Starting phenix.real_space_refine on Fri Mar 22 20:26:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0w_25583/03_2024/7t0w_25583_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0w_25583/03_2024/7t0w_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0w_25583/03_2024/7t0w_25583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0w_25583/03_2024/7t0w_25583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0w_25583/03_2024/7t0w_25583_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0w_25583/03_2024/7t0w_25583_trim.pdb" } 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 Residue "C TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 15.54, per 1000 atoms: 0.45 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 - 3.50 Amino acid : False - 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 G 1 " - " ASN C 80 " " NAG I 1 " - " ASN C 149 " " NAG J 1 " - " ASN D 111 " " NAG K 1 " - " ASN E 208 " " NAG N 1 " - " ASN B 111 " Time building additional restraints: 29.20 Conformation dependent library (CDL) restraints added in 4.1 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: 2.54 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: 12.71 Time building geometry restraints manager: 30.15 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: 97.75 - 105.06: 351 105.06 - 112.37: 39160 112.37 - 119.69: 9440 119.69 - 127.00: 13393 127.00 - 134.31: 227 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: 2402 0.066 - 0.133: 373 0.133 - 0.199: 34 0.199 - 0.266: 5 0.266 - 0.332: 1 Chirality restraints: 2815 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 2812 not shown) Planarity restraints: 5044 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 5041 not shown) Histogram of nonbonded interaction distances: 0.59 - 1.39: 2 1.39 - 2.19: 2382 2.19 - 3.00: 98022 3.00 - 3.80: 146777 3.80 - 4.60: 248897 Warning: very small nonbonded interaction distances. Nonbonded interactions: 496080 Sorted by model distance: nonbonded pdb="HD22 ASN A 149 " pdb=" C1 NAG M 1 " model vdw 0.589 2.750 nonbonded pdb="HD22 ASN A 80 " pdb=" C1 NAG F 1 " model vdw 0.599 2.750 nonbonded pdb=" ND2 ASN A 149 " pdb=" C1 NAG M 1 " model vdw 1.447 3.250 nonbonded pdb=" ND2 ASN A 80 " pdb=" C1 NAG F 1 " model vdw 1.455 3.250 nonbonded pdb=" OH TYRH2 60 " pdb=" H METH2 70 " model vdw 1.494 1.850 ... (remaining 496075 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 2.090 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: 0.500 Extract box with map and model: 7.550 Check model and map are aligned: 0.560 Set scattering table: 0.310 Process input model: 109.820 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.250 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:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.020 ------------------------------------------------------------------------------- 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 17859 Z= 0.439 Angle : 0.790 9.427 24294 Z= 0.446 Chirality : 0.049 0.332 2815 Planarity : 0.006 0.080 2998 Dihedral : 14.131 106.340 6775 Min Nonbonded Distance : 1.447 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 *********************** 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 fitting. rotamer outliers: 6 poor density : 310 time to evaluate : 2.714 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: 2.3772 time to fit residues: 851.0929 Evaluate side-chains 253 residues out of total 1885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 247 time to evaluate : 3.148 ------------------------------------------------------------------------------- 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: 0.7980 chunk 159 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 L 80 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17859 Z= 0.207 Angle : 0.575 9.336 24294 Z= 0.292 Chirality : 0.043 0.194 2815 Planarity : 0.005 0.066 2998 Dihedral : 8.717 76.935 2874 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.54 % Allowed : 8.17 % Favored : 90.29 % 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: -0.67 (0.19), residues: 2121 helix: 1.46 (0.21), residues: 611 sheet: -1.21 (0.20), residues: 637 loop : -1.12 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPL2 92 HIS 0.004 0.001 HIS B 56 PHE 0.019 0.001 PHE A 306 TYR 0.020 0.001 TYR A 299 ARG 0.010 0.001 ARG H 87 *********************** 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 291 residues out of total 1885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 262 time to evaluate : 3.