pdb=" N ASP L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 51 removed outlier: 6.532A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 56 through 68 current: chain 'A' and resid 123 through 135 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.796A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 39 through 49 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 39 through 49 current: chain 'B' and resid 59 through 71 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 59 through 71 current: chain 'B' and resid 126 through 138 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 99 through 101 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 150 through 159 current: chain 'B' and resid 209 through 221 Processing sheet with id=AA5, first strand: chain 'C' and resid 36 through 51 removed outlier: 6.501A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 56 through 68 current: chain 'C' and resid 123 through 135 Processing sheet with id=AA6, first strand: chain 'C' and resid 96 through 98 removed outlier: 4.029A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY C 203 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 42 through 49 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 42 through 49 current: chain 'D' and resid 59 through 71 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 71 current: chain 'D' and resid 126 through 138 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.126A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 51 through 59 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 51 through 59 current: chain 'E' and resid 71 through 83 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 71 through 83 current: chain 'E' and resid 138 through 150 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 111 through 112 removed outlier: 4.494A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L2' and resid 9 through 10 removed outlier: 6.316A pdb=" N TRPL2 36 " --> pdb=" O LEUL2 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L2' and resid 18 through 23 Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.610A pdb=" N GLU H 10 " --> pdb=" O VAL H 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AB6, first strand: chain 'H' and resid 45 through 49 removed outlier: 5.000A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 101 through 103 Processing sheet with id=AB8, first strand: chain 'H2' and resid 3 through 6 removed outlier: 3.800A pdb=" N VALH2 20 " --> pdb=" O METH2 81 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H2' and resid 10 through 11 removed outlier: 6.179A pdb=" N GLUH2 10 " --> pdb=" O VALH2 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'H2' and resid 45 through 51 removed outlier: 6.702A pdb=" N TRPH2 36 " --> pdb=" O METH2 48 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N GLYH2 50 " --> pdb=" O ILEH2 34 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILEH2 34 " --> pdb=" O GLYH2 50 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASPH2 33 " --> pdb=" O GLYH2 99 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 12 current: chain 'L' and resid 46 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 46 through 49 current: chain 'L' and resid 99 through 102 No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'L' and resid 18 through 23 650 hydrogen bonds defined for protein. 1842 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: 12.34 Time building geometry restraints manager: 12.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 16571 1.03 - 1.23: 701 1.23 - 1.43: 7385 1.43 - 1.63: 10007 1.63 - 1.82: 163 Bond restraints: 34827 Sorted by residual: bond pdb=" N ASP L 94 " pdb=" H ASP L 94 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.83e+01 bond pdb=" N MET H 51 " pdb=" H MET H 51 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.83e+01 bond pdb=" N TYR D 169 " pdb=" H TYR D 169 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.80e+01 bond pdb=" N TYR H 32 " pdb=" H TYR H 32 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.79e+01 bond pdb=" N ASNH2 57 " pdb=" H ASNH2 57 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.79e+01 ... (remaining 34822 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 61414 1.89 - 3.77: 981 3.77 - 5.66: 145 5.66 - 7.54: 27 7.54 - 9.43: 4 Bond angle restraints: 62571 Sorted by residual: angle pdb=" O LEUL2 96 " pdb=" C LEUL2 96 " pdb=" N LYSL2 97 " ideal model delta sigma weight residual 122.81 116.31 6.50 1.42e+00 4.96e-01 2.10e+01 angle pdb=" CA ASPH2 52 " pdb=" C ASPH2 52 " pdb=" O ASPH2 52 " ideal model delta sigma weight residual 119.76 115.69 4.07 8.90e-01 1.26e+00 2.09e+01 angle pdb=" CA LEU L 96 " pdb=" C LEU L 96 " pdb=" O LEU L 96 " ideal model delta sigma weight residual 120.99 115.91 5.08 1.12e+00 7.97e-01 2.06e+01 angle pdb=" CA LEU L 96 " pdb=" C LEU L 96 " pdb=" N LYS L 97 " ideal model delta sigma weight residual 115.61 122.16 -6.55 1.45e+00 4.76e-01 2.04e+01 angle pdb=" N GLY H 56 " pdb=" CA GLY H 56 " pdb=" C GLY H 56 " ideal model delta sigma weight residual 115.21 109.38 5.83 1.30e+00 5.92e-01 2.01e+01 ... (remaining 62566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.27: 15717 21.27 - 42.54: 880 42.54 - 63.80: 235 63.80 - 85.07: 34 85.07 - 106.34: 13 Dihedral angle restraints: 16879 sinusoidal: 9203 harmonic: 7676 Sorted by residual: dihedral pdb=" CB CYSH2 22 " pdb=" SG CYSH2 22 " pdb=" SG CYSH2 96 " pdb=" CB CYSH2 96 " ideal model delta sinusoidal sigma weight residual 93.00 145.43 -52.43 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CA CYS D 153 " pdb=" C CYS D 153 " pdb=" N PRO D 154 " pdb=" CA PRO D 154 " ideal model delta harmonic sigma weight residual 180.00 -158.72 -21.28 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CB CYS E 151 " pdb=" SG CYS E 151 " pdb=" SG CYS E 165 " pdb=" CB CYS E 165 " ideal model delta sinusoidal sigma