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ILE cc_start: 0.9158 (tt) cc_final: 0.8856 (pt) REVERT: A 241 TRP cc_start: 0.6445 (m-10) cc_final: 0.5930 (m-10) REVERT: A 310 PRO cc_start: 0.7815 (Cg_endo) cc_final: 0.7591 (Cg_exo) REVERT: A 323 PHE cc_start: 0.7042 (m-80) cc_final: 0.6838 (m-80) REVERT: B 124 ASP cc_start: 0.7829 (t0) cc_final: 0.7592 (t0) REVERT: B 174 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7604 (tt0) REVERT: C 283 MET cc_start: 0.8219 (mmm) cc_final: 0.7850 (mmm) REVERT: C 286 MET cc_start: 0.7782 (tpp) cc_final: 0.7546 (tpt) REVERT: C 297 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7591 (mp) REVERT: C 305 ILE cc_start: 0.8324 (tp) cc_final: 0.8009 (tp) REVERT: D 83 VAL cc_start: 0.9359 (OUTLIER) cc_final: 0.9103 (t) REVERT: D 304 PHE cc_start: 0.7908 (t80) cc_final: 0.7643 (t80) REVERT: E 52 LEU cc_start: 0.8954 (tp) cc_final: 0.8724 (tp) REVERT: E 152 GLN cc_start: 0.7008 (mm-40) cc_final: 0.6649 (mm-40) REVERT: E 313 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6645 (tp30) REVERT: H 51 MET cc_start: 0.8288 (ppp) cc_final: 0.7982 (ttp) REVERT: H 80 TYR cc_start: 0.6814 (OUTLIER) cc_final: 0.5654 (p90) REVERT: H2 62 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7777 (tm-30) REVERT: H2 100 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7532 (mt-10) REVERT: L 84 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7861 (tm-30) outliers start: 29 outliers final: 12 residues processed: 275 average time/residue: 2.2623 time to fit residues: 713.6806 Evaluate side-chains 264 residues out of total 1885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 248 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 55 ASP 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 D residue 43 THR Chi-restraints excluded: chain D residue 83 VAL 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 106 optimal weight: 2.9990 chunk 59 optimal weight: 0.0470 chunk 159 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 HIS C 224 GLN D 56 HIS E 135 ASN L2 16 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17859 Z= 0.277 Angle : 0.557 9.251 24294 Z= 0.285 Chirality : 0.042 0.160 2815 Planarity : 0.004 0.056 2998 Dihedral : 6.933 67.036 2861 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.75 % Allowed : 9.50 % Favored : 88.75 % 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: -0.53 (0.19), residues: 2121 helix: 1.60 (0.21), residues: 613 sheet: -1.17 (0.20), residues: 654 loop : -1.02 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 36 HIS 0.004 0.001 HIS B 56 PHE 0.018 0.001 PHE A 306 TYR 0.020 0.001 TYR A 299 ARG 0.008 0.000 ARG C 269 *********************** 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 fitting. rotamer outliers: 33 poor density : 250 time to evaluate : 3.009 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: 0.9171 (tt) cc_final: 0.8869 (pt) REVERT: A 241 TRP cc_start: 0.6489 (m-10) cc_final: 0.5978 (m-10) REVERT: A 310 PRO cc_start: 0.7824 (Cg_endo) cc_final: 0.7616 (Cg_exo) REVERT: B 124 ASP cc_start: 0.7842 (t0) cc_final: 0.7624 (t0) REVERT: C 224 GLN cc_start: 0.8206 (tp40) cc_final: 0.7501 (tm-30) REVERT: C 283 MET cc_start: 0.8249 (mmm) cc_final: 0.7731 (mmm) REVERT: C 297 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7592 (mp) REVERT: D 83 VAL cc_start: 0.9354 (OUTLIER) cc_final: 0.9099 (t) REVERT: E 313 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6721 (tp30) REVERT: L2 86 ASP cc_start: 0.8085 (m-30) cc_final: 0.7593 (m-30) REVERT: H 51 MET cc_start: 0.8445 (ppp) cc_final: 0.8067 (ttp) REVERT: H 80 TYR cc_start: 0.6745 (OUTLIER) cc_final: 0.5548 (p90) REVERT: H2 62 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7750 (tm-30) REVERT: H2 100 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7496 (mt-10) REVERT: L 84 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7828 (tm-30) outliers start: 33 outliers final: 14 residues processed: 266 average time/residue: 2.2223 time to fit residues: 679.3838 Evaluate side-chains 256 residues out of total 1885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 239 time to evaluate : 2.