weight residual 93.00 57.96 35.04 1 1.00e+01 1.00e-02 1.74e+01 ... (remaining 16876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2404 0.066 - 0.133: 373 0.133 - 0.199: 34 0.199 - 0.266: 5 0.266 - 0.332: 1 Chirality restraints: 2817 Sorted by residual: chirality pdb=" CA ASP H 113 " pdb=" N ASP H 113 " pdb=" C ASP H 113 " pdb=" CB ASP H 113 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 2814 not shown) Planarity restraints: 5046 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN H 57 " 0.297 2.00e-02 2.50e+03 3.09e-01 1.43e+03 pdb=" CG ASN H 57 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN H 57 " -0.290 2.00e-02 2.50e+03 pdb=" ND2 ASN H 57 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN H 57 " -0.445 2.00e-02 2.50e+03 pdb="HD22 ASN H 57 " 0.451 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASNH2 57 " -0.197 2.00e-02 2.50e+03 1.94e-01 5.64e+02 pdb=" CG ASNH2 57 " 0.007 2.00e-02 2.50e+03 pdb=" OD1 ASNH2 57 " 0.192 2.00e-02 2.50e+03 pdb=" ND2 ASNH2 57 " 0.006 2.00e-02 2.50e+03 pdb="HD21 ASNH2 57 " -0.277 2.00e-02 2.50e+03 pdb="HD22 ASNH2 57 " 0.270 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASPH2 52 " -0.019 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C ASPH2 52 " 0.064 2.00e-02 2.50e+03 pdb=" O ASPH2 52 " -0.023 2.00e-02 2.50e+03 pdb=" N PROH2 53 " -0.022 2.00e-02 2.50e+03 ... (remaining 5043 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 1076 2.11 - 2.74: 62001 2.74 - 3.36: 98731 3.36 - 3.98: 130277 3.98 - 4.60: 203985 Nonbonded interactions: 496070 Sorted by model distance: nonbonded pdb=" OH TYRH2 60 " pdb=" H METH2 70 " model vdw 1.494 2.450 nonbonded pdb=" O THR C 233 " pdb=" HG SER C 236 " model vdw 1.527 2.450 nonbonded pdb=" O ALA E 295 " pdb=" HH TYR E 350 " model vdw 1.541 2.450 nonbonded pdb=" OE1 GLU A 155 " pdb="HH21 ARG A 207 " model vdw 1.562 2.450 nonbonded pdb=" OD1 ASP C 121 " pdb=" HG1 THR C 123 " model vdw 1.574 2.450 ... (remaining 496065 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'H2' } ncs_group { reference = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'L' selection = (chain 'L2' and ((resid 3 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 4 through 21 or (resid 22 \ and (name N or name CA or name C or name O or name CB or name SG or name H or n \ ame HA or name HB2 or name HB3)) or resid 23 through 88 or (resid 89 and (name N \ or name CA or name C or name O or name CB or name SG or name H or name HA or na \ me HB2 or name HB3)) or resid 90 through 96 or (resid 97 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name CE or name NZ or na \ me H or name HA )) or resid 98 through 112)) } 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: 1.290 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: 0.650 Extract box with map and model: 1.480 Check model and map are aligned: 0.280 Set scattering table: 0.340 Process input model: 74.790 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.150 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:11.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 17891 Z= 0.325 Angle : 0.806 9.427 24382 Z= 0.448 Chirality : 0.049 0.332 2817 Planarity : 0.006 0.080 2998 Dihedral : 14.131 106.340 6775 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.32 % Allowed : 0.53 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.24 % 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: -1.01 (0.18), residues: 2121 helix: 1.13 (0.21), residues: 607 sheet: -1.43 (0.19), residues: 661 loop : -1.24 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRPL2 92 HIS 0.007 0.001 HIS A 119 PHE 0.036 0.002 PHE B 146 TYR 0.030 0.002 TYRH2 60 ARG 0.011 0.001 ARG L 107 Details of bonding type rmsd link_NAG-ASN : bond 0.01269 ( 7) link_NAG-ASN : angle 3.23520 ( 21) link_ALPHA1-6 : bond 0.00311 ( 2) link_ALPHA1-6 : angle 2.64596 ( 6) link_BETA1-4 : bond 0.00631 ( 10) link_BETA1-4 : angle 2.80902 ( 30) link_ALPHA1-2 : bond 0.00524 ( 3) link_ALPHA1-2 : angle 2.73845 ( 9) link_ALPHA1-3 : bond 0.00430 ( 2) link_ALPHA1-3 : angle 2.30828 ( 6) hydrogen bonds : bond 0.11576 ( 650) hydrogen bonds : angle 5.81920 ( 1842) SS BOND : bond 0.00371 ( 8) SS BOND : angle 1.83534 ( 16) covalent geometry : bond 0.00671 (17859) covalent geometry : angle 0.79040 (24294) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 316 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 310 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ILE cc_start: 0.9166 (tt) cc_final: 0.8868 (pt) REVERT: A 241 TRP cc_start: 0.6347 (m-10) cc_final: 0.5763 (m-10) REVERT: A 310 PRO cc_start: 0.7754 (Cg_endo) cc_final: 0.7519 (Cg_exo) REVERT: A 319 TRP cc_start: 0.6582 (t60) cc_final: 0.6290 (t60) REVERT: B 124 ASP cc_start: 0.7783 (t0) cc_final: 0.7553 (t0) REVERT: B 174 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: C 231 LEU cc_start: 0.8395 (mt) cc_final: 0.8081 (mt) REVERT: C 283 MET cc_start: 0.8250 (mmm) cc_final: 0.7925 (mmm) REVERT: C 286 MET cc_start: 0.7884 (tpp) cc_final: 0.7680 (tpt) REVERT: C 305 ILE cc_start: 0.8301 (tp) cc_final: 0.8001 (tp) REVERT: E 52 LEU cc_start: 0.8962 (tp) cc_final: 0.8759 (tp) REVERT: E 152 GLN cc_start: 0.6901 (mm-40) cc_final: 0.6589 (mm-40) REVERT: E 313 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6658 (tp30) REVERT: H 51 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7990 (ttp) REVERT: H 62 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7739 (tm-30) REVERT: H2 62 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7865 (tm-30) REVERT: H2 81 MET cc_start: 0.8477 (ptm) cc_final: 0.8080 (ptm) REVERT: L 84 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7809 (tm-30) outliers start: 6 outliers final: 4 residues processed: 314 average time/residue: 2.4368 time to fit residues: 877.1559 Evaluate side-chains 253 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 247 time to evaluate : 2.