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 79 LEU 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 D residue 83 VAL 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 H2 residue 57 ASN Chi-restraints excluded: chain H2 residue 110 ASP 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 189 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 203 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 54 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 56 HIS 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17859 Z= 0.175 Angle : 0.514 9.309 24294 Z= 0.261 Chirality : 0.041 0.189 2815 Planarity : 0.004 0.061 2998 Dihedral : 6.130 59.168 2859 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.38 % Allowed : 10.72 % Favored : 87.90 % 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: -0.31 (0.19), residues: 2121 helix: 1.82 (0.21), residues: 613 sheet: -1.05 (0.20), residues: 634 loop : -0.93 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 319 HIS 0.002 0.000 HIS A 267 PHE 0.013 0.001 PHE A 306 TYR 0.019 0.001 TYR A 299 ARG 0.008 0.000 ARGL2 17 *********************** 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 271 residues out of total 1885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 245 time to evaluate : 2.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ILE cc_start: 0.9163 (tt) cc_final: 0.8862 (pt) REVERT: A 241 TRP cc_start: 0.6597 (m-10) cc_final: 0.6080 (m-10) REVERT: A 286 MET cc_start: 0.7375 (tpp) cc_final: 0.7079 (tpp) REVERT: A 307 PHE cc_start: 0.6594 (OUTLIER) cc_final: 0.6365 (p90) REVERT: A 310 PRO cc_start: 0.7774 (Cg_endo) cc_final: 0.7573 (Cg_exo) REVERT: B 124 ASP cc_start: 0.7837 (t0) cc_final: 0.7597 (t0) REVERT: B 282 TYR cc_start: 0.7356 (p90) cc_final: 0.6927 (p90) REVERT: C 40 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8198 (mtt) REVERT: C 283 MET cc_start: 0.8257 (mmm) cc_final: 0.7728 (mmm) REVERT: C 297 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7578 (mp) REVERT: D 83 VAL cc_start: 0.9340 (OUTLIER) cc_final: 0.9079 (t) REVERT: E 313 GLU cc_start: 0.7377 (tm-30) cc_final: 0.6840 (tp30) REVERT: L2 86 ASP cc_start: 0.8174 (m-30) cc_final: 0.7688 (m-30) REVERT: H 51 MET cc_start: 0.8450 (ppp) cc_final: 0.8089 (ttp) REVERT: H 80 TYR cc_start: 0.6704 (OUTLIER) cc_final: 0.5629 (p90) REVERT: H2 10 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: H2 38 ARG cc_start: 0.8477 (ttm170) cc_final: 0.8250 (ttm170) REVERT: H2 62 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7734 (tm-30) REVERT: H2 100 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7465 (mt-10) REVERT: L 84 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7822 (tm-30) outliers start: 26 outliers final: 13 residues processed: 257 average time/residue: 2.2743 time to fit residues: 667.6350 Evaluate side-chains 255 residues out of total 1885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 236 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 172 ASP 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 D residue 304 PHE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 337 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 10 GLU Chi-restraints excluded: chain H2 residue 57 ASN Chi-restraints excluded: chain H2 residue 110 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 169 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 174 optimal weight: 0.0470 chunk 140 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 56 HIS E 135 ASN L2 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17859 Z= 0.249 Angle : 0.528 9.023 24294 Z= 0.268 Chirality : 0.041 0.202 2815 Planarity : 0.004 0.061 2998 Dihedral : 6.037 59.323 2859 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.38 % Allowed : 11.83 % Favored : 86.79 % 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: -0.30 (0.19), residues: 2121 helix: 1.87 (0.21), residues: 613 sheet: -1.16 (0.20), residues: 670 loop : -0.81 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 319 HIS 0.002 0.001 HIS A 267 PHE 0.015 0.001 PHE A 306 TYR 0.018 0.001 TYR A 299 ARG 0.006 0.000 ARGL2 17 *********************** 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 265 residues out of total 1885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 239 time to evaluate : 2.903 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 25 ILE cc_start: 0.9170 (tt) cc_final: 0.8871 (pt) REVERT: A 138 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7286 (mtt) REVERT: A 241 TRP cc_start: 0.6697 (m-10) cc_final: 0.6146 (m-10) REVERT: A 286 MET cc_start: 0.7388 (tpp) cc_final: 0.7123 (tpp) REVERT: B 58 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8234 (mtt) REVERT: B 124 ASP cc_start: 0.7846 (t0) cc_final: 0.7579 (t0) REVERT: B 282 TYR cc_start: 0.7475 (p90) cc_final: 0.7039 (p90) REVERT: C 40 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8169 (mtt) REVERT: C 283 MET cc_start: 0.8287 (mmm) cc_final: 0.7734 (mmm) REVERT: C 297 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7646 (mp) REVERT: D 83 VAL cc_start: 0.9347 (OUTLIER) cc_final: 0.9087 (t) REVERT: E 313 GLU cc_start: 0.7363 (tm-30) cc_final: 0.6769 (tp30) REVERT: L2 86 ASP cc_start: 0.8204 (m-30) cc_final: 0.7697 (m-30) REVERT: H 51 MET cc_start: 0.8436 (ppp) cc_final: 0.8157 (ttp) REVERT: H 80 TYR cc_start: 0.6756 (OUTLIER) cc_final: 0.5561 (p90) REVERT: H2 62 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7709 (tm-30) REVERT: H2 100 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7536 (mt-10) REVERT: L 84 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7810 (tm-30) outliers start: 26 outliers final: 9 residues processed: 251 average time/residue: 2.3192 time to fit residues: 668.3040 Evaluate side-chains 248 residues out of total 1885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 233 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET 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 E residue 126 THR 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 H residue 110 ASP Chi-restraints excluded: chain H2 residue 110 ASP 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 68 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 204 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 267 HIS D 56 HIS E 135 ASN L2 16 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17859 Z= 0.269 Angle : 0.535 9.378 24294 Z= 0.272 Chirality : 0.042 0.208 2815 Planarity : 0.004 0.062 2998 Dihedral : 6.020 58.999 2859 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.75 % Allowed : 12.20 % 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: -0.23 (0.19), residues: 2121 helix: 1.90 (0.21), residues: 613 sheet: -1.15 (0.20), residues: 658 loop : -0.73 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 319 HIS 0.003 0.001 HIS D 218 PHE 0.015 0.001 PHEH2 64 TYR 0.025 0.001 TYR A 244 ARG 0.008 0.000 ARGL2 17 *********************** 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 273 residues out of total 1885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 240 time to evaluate : 3.314 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 25 ILE cc_start: 0.9186 (tt) cc_final: 0.8875 (pt) REVERT: A 138 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7269 (mtt) REVERT: A 241 TRP cc_start: 0.6676 (m-10) cc_final: 0.6141 (m-10) REVERT: A 286 MET cc_start: 0.7388 (tpp) cc_final: 0.6987 (tpp) REVERT: B 58 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8243 (mtt) REVERT: B 124 ASP cc_start: 0.7848 (t0) cc_final: 0.7570 (t0) REVERT: B 282 TYR cc_start: 0.7602 (p90) cc_final: 0.7160 (p90) REVERT: C 40 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8142 (mtt) REVERT: C 283 MET cc_start: 0.8250 (mmm) cc_final: 0.7671 (mmm) REVERT: C 297 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7654 (mp) REVERT: D 63 ASP cc_start: 0.7437 (t0) cc_final: 0.7151 (t0) REVERT: D 83 VAL cc_start: 0.9349 (OUTLIER) cc_final: 0.9084 (t) REVERT: E 296 MET cc_start: 0.7115 (tpp) cc_final: 0.6879 (tpp) REVERT: E 297 ASP cc_start: 0.6899 (OUTLIER) cc_final: 0.6636 (t0) REVERT: E 313 GLU cc_start: 0.7356 (tm-30) cc_final: 0.6736 (tp30) REVERT: L2 86 ASP cc_start: 0.8223 (m-30) cc_final: 0.7710 (m-30) REVERT: H 80 TYR cc_start: 0.6824 (OUTLIER) cc_final: 0.5650 (p90) REVERT: H2 10 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: H2 62 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7834 (tm-30) REVERT: L 84 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7856 (tm-30) outliers start: 33 outliers final: 13 residues processed: 257 average time/residue: 2.3035 time to fit residues: 677.8008 Evaluate side-chains 251 residues out of total 1885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 230 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET 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 46 SER 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 131 MET Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 126 THR 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 H residue 110 ASP Chi-restraints excluded: chain H2 residue 10 GLU Chi-restraints excluded: chain H2 residue 110 ASP 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 