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 175 PRO Chi-restraints excluded: chain H residue 51 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 HIS B 229 GLN D 56 HIS E 135 ASN L2 16 GLN L2 80 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.118676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.087200 restraints weight = 76732.301| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.47 r_work: 0.2993 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17891 Z= 0.148 Angle : 0.594 9.197 24382 Z= 0.304 Chirality : 0.043 0.198 2817 Planarity : 0.005 0.062 2998 Dihedral : 8.593 75.940 2874 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.43 % Allowed : 8.70 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.18), residues: 2121 helix: 1.37 (0.21), residues: 611 sheet: -1.37 (0.20), residues: 643 loop : -1.15 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPL2 92 HIS 0.004 0.001 HIS B 56 PHE 0.019 0.001 PHE A 306 TYR 0.022 0.001 TYR A 299 ARG 0.010 0.001 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 7) link_NAG-ASN : angle 2.46358 ( 21) link_ALPHA1-6 : bond 0.00472 ( 2) link_ALPHA1-6 : angle 1.79866 ( 6) link_BETA1-4 : bond 0.00330 ( 10) link_BETA1-4 : angle 2.06408 ( 30) link_ALPHA1-2 : bond 0.00189 ( 3) link_ALPHA1-2 : angle 1.91429 ( 9) link_ALPHA1-3 : bond 0.00723 ( 2) link_ALPHA1-3 : angle 1.82577 ( 6) hydrogen bonds : bond 0.04005 ( 650) hydrogen bonds : angle 5.02742 ( 1842) SS BOND : bond 0.00236 ( 8) SS BOND : angle 1.32064 ( 16) covalent geometry : bond 0.00341 (17859) covalent geometry : angle 0.58219 (24294) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 298 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 271 time to evaluate : 2.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ILE cc_start: 0.9114 (tt) cc_final: 0.8796 (pt) REVERT: A 164 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8743 (mt) REVERT: A 241 TRP cc_start: 0.6361 (m-10) cc_final: 0.5816 (m-10) REVERT: A 310 PRO cc_start: 0.7527 (Cg_endo) cc_final: 0.7286 (Cg_exo) REVERT: B 21 ARG cc_start: 0.7690 (mmp80) cc_final: 0.7377 (mmp-170) REVERT: B 58 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8624 (mtt) REVERT: B 124 ASP cc_start: 0.8306 (t0) cc_final: 0.7996 (t0) REVERT: B 173 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8446 (mmt90) REVERT: B 174 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8100 (tt0) REVERT: C 283 MET cc_start: 0.8398 (mmm) cc_final: 0.7943 (mmm) REVERT: C 286 MET cc_start: 0.8060 (tpp) cc_final: 0.7827 (tpt) REVERT: C 297 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7482 (mp) REVERT: E 52 LEU cc_start: 0.9002 (tp) cc_final: 0.8751 (tp) REVERT: E 152 GLN cc_start: 0.7055 (mm-40) cc_final: 0.6622 (mm-40) REVERT: E 258 ASN cc_start: 0.7748 (t0) cc_final: 0.7349 (t0) REVERT: E 313 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6554 (tp30) REVERT: H 51 MET cc_start: 0.8666 (ppp) cc_final: 0.8437 (ttp) REVERT: H 62 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7810 (tm-30) REVERT: H 80 TYR cc_start: 0.6854 (OUTLIER) cc_final: 0.5773 (p90) REVERT: H2 33 ASP cc_start: 0.8248 (p0) cc_final: 0.7990 (p0) REVERT: H2 62 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8023 (tm-30) REVERT: H2 100 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8177 (mt-10) REVERT: L 84 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8170 (tm-30) outliers start: 27 outliers final: 12 residues processed: 284 average time/residue: 2.3544 time to fit residues: 768.0060 Evaluate side-chains 268 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 250 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H2 residue 23 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 69 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 106 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN B 56 HIS C 224 GLN D 56 HIS E 135 ASN L2 16 GLN L2 32 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.117775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.086389 restraints weight = 76892.956| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.48 r_work: 0.2981 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17891 Z= 0.153 Angle : 0.561 9.184 24382 Z= 0.286 Chirality : 0.042 0.167 2817 Planarity : 0.004 0.057 2998 Dihedral : 7.044 66.939 2863 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.49 % Allowed : 10.29 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.24 % 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: -0.62 (0.19), residues: 2121 helix: 1.57 (0.21), residues: 613 sheet: -1.33 (0.20), residues: 620 loop : -1.05 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 319 HIS 0.003 0.001 HIS B 56 PHE 0.017 0.001 PHE A 306 TYR 0.021 0.001 TYR A 299 ARG 0.006 0.000 ARG C 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 7) link_NAG-ASN : angle 2.41577 ( 21) link_ALPHA1-6 : bond 0.00284 ( 2) link_ALPHA1-6 : angle 2.00846 ( 6) link_BETA1-4 : bond 0.00275 ( 10) link_BETA1-4 : angle 1.86272 ( 30) link_ALPHA1-2 : bond 0.00210 ( 3) link_ALPHA1-2 : angle 2.06745 ( 9) link_ALPHA1-3 : bond 0.00585 ( 2) link_ALPHA1-3 : angle 1.85837 ( 6) hydrogen bonds : bond 0.03650 ( 650) hydrogen bonds : angle 4.79608 ( 1842) SS BOND : bond 0.00764 ( 8) SS BOND : angle 1.30637 ( 16) covalent geometry : bond 0.00352 (17859) covalent geometry : angle 0.54983 (24294) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 255 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8736 (mt) REVERT: A 241 TRP cc_start: 0.6395 (m-10) cc_final: 0.5869 (m-10) REVERT: A 310 PRO cc_start: 0.7559 (Cg_endo) cc_final: 0.7332 (Cg_exo) REVERT: B 21 ARG cc_start: 0.7638 (mmp80) cc_final: 0.7292 (mmp-170) REVERT: B 124 ASP cc_start: 0.8313 (t0) cc_final: 0.7966 (t0) REVERT: B 173 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8567 (mmt90) REVERT: C 224 GLN cc_start: 0.8439 (tp40) cc_final: 0.7799 (tm-30) REVERT: C 