196 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN C 224 GLN E 135 ASN L2 16 GLN L 80 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17859 Z= 0.319 Angle : 0.556 9.529 24294 Z= 0.283 Chirality : 0.042 0.205 2815 Planarity : 0.005 0.074 2998 Dihedral : 6.185 59.522 2859 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.59 % Allowed : 13.00 % Favored : 85.41 % 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: -0.34 (0.19), residues: 2121 helix: 1.70 (0.21), residues: 629 sheet: -1.13 (0.20), residues: 658 loop : -0.83 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 319 HIS 0.003 0.001 HIS D 218 PHE 0.015 0.001 PHE H 112 TYR 0.018 0.002 TYR A 299 ARG 0.009 0.001 ARGL2 17 *********************** 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 266 residues out of total 1885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 236 time to evaluate : 2.867 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 25 ILE cc_start: 0.9201 (tt) cc_final: 0.8865 (pt) REVERT: A 138 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7199 (mtt) REVERT: A 241 TRP cc_start: 0.6733 (m-10) cc_final: 0.6188 (m-10) REVERT: A 286 MET cc_start: 0.7402 (tpp) cc_final: 0.7033 (tpp) REVERT: B 58 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8261 (mtt) REVERT: B 124 ASP cc_start: 0.7877 (t0) cc_final: 0.7565 (t0) REVERT: B 282 TYR cc_start: 0.7687 (p90) cc_final: 0.7262 (p90) REVERT: C 40 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8121 (mtt) REVERT: C 224 GLN cc_start: 0.8179 (tp40) cc_final: 0.7974 (tp40) REVERT: C 283 MET cc_start: 0.8273 (mmm) cc_final: 0.7685 (mmm) REVERT: C 297 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7692 (mp) REVERT: D 63 ASP cc_start: 0.7443 (t0) cc_final: 0.7174 (t0) REVERT: D 83 VAL cc_start: 0.9354 (OUTLIER) cc_final: 0.9088 (t) REVERT: E 296 MET cc_start: 0.7182 (tpp) cc_final: 0.6954 (tpp) REVERT: E 313 GLU cc_start: 0.7369 (tm-30) cc_final: 0.6709 (tp30) REVERT: L2 86 ASP cc_start: 0.8208 (m-30) cc_final: 0.7681 (m-30) REVERT: H 51 MET cc_start: 0.8521 (ptm) cc_final: 0.8241 (ttp) REVERT: H 80 TYR cc_start: 0.6910 (OUTLIER) cc_final: 0.5769 (p90) REVERT: H2 80 TYR cc_start: 0.7634 (OUTLIER) cc_final: 0.5861 (p90) REVERT: L 84 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7885 (tm-30) outliers start: 30 outliers final: 13 residues processed: 253 average time/residue: 2.1638 time to fit residues: 631.4741 Evaluate side-chains 254 residues out of total 1885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 234 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET 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 46 SER 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 131 MET Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain E residue 126 THR 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 H residue 110 ASP Chi-restraints excluded: chain H2 residue 80 TYR Chi-restraints excluded: chain H2 residue 110 ASP 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 125 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 309 GLN E 135 ASN L2 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 17859 Z= 0.475 Angle : 0.619 10.272 24294 Z= 0.318 Chirality : 0.045 0.219 2815 Planarity : 0.005 0.064 2998 Dihedral : 6.704 65.120 2859 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.75 % Allowed : 13.63 % Favored : 84.62 % 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 (0.18), residues: 2121 helix: 1.46 (0.21), residues: 629 sheet: -1.24 (0.20), residues: 658 loop : -0.99 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 319 HIS 0.005 0.001 HIS B 110 PHE 0.020 0.002 PHE D 304 TYR 0.024 0.002 TYR A 244 ARG 0.007 0.001 ARGL2 17 *********************** 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 269 residues out of total 1885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 236 time to evaluate : 3.079 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: 0.9225 (tt) cc_final: 0.8889 (pt) REVERT: A 40 MET cc_start: 0.8640 (mmt) cc_final: 0.8013 (mpt) REVERT: A 238 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7946 (t) REVERT: A 241 TRP cc_start: 0.6739 (m-10) cc_final: 0.6199 (m-10) REVERT: A 286 MET cc_start: 0.7441 (tpp) cc_final: 0.7149 (tpp) REVERT: B 58 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8279 (mtt) REVERT: B 124 ASP cc_start: 0.7866 (t0) cc_final: 0.7514 (t0) REVERT: B 282 TYR cc_start: 0.7799 (p90) cc_final: 0.7223 (p90) REVERT: C 40 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8092 (mtt) REVERT: C 283 MET cc_start: 0.8200 (mmm) cc_final: 0.7590 (mmm) REVERT: C 297 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7799 (mp) REVERT: D 63 ASP cc_start: 0.7467 (t0) cc_final: 0.7200 (t0) REVERT: D 83 VAL cc_start: 0.9360 (OUTLIER) cc_final: 0.9092 (t) REVERT: E 235 TYR cc_start: 0.6768 (t80) cc_final: 0.6487 (t80) REVERT: E 296 MET cc_start: 0.7339 (tpp) cc_final: 0.7015 (tpp) REVERT: E 297 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6744 (t0) REVERT: E 313 GLU cc_start: 0.7446 (tm-30) cc_final: 0.6784 (tp30) REVERT: L2 86 ASP cc_start: 0.8278 (m-30) cc_final: 0.7728 (m-30) REVERT: H 51 MET cc_start: 0.8519 (ptm) cc_final: 0.8234 (ttp) REVERT: H 80 TYR cc_start: 0.7004 (OUTLIER) cc_final: 0.5758 (p90) REVERT: H2 10 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: H2 80 TYR cc_start: 0.7640 (OUTLIER) cc_final: 0.6077 (p90) REVERT: L 84 GLU cc_start: 0.8334 (tm-30) cc_final: 0.8037 (tm-30) outliers start: 33 outliers final: 19 residues processed: 257 average time/residue: 2.2694 time to fit residues: 671.5313 Evaluate side-chains 255 residues out of total 1885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 227 time to evaluate : 2.887 ------------------------------------------------------------------------------- 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 A residue 238 VAL 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 41 ASN Chi-restraints excluded: chain C residue 46 SER 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 131 MET Chi-restraints excluded: chain E residue 126 THR 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 H residue 110 ASP Chi-restraints excluded: chain H2 residue 10 GLU Chi-restraints excluded: chain H2 residue 80 TYR Chi-restraints excluded: chain H2 residue 110 ASP 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 194 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 189 optimal weight: 0.8980 chunk 114 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 188 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 224 GLN C 309 GLN E 135 ASN E 152 GLN L2 16 GLN L2 80 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17859 Z= 0.194 Angle : 0.538 10.402 24294 Z= 0.272 Chirality : 0.041 0.186 2815 Planarity : 0.004 0.066 2998 Dihedral : 6.272 59.694 2859 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.11 % Allowed : 14.75 % Favored : 84.14 % 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: 1.73 (0.21), residues: 629 sheet: -1.15 (0.20), residues: 662 loop : -0.83 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 319 HIS 0.002 0.000 HIS D 218 PHE 0.013 0.001 PHE D 304 TYR 0.020 0.001 TYR C 299 ARG 0.009 0.000 ARGL2 17 *********************** 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 260 residues out of total 1885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 239 time to evaluate : 2.600 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 25 ILE cc_start: 0.9188 (tt) cc_final: 0.8865 (pt) REVERT: A 40 MET cc_start: 0.8602 (mmt) cc_final: 0.7906 (mpt) REVERT: A 138 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7204 (mtt) REVERT: A 241 TRP cc_start: 0.6725 (m-10) cc_final: 0.6188 (m-10) REVERT: A 286 MET cc_start: 0.7383 (tpp) cc_final: 0.7102 (tpp) REVERT: B 124 ASP cc_start: 0.7821 (t0) cc_final: 0.7502 (t0) REVERT: B 282 TYR cc_start: 0.7766 (p90) cc_final: 0.7133 (p90) REVERT: C 40 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8108 (mtt) REVERT: C 283 MET cc_start: 0.8180 (mmm) cc_final: 0.7972 (mmm) REVERT: D 63 ASP cc_start: 0.7493 (t0) cc_final: 0.7147 (t0) REVERT: D 83 VAL cc_start: 0.9337 (OUTLIER) cc_final: 0.9062 (t) REVERT: E 235 TYR cc_start: 0.6656 (t80) cc_final: 0.6367 (t80) REVERT: E 296 MET cc_start: 0.7290 (tpp) cc_final: 0.6957 (tpp) REVERT: E 297 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6761 (t0) REVERT: E 313 GLU cc_start: 0.7471 (tm-30) cc_final: 0.6773 (tp30) REVERT: L2 86 ASP cc_start: 0.8311 (m-30) cc_final: 0.7780 (m-30) REVERT: H 51 MET cc_start: 0.8479 (ptm) cc_final: 0.8184 (ttp) REVERT: H 80 TYR cc_start: 0.7034 (OUTLIER) cc_final: 0.5813 (p90) REVERT: H2 80 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.5883 (p90) REVERT: H2 100 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7660 (mt-10) REVERT: L 84 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8008 (tm-30) outliers start: 21 