235 LEU cc_start: 0.8251 (tt) cc_final: 0.8047 (mt) REVERT: C 283 MET cc_start: 0.8371 (mmm) cc_final: 0.7872 (mmm) REVERT: C 286 MET cc_start: 0.7970 (tpp) cc_final: 0.7768 (tpt) REVERT: C 297 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7465 (mp) REVERT: E 52 LEU cc_start: 0.9004 (tp) cc_final: 0.8783 (tp) REVERT: E 258 ASN cc_start: 0.7743 (t0) cc_final: 0.7360 (t0) REVERT: E 313 GLU cc_start: 0.7156 (tm-30) cc_final: 0.6615 (tp30) REVERT: L2 86 ASP cc_start: 0.8287 (m-30) cc_final: 0.7841 (m-30) REVERT: H 51 MET cc_start: 0.8817 (ppp) cc_final: 0.8538 (ttp) REVERT: H 62 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7742 (tm-30) REVERT: H 80 TYR cc_start: 0.6853 (OUTLIER) cc_final: 0.5759 (p90) REVERT: H 90 ASP cc_start: 0.8028 (m-30) cc_final: 0.7784 (m-30) REVERT: H2 33 ASP cc_start: 0.8342 (p0) cc_final: 0.7992 (p0) REVERT: H2 62 GLN cc_start: 0.8491 (tm-30) cc_final: 0.7967 (tm-30) REVERT: H2 63 LYS cc_start: 0.8932 (ttmt) cc_final: 0.8708 (tmmt) REVERT: H2 89 GLU cc_start: 0.7703 (pm20) cc_final: 0.7493 (mp0) REVERT: H2 100 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8168 (mt-10) REVERT: L 84 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8182 (tm-30) outliers start: 28 outliers final: 13 residues processed: 268 average time/residue: 2.3788 time to fit residues: 727.5164 Evaluate side-chains 261 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 244 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 181 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 135 ASN L2 16 GLN L2 80 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.116384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.085142 restraints weight = 77201.841| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.46 r_work: 0.2958 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17891 Z= 0.200 Angle : 0.571 9.157 24382 Z= 0.291 Chirality : 0.043 0.192 2817 Planarity : 0.005 0.061 2998 Dihedral : 6.633 62.506 2863 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.54 % Allowed : 10.88 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.24 % 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: -0.62 (0.19), residues: 2121 helix: 1.61 (0.21), residues: 613 sheet: -1.38 (0.20), residues: 624 loop : -1.02 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 319 HIS 0.003 0.001 HIS A 267 PHE 0.015 0.001 PHE A 306 TYR 0.020 0.002 TYR A 299 ARG 0.008 0.000 ARG D 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00405 ( 7) link_NAG-ASN : angle 2.50526 ( 21) link_ALPHA1-6 : bond 0.00418 ( 2) link_ALPHA1-6 : angle 2.15502 ( 6) link_BETA1-4 : bond 0.00299 ( 10) link_BETA1-4 : angle 1.83161 ( 30) link_ALPHA1-2 : bond 0.00327 ( 3) link_ALPHA1-2 : angle 2.18238 ( 9) link_ALPHA1-3 : bond 0.00478 ( 2) link_ALPHA1-3 : angle 2.01917 ( 6) hydrogen bonds : bond 0.03596 ( 650) hydrogen bonds : angle 4.66790 ( 1842) SS BOND : bond 0.00277 ( 8) SS BOND : angle 1.42220 ( 16) covalent geometry : bond 0.00463 (17859) covalent geometry : angle 0.55938 (24294) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 252 time to evaluate : 3.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7673 (mtt) REVERT: A 164 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8732 (tt) REVERT: A 241 TRP cc_start: 0.6575 (m-10) cc_final: 0.6009 (m-10) REVERT: A 310 PRO cc_start: 0.7642 (Cg_endo) cc_final: 0.7431 (Cg_exo) REVERT: B 21 ARG cc_start: 0.7733 (mmp80) cc_final: 0.7380 (mmp-170) REVERT: B 58 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8617 (mtt) REVERT: B 124 ASP cc_start: 0.8329 (t0) cc_final: 0.7931 (t0) REVERT: B 199 ASP cc_start: 0.8036 (t0) cc_final: 0.7793 (t0) REVERT: C 40 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8703 (mtt) REVERT: C 283 MET cc_start: 0.8444 (mmm) cc_final: 0.7879 (mmm) REVERT: C 286 MET cc_start: 0.7997 (tpp) cc_final: 0.7784 (tpt) REVERT: C 297 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7544 (mp) REVERT: D 83 VAL cc_start: 0.9417 (OUTLIER) cc_final: 0.9186 (t) REVERT: E 258 ASN cc_start: 0.7822 (t0) cc_final: 0.7407 (t0) REVERT: E 313 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6580 (tp30) REVERT: L2 86 ASP cc_start: 0.8420 (m-30) cc_final: 0.7923 (m-30) REVERT: H 62 GLN cc_start: 0.7966 (tm-30) cc_final: 0.7692 (tm-30) REVERT: H 80 TYR cc_start: 0.6917 (OUTLIER) cc_final: 0.5828 (p90) REVERT: H 90 ASP cc_start: 0.7994 (m-30) cc_final: 0.7737 (m-30) REVERT: H2 10 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: H2 33 ASP cc_start: 0.8337 (p0) cc_final: 0.7953 (p0) REVERT: H2 62 GLN cc_start: 0.8505 (tm-30) cc_final: 0.7965 (tm-30) REVERT: H2 100 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8220 (mt-10) REVERT: L 84 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8186 (tm-30) outliers start: 29 outliers final: 10 residues processed: 264 average time/residue: 2.4123 time to fit residues: 730.1062 Evaluate side-chains 255 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 237 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H2 residue 10 GLU Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 135 ASN L2 16 GLN L2 80 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.116180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.085052 restraints weight = 76949.947| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.45 r_work: 0.2952 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17891 Z= 0.175 Angle : 0.555 9.395 24382 Z= 0.282 Chirality : 0.042 0.196 2817 Planarity : 0.004 0.063 2998 Dihedral : 6.238 60.071 2859 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.27 % Allowed : 11.78 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.24 % 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: -0.55 (0.19), residues: 2121 helix: 1.69 (0.21), residues: 614 sheet: -1.38 (0.20), residues: 624 loop : -0.97 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 319 HIS 0.003 0.001 HIS A 267 PHE 0.015 0.001 PHE A 306 TYR 0.020 0.001 TYR A 299 ARG 0.007 0.000 ARG D 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 7) link_NAG-ASN : angle 2.51915 ( 21) link_ALPHA1-6 : bond 0.00330 ( 2) link_ALPHA1-6 : angle 2.07147 ( 6) link_BETA1-4 : bond 0.00274 ( 10) link_BETA1-4 : angle 1.71968 ( 30) link_ALPHA1-2 : bond 0.00217 ( 3) link_ALPHA1-2 : angle 2.03033 ( 9) link_ALPHA1-3 : bond 0.00608 ( 2) link_ALPHA1-3 : angle 1.80580 ( 6) hydrogen bonds : bond 0.03476 ( 650) hydrogen bonds : angle 4.55774 ( 1842) SS BOND : bond 0.00292 ( 8) SS BOND : angle 1.31442 ( 16) covalent geometry : bond 0.00405 (17859) covalent geometry : angle 0.54353 (24294) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 270 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 246 time to evaluate : 2.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.9175 (mpt) cc_final: 0.8193 (mpt) REVERT: A 138 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7621 (mtt) REVERT: A 241 TRP cc_start: 0.6641 (m-10) cc_final: 0.6077 (m-10) REVERT: A 286 MET cc_start: 0.7475 (tpp) cc_final: 0.7253 (tpp) REVERT: A 310 PRO cc_start: 0.7618 (Cg_endo) cc_final: 0.7413 (Cg_exo) REVERT: B 21 ARG cc_start: 0.7748 (mmp80) cc_final: 0.7372 (mmp-170) REVERT: B 124 ASP cc_start: 0.8326 (t0) cc_final: 0.7915 (t0) REVERT: B 199 ASP cc_start: 0.7950 (t0) cc_final: 0.7683 (t0) REVERT: C 40 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8683 (mtt) REVERT: C 283 MET cc_start: 0.8403 (mmm) cc_final: 0.7805 (mmm) REVERT: C 286 MET cc_start: 0.7945 (tpp) cc_final: 0.7717 (tpt) REVERT: C 297 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7562 (mp) REVERT: D 83 VAL cc_start: 0.9403 (OUTLIER) cc_final: 0.9169 (t) REVERT: E 258 ASN cc_start: 0.7833 (t0) cc_final: 0.7409 (t0) REVERT: E 313 GLU cc_start: 0.7255 (tm-30) cc_final: 0.6521 (tp30) REVERT: L2 86 ASP cc_start: 0.8367 (m-30) cc_final: 0.7874 (m-30) REVERT: H 51 MET cc_start: 0.8870 (ttp) cc_final: 0.8669 (ttp) REVERT: H 62 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7663 (tm-30) REVERT: H 80 TYR cc_start: 0.6922 (OUTLIER) cc_final: 0.5867 (p90) REVERT: H 90 ASP cc_start: 0.8056 (m-30) cc_final: 0.7775 (m-30) REVERT: H2 33 ASP cc_start: 0.8305 (p0) cc_final: 0.7857 (p0) REVERT: H2 62 GLN cc_start: 0.8508 (tm-30) cc_final: 0.7923 (tm-30) REVERT: L 84 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8163 (tm-30) outliers start: 24 outliers final: 10 residues processed: 260 average time/residue: 2.3471 time to fit residues: 698.2341 Evaluate side-chains 253 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 238 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain L2 residue 57 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 35 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 153 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 GLN E 135 ASN L2 16 GLN L2 80 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.116483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.085463 restraints weight = 76825.931| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.45 r_work: 0.2967 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17891 Z= 0.151 Angle : 0.547 9.228 24382 Z= 0.278 Chirality : 0.042 0.200 2817 Planarity : 0.004 0.064 2998 Dihedral : 6.017 59.596 2859 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.33 % Allowed : 12.63 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.24 % 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: -0.46 (0.19), residues: 2121 helix: 1.80 (0.21), residues: 614 sheet: -1.35 (0.20), residues: 624 loop : -0.92 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 319 HIS 0.002 0.001 HIS A 267 PHE 0.013 0.001 PHE A 306 TYR 0.020 0.001 TYR A 244 ARG 0.008 0.000 ARGL2 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 7) link_NAG-ASN : angle 2.51512 ( 21) link_ALPHA1-6 : bond 0.00302 ( 2) link_ALPHA1-6 : angle 2.01885 ( 6) link_BETA1-4 : bond 0.00270 ( 10) link_BETA1-4 : angle 1.67154 ( 30) link_ALPHA1-2 : bond 0.00147 ( 3) link_ALPHA1-2 : angle 1.97812 ( 9) link_ALPHA1-3 : bond 0.00573 ( 2) link_ALPHA1-3 : angle 1.78435 ( 6) hydrogen bonds : bond 0.03303 ( 650) hydrogen bonds : angle 4.46977 ( 1842) SS BOND : bond 0.00261 ( 8) SS BOND : angle 1.21242 ( 16) covalent geometry : bond 0.00350 (17859) covalent geometry : angle 0.53619 (24294) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 3.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.9146 (mpt) cc_final: 0.8271 (mpt) REVERT: A 138 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7619 (mtt) REVERT: A 241 TRP cc_start: 0.6621 (m-10) cc_final: 0.6060 (m-10) REVERT: A 286 MET cc_start: 0.7509 (tpp) cc_final: 0.7214 (tpp) REVERT: A 310 PRO cc_start: 0.7609 (Cg_endo) cc_final: 0.7406 (Cg_exo) REVERT: B 21 ARG cc_start: 0.7794 (mmp80) cc_final: 0.7414 (mmp-170) REVERT: B 124 ASP cc_start: 0.8349 (t0) cc_final: 0.7929 (t0) REVERT: B 199 ASP cc_start: 0.7952 (t0) cc_final: 0.7720 (t0) REVERT: B 282 TYR cc_start: 0.7711 (p90) cc_final: 0.7414 (p90) REVERT: C 40 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8684 (mtt) REVERT: C 111 VAL cc_start: 0.8969 (m) cc_final: 0.8714 (p) REVERT: C 224 GLN cc_start: 0.8446 (tp40) cc_final: 0.7834 (tm-30) REVERT: C 283 MET cc_start: 0.8420 (mmm) cc_final: 0.7814 (mmm) REVERT: C 286 MET cc_start: 0.7983 (tpp) cc_final: 0.7727 (tpt) REVERT: C 297 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7599 (mp) REVERT: D 83 VAL cc_start: 0.9401 (OUTLIER) cc_final: 0.9166 (t) REVERT: E 258 ASN cc_start: 0.7829 (t0) cc_final: 0.7402 (t0) REVERT: E 297 ASP cc_start: 0.7016 (OUTLIER) cc_final: 0.6782 (t0) REVERT: E 313 GLU cc_start: 0.7308 (tm-30) cc_final: 0.6707 (tp30) REVERT: L2 86 ASP cc_start: 0.8419 (m-30) cc_final: 0.7931 (m-30) REVERT: H 62 GLN cc_start: 0.7920 (tm-30) cc_final: 0.7666 (tm-30) REVERT: H 80 TYR cc_start: 0.7086 (OUTLIER) cc_final: 0.6079 (p90) REVERT: H 90 ASP cc_start: 0.8105 (m-30) cc_final: 0.7851 (m-30) REVERT: H2 10 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: H2 33 ASP cc_start: 0.8317 (p0) cc_final: 0.7827 (p0) REVERT: H2 100 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8179 (mt-10) REVERT: L 84 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8163 (tm-30) outliers start: 25 outliers final: 9 residues processed: 252 average time/residue: 2.3579 time to fit residues: 680.0565 Evaluate side-chains 252 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain L2 residue 57 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H2 residue 10 GLU Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 183 optimal weight: 0.0770 chunk 90 optimal weight: 4.9990 chunk 206 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN C 309 GLN E 135 ASN L2 16 GLN L2 38 GLN L2 80 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.114469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.083571 restraints weight = 77657.027| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.39 r_work: 0.2933 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 17891 Z= 0.252 Angle : 0.595 9.440 24382 Z= 0.303 Chirality : 0.043 0.177 2817 Planarity : 0.005 0.073 2998 Dihedral : 6.358 61.543 2859 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.80 % Allowed : 13.00 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.24 % 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: -0.59 (0.19), residues: 2121 helix: 1.69 (0.21), residues: 615 sheet: -1.48 (0.19), residues: 644 loop : -0.94 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 319 HIS 0.004 0.001 HIS A 267 PHE 0.018 0.002 PHE H 112 TYR 0.019 0.002 TYR A 299 ARG 0.008 0.001 ARG A 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 7) link_NAG-ASN : angle 2.82485 ( 21) link_ALPHA1-6 : bond 0.00575 ( 2) link_ALPHA1-6 : angle 2.34575 ( 6) link_BETA1-4 : bond 0.00301 ( 10) link_BETA1-4 : angle 1.94452 ( 30) link_ALPHA1-2 : bond 0.00433 ( 3) link_ALPHA1-2 : angle 2.31568 ( 9) link_ALPHA1-3 : bond 0.00365 ( 2) link_ALPHA1-3 : angle 2.09285 ( 6) hydrogen bonds : bond 0.03568 ( 650) hydrogen bonds : angle 4.54897 ( 1842) SS BOND : bond 0.00343 ( 8) SS BOND : angle 1.54434 ( 16) covalent geometry : bond 0.00581 (17859) covalent geometry : angle 0.58147 (24294) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 244 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.9119 (mpt) cc_final: 0.8222 (mpt) REVERT: A 138 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7744 (mtt) REVERT: A 241 TRP cc_start: 0.6649 (m-10) cc_final: 0.6102 (m-10) REVERT: A 286 MET cc_start: 0.7510 (tpp) cc_final: 0.7194 (tpp) REVERT: B 21 ARG cc_start: 0.7732 (mmp80) cc_final: 0.7333 (mmp-170) REVERT: B 58 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8563 (mtt) REVERT: B 124 ASP cc_start: 0.8360 (t0) cc_final: 0.7944 (t0) REVERT: C 40 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8672 (mtt) REVERT: C 270 GLU cc_start: 0.7025 (mp0) cc_final: 0.6820 (mp0) REVERT: C 283 MET cc_start: 0.8379 (mmm) cc_final: 0.7756 (mmm) REVERT: C 297 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7627 (mp) REVERT: D 36 GLU cc_start: 0.8384 (mp0) cc_final: 0.8070 (mp0) REVERT: D 83 VAL cc_start: 0.9401 (OUTLIER) cc_final: 0.9165 (t) REVERT: D 112 MET cc_start: 0.9036 (tpp) cc_final: 0.8827 (tpp) REVERT: E 258 ASN cc_start: 0.7822 (t0) cc_final: 0.7368 (t0) REVERT: E 313 GLU cc_start: 0.7333 (tm-30) cc_final: 0.6705 (tp30) REVERT: L2 86 ASP cc_start: 0.8464 (m-30) cc_final: 0.7940 (m-30) REVERT: H 62 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7637 (tm-30) REVERT: H 80 TYR cc_start: 0.7147 (OUTLIER) cc_final: 0.5969 (p90) REVERT: H 90 ASP cc_start: 0.8041 (m-30) cc_final: 0.7737 (m-30) REVERT: H2 33 ASP cc_start: 0.8336 (p0) cc_final: 0.7848 (p0) REVERT: H2 80 TYR cc_start: 0.7474 (OUTLIER) cc_final: 0.5744 (p90) REVERT: H2 100 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8170 (mt-10) REVERT: L 84 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8246 (tm-30) outliers start: 34 outliers final: 15 residues processed: 260 average time/residue: 2.2504 time to fit residues: 673.4012 Evaluate side-chains 258 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 236 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain L2 residue 57 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H2 residue 80 TYR Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 113 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 150 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 189 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 GLN E 135 ASN E 152 GLN L2 16 GLN L2 80 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.116429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.085686 restraints weight = 76911.123| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.40 r_work: 0.2970 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17891 Z= 0.129 Angle : 0.544 9.839 24382 Z= 0.275 Chirality : 0.042 0.193 2817 Planarity : 0.005 0.066 2998 Dihedral : 5.933 56.864 2859 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.22 % Allowed : 13.74 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.24 % 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: -0.40 (0.19), residues: 2121 helix: 1.89 (0.21), residues: 615 sheet: -1.41 (0.19), residues: 642 loop : -0.83 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 319 HIS 0.002 0.000 HIS A 267 PHE 0.019 0.001 PHE D 304 TYR 0.021 0.001 TYR A 244 ARG 0.009 0.000 ARGL2 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 7) link_NAG-ASN : angle 2.46924 ( 21) link_ALPHA1-6 : bond 0.00300 ( 2) link_ALPHA1-6 : angle 1.88808 ( 6) link_BETA1-4 : bond 0.00296 ( 10) link_BETA1-4 : angle 1.59146 ( 30) link_ALPHA1-2 : bond 0.00178 ( 3) link_ALPHA1-2 : angle 1.85083 ( 9) link_ALPHA1-3 : bond 0.00843 ( 2) link_ALPHA1-3 : angle 1.60754 ( 6) hydrogen bonds : bond 0.03191 ( 650) hydrogen bonds : angle 4.40152 ( 1842) SS BOND : bond 0.00254 ( 8) SS BOND : angle 1.10956 ( 16) covalent geometry : bond 0.00299 (17859) covalent geometry : angle 0.53397 (24294) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 272 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 249 time to evaluate : 2.