outliers final: 9 residues processed: 251 average time/residue: 2.1549 time to fit residues: 624.6204 Evaluate side-chains 247 residues out of total 1885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 232 time to evaluate : 2.766 ------------------------------------------------------------------------------- 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 324 PHE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain E residue 126 THR 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 H2 residue 110 ASP 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 200 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 210 optimal weight: 0.7980 chunk 193 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 129 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 309 GLN E 135 ASN L2 16 GLN L2 80 GLN L 80 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17859 Z= 0.181 Angle : 0.525 11.221 24294 Z= 0.264 Chirality : 0.041 0.197 2815 Planarity : 0.004 0.064 2998 Dihedral : 5.950 59.700 2859 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.01 % Allowed : 15.17 % Favored : 83.82 % 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: -0.12 (0.19), residues: 2121 helix: 2.00 (0.21), residues: 614 sheet: -1.10 (0.20), residues: 672 loop : -0.65 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 319 HIS 0.002 0.000 HIS A 267 PHE 0.019 0.001 PHE D 304 TYR 0.022 0.001 TYR A 244 ARG 0.009 0.000 ARGL2 17 ********************** 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 252 residues out of total 1885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 233 time to evaluate : 3.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ILE cc_start: 0.9176 (tt) cc_final: 0.8868 (pt) REVERT: A 137 MET cc_start: 0.7053 (tpt) cc_final: 0.6813 (tpt) REVERT: A 241 TRP cc_start: 0.6717 (m-10) cc_final: 0.6194 (m-10) REVERT: A 286 MET cc_start: 0.7335 (tpp) cc_final: 0.6953 (tpp) REVERT: B 124 ASP cc_start: 0.7923 (t0) cc_final: 0.7613 (t0) REVERT: B 282 TYR cc_start: 0.7814 (p90) cc_final: 0.7114 (p90) REVERT: C 40 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8132 (mtt) REVERT: C 283 MET cc_start: 0.8152 (mmm) cc_final: 0.7545 (mmm) REVERT: D 83 VAL cc_start: 0.9340 (OUTLIER) cc_final: 0.9072 (t) REVERT: E 235 TYR cc_start: 0.6646 (t80) cc_final: 0.6330 (t80) REVERT: E 296 MET cc_start: 0.7286 (tpp) cc_final: 0.6957 (tpp) REVERT: E 297 ASP cc_start: 0.7133 (OUTLIER) cc_final: 0.6746 (t0) REVERT: E 313 GLU cc_start: 0.7430 (tm-30) cc_final: 0.6755 (tp30) REVERT: L2 86 ASP cc_start: 0.8275 (m-30) cc_final: 0.7766 (m-30) REVERT: H 51 MET cc_start: 0.8483 (ptm) cc_final: 0.8225 (ttp) REVERT: H 80 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.5908 (p90) REVERT: H2 10 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: H2 80 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.6039 (p90) REVERT: L 84 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7999 (tm-30) outliers start: 19 outliers final: 10 residues processed: 243 average time/residue: 2.2241 time to fit residues: 625.5901 Evaluate side-chains 244 residues out of total 1885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 228 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 10 GLU Chi-restraints excluded: chain H2 residue 80 TYR Chi-restraints excluded: chain H2 residue 110 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 154 optimal weight: 0.0980 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 309 GLN E 135 ASN L2 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.117275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.086169 restraints weight = 76873.954| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.44 r_work: 0.2967 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17859 Z= 0.213 Angle : 0.526 11.582 24294 Z= 0.265 Chirality : 0.041 0.204 2815 Planarity : 0.004 0.064 2998 Dihedral : 5.925 58.910 2859 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.01 % Allowed : 15.38 % Favored : 83.61 % 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: -0.06 (0.19), residues: 2121 helix: 2.05 (0.21), residues: 615 sheet: -1.05 (0.20), residues: 676 loop : -0.64 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 319 HIS 0.002 0.000 HIS A 267 PHE 0.019 0.001 PHE D 304 TYR 0.019 0.001 TYR C 299 ARG 0.008 0.000 ARGL2 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11958.72 seconds wall clock time: 209 minutes 32.58 seconds (12572.58 seconds total)