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.9073 (mpt) cc_final: 0.8199 (mpt) REVERT: A 138 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7863 (mtt) REVERT: A 185 GLN cc_start: 0.7982 (tt0) cc_final: 0.7753 (tt0) REVERT: A 241 TRP cc_start: 0.6644 (m-10) cc_final: 0.6098 (m-10) REVERT: A 286 MET cc_start: 0.7444 (tpp) cc_final: 0.7194 (tpp) REVERT: B 21 ARG cc_start: 0.7772 (mmp80) cc_final: 0.7404 (mmp-170) REVERT: B 124 ASP cc_start: 0.8320 (t0) cc_final: 0.7874 (t0) REVERT: C 40 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8692 (mtt) REVERT: C 111 VAL cc_start: 0.8937 (m) cc_final: 0.8688 (p) REVERT: C 283 MET cc_start: 0.8349 (mmm) cc_final: 0.8130 (mmm) REVERT: D 83 VAL cc_start: 0.9394 (OUTLIER) cc_final: 0.9154 (t) REVERT: D 229 GLN cc_start: 0.8972 (tp40) cc_final: 0.8752 (tp40) REVERT: E 258 ASN cc_start: 0.7803 (t0) cc_final: 0.7349 (t0) REVERT: E 297 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6787 (t0) REVERT: E 313 GLU cc_start: 0.7400 (tm-30) cc_final: 0.6748 (tp30) REVERT: L2 86 ASP cc_start: 0.8501 (m-30) cc_final: 0.7989 (m-30) REVERT: H 62 GLN cc_start: 0.7881 (tm-30) cc_final: 0.7589 (tm-30) REVERT: H 80 TYR cc_start: 0.7126 (OUTLIER) cc_final: 0.5964 (p90) REVERT: H 90 ASP cc_start: 0.8103 (m-30) cc_final: 0.7862 (m-30) REVERT: H2 33 ASP cc_start: 0.8267 (p0) cc_final: 0.7766 (p0) REVERT: H2 80 TYR cc_start: 0.7328 (OUTLIER) cc_final: 0.5693 (p90) REVERT: H2 100 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8145 (mt-10) REVERT: L 84 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8198 (tm-30) outliers start: 23 outliers final: 16 residues processed: 260 average time/residue: 2.1910 time to fit residues: 656.9633 Evaluate side-chains 259 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain L2 residue 57 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H2 residue 80 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 111 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 51 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 209 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 HIS B 116 ASN E 152 GLN L2 16 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.116295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.085306 restraints weight = 76995.556| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.44 r_work: 0.2969 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17891 Z= 0.130 Angle : 0.545 9.293 24382 Z= 0.274 Chirality : 0.041 0.193 2817 Planarity : 0.004 0.064 2998 Dihedral : 5.804 56.124 2859 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.17 % Allowed : 14.48 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.24 % 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: -0.33 (0.19), residues: 2121 helix: 1.95 (0.21), residues: 615 sheet: -1.38 (0.20), residues: 644 loop : -0.77 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 319 HIS 0.010 0.001 HIS B 56 PHE 0.018 0.001 PHE D 304 TYR 0.020 0.001 TYR A 299 ARG 0.009 0.000 ARGL2 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 7) link_NAG-ASN : angle 2.48684 ( 21) link_ALPHA1-6 : bond 0.00260 ( 2) link_ALPHA1-6 : angle 1.95461 ( 6) link_BETA1-4 : bond 0.00305 ( 10) link_BETA1-4 : angle 1.61886 ( 30) link_ALPHA1-2 : bond 0.00141 ( 3) link_ALPHA1-2 : angle 1.92115 ( 9) link_ALPHA1-3 : bond 0.00601 ( 2) link_ALPHA1-3 : angle 1.72667 ( 6) hydrogen bonds : bond 0.03127 ( 650) hydrogen bonds : angle 4.36504 ( 1842) SS BOND : bond 0.00236 ( 8) SS BOND : angle 1.09194 ( 16) covalent geometry : bond 0.00301 (17859) covalent geometry : angle 0.53454 (24294) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 264 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 242 time to evaluate : 2.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.9052 (mpt) cc_final: 0.8256 (mpt) REVERT: A 138 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7903 (mtt) REVERT: A 185 GLN cc_start: 0.7983 (tt0) cc_final: 0.7770 (tt0) REVERT: A 241 TRP cc_start: 0.6674 (m-10) cc_final: 0.6113 (m-10) REVERT: A 286 MET cc_start: 0.7468 (tpp) cc_final: 0.7225 (tpp) REVERT: B 21 ARG cc_start: 0.7800 (mmp80) cc_final: 0.7420 (mmp-170) REVERT: B 58 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8519 (mtt) REVERT: B 78 LYS cc_start: 0.9083 (ttmt) cc_final: 0.8697 (mmmm) REVERT: B 124 ASP cc_start: 0.8316 (t0) cc_final: 0.7878 (t0) REVERT: B 279 LYS cc_start: 0.8068 (mptt) cc_final: 0.7809 (mptt) REVERT: C 40 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8687 (mtt) REVERT: C 111 VAL cc_start: 0.8953 (m) cc_final: 0.8702 (p) REVERT: D 83 VAL cc_start: 0.9402 (OUTLIER) cc_final: 0.9163 (t) REVERT: D 229 GLN cc_start: 0.8962 (tp40) cc_final: 0.8732 (tp40) REVERT: E 258 ASN cc_start: 0.7828 (t0) cc_final: 0.7377 (t0) REVERT: E 297 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6854 (t0) REVERT: E 313 GLU cc_start: 0.7398 (tm-30) cc_final: 0.6721 (tp30) REVERT: L2 86 ASP cc_start: 0.8508 (m-30) cc_final: 0.8014 (m-30) REVERT: H 62 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7590 (tm-30) REVERT: H 80 TYR cc_start: 0.7162 (OUTLIER) cc_final: 0.6108 (p90) REVERT: H 90 ASP cc_start: 0.8110 (m-30) cc_final: 0.7871 (m-30) REVERT: H2 33 ASP cc_start: 0.8279 (p0) cc_final: 0.7761 (p0) REVERT: H2 80 TYR cc_start: 0.7389 (OUTLIER) cc_final: 0.5836 (p90) REVERT: H2 100 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8203 (mt-10) REVERT: L 84 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8198 (tm-30) outliers start: 22 outliers final: 14 residues processed: 251 average time/residue: 2.2065 time to fit residues: 636.2598 Evaluate side-chains 261 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 240 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain L2 residue 57 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H2 residue 80 TYR Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 HIS L2 16 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.115455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.084690 restraints weight = 77136.176| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.39 r_work: 0.2952 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17891 Z= 0.180 Angle : 0.568 10.402 24382 Z= 0.287 Chirality : 0.042 0.210 2817 Planarity : 0.005 0.064 2998 Dihedral : 5.900 55.408 2859 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.27 % Allowed : 14.80 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.24 % 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: -0.37 (0.19), residues: 2121 helix: 1.92 (0.21), residues: 615 sheet: -1.38 (0.20), residues: 644 loop : -0.82 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 319 HIS 0.006 0.001 HIS B 56 PHE 0.019 0.001 PHE D 304 TYR 0.024 0.002 TYR A 244 ARG 0.009 0.000 ARGL2 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 7) link_NAG-ASN : angle 2.60863 ( 21) link_ALPHA1-6 : bond 0.00436 ( 2) link_ALPHA1-6 : angle 2.15862 ( 6) link_BETA1-4 : bond 0.00300 ( 10) link_BETA1-4 : angle 1.72788 ( 30) link_ALPHA1-2 : bond 0.00233 ( 3) link_ALPHA1-2 : angle 2.07894 ( 9) link_ALPHA1-3 : bond 0.00538 ( 2) link_ALPHA1-3 : angle 1.82996 ( 6) hydrogen bonds : bond 0.03232 ( 650) hydrogen bonds : angle 4.37803 ( 1842) SS BOND : bond 0.00278 ( 8) SS BOND : angle 1.24845 ( 16) covalent geometry : bond 0.00418 (17859) covalent geometry : angle 0.55627 (24294) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 265 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 241 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.9075 (mpt) cc_final: 0.8271 (mpt) REVERT: A 138 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7891 (mtt) REVERT: A 241 TRP cc_start: 0.6658 (m-10) cc_final: 0.6071 (m-10) REVERT: A 286 MET cc_start: 0.7480 (tpp) cc_final: 0.7241 (tpp) REVERT: B 21 ARG cc_start: 0.7765 (mmp80) cc_final: 0.7362 (mmp-170) REVERT: B 58 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8507 (mtt) REVERT: B 124 ASP cc_start: 0.8310 (t0) cc_final: 0.7856 (t0) REVERT: B 279 LYS cc_start: 0.8137 (mptt) cc_final: 0.7916 (mptt) REVERT: C 40 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8694 (mtt) REVERT: D 36 GLU cc_start: 0.8369 (mp0) cc_final: 0.8087 (mp0) REVERT: D 83 VAL cc_start: 0.9401 (OUTLIER) cc_final: 0.9163 (t) REVERT: D 229 GLN cc_start: 0.9015 (tp40) cc_final: 0.8751 (tp40) REVERT: E 258 ASN cc_start: 0.7806 (t0) cc_final: 0.7345 (t0) REVERT: E 297 ASP cc_start: 0.7172 (OUTLIER) cc_final: 0.6862 (t0) REVERT: E 313 GLU cc_start: 0.7378 (tm-30) cc_final: 0.6739 (tp30) REVERT: L2 86 ASP cc_start: 0.8479 (m-30) cc_final: 0.7957 (m-30) REVERT: H 62 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7612 (tm-30) REVERT: H 80 TYR cc_start: 0.7137 (OUTLIER) cc_final: 0.5983 (p90) REVERT: H 90 ASP cc_start: 0.7971 (m-30) cc_final: 0.7697 (m-30) REVERT: H2 33 ASP cc_start: 0.8251 (p0) cc_final: 0.7726 (p0) REVERT: H2 80 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.5958 (p90) REVERT: H2 100 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8190 (mt-10) REVERT: L 84 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8250 (tm-30) outliers start: 24 outliers final: 16 residues processed: 252 average time/residue: 2.2676 time to fit residues: 658.6464 Evaluate side-chains 259 residues out of total 1885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 236 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 58 MET Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain L2 residue 57 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H2 residue 80 TYR Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 209 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 142 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 205 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 180 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L2 16 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.116214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.085399 restraints weight = 77118.247| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.43 r_work: 0.2963 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17891 Z= 0.133 Angle : 0.549 11.912 24382 Z= 0.276 Chirality : 0.042 0.201 2817 Planarity : 0.004 0.065 2998 Dihedral : 5.712 54.667 2859 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.11 % Allowed : 15.12 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.62 % Cis-general : 0.24 % 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: -0.28 (0.19), residues: 2121 helix: 2.01 (0.21), residues: 615 sheet: -1.34 (0.20), residues: 644 loop : -0.77 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 319 HIS 0.002 0.000 HIS B 56 PHE 0.021 0.001 PHE D 304 TYR 0.020 0.001 TYR A 299 ARG 0.008 0.000 ARGL2 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 7) link_NAG-ASN : angle 2.43385 ( 21) link_ALPHA1-6 : bond 0.00270 ( 2) link_ALPHA1-6 : angle 1.95728 ( 6) link_BETA1-4 : bond 0.00283 ( 10) link_BETA1-4 : angle 1.59192 ( 30) link_ALPHA1-2 : bond 0.00151 ( 3) link_ALPHA1-2 : angle 1.89104 ( 9) link_ALPHA1-3 : bond 0.00776 ( 2) link_ALPHA1-3 : angle 1.66553 ( 6) hydrogen bonds : bond 0.03091 ( 650) hydrogen bonds : angle 4.30967 ( 1842) SS BOND : bond 0.00254 ( 8) SS BOND : angle 1.08872 ( 16) covalent geometry : bond 0.00310 (17859) covalent geometry : angle 0.53855 (24294) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23761.45 seconds wall clock time: 401 minutes 32.16 seconds (24092.16 seconds total)