Starting phenix.real_space_refine on Mon Apr 15 11:01:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si9_40503/04_2024/8si9_40503_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si9_40503/04_2024/8si9_40503.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si9_40503/04_2024/8si9_40503_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si9_40503/04_2024/8si9_40503_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si9_40503/04_2024/8si9_40503_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si9_40503/04_2024/8si9_40503.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si9_40503/04_2024/8si9_40503.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si9_40503/04_2024/8si9_40503_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si9_40503/04_2024/8si9_40503_trim_updated.pdb" } resolution = 2.98 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= 0.002 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 97 5.16 5 C 11259 2.51 5 N 2827 2.21 5 O 3237 1.98 5 H 16954 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" Residue "D PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 34374 Number of models: 1 Model: "" Number of chains: 17 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: 5443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5443 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 321} 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: 5443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5443 Classifications: {'peptide': 337} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 321} 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: "I" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1573 Classifications: {'peptide': 105} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "J" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1784 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1595 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1798 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "F" 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: "G" 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 Chain: "H" 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: "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: 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: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'Y4B': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {'ABU': 1, 'NAG': 1, 'Y4B': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 14.90, per 1000 atoms: 0.43 Number of scatterers: 34374 At special positions: 0 Unit cell: (149.8, 127.33, 126.26, 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 97 16.00 O 3237 8.00 N 2827 7.00 C 11259 6.00 H 16954 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.05 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " 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 G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " " MAN G 8 " - " MAN G 9 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 7 " - " MAN G 10 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 8 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 401 " - " ASN A 80 " " NAG C 401 " - " ASN C 80 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG M 1 " - " ASN D 111 " " NAG N 1 " - " ASN E 208 " Time building additional restraints: 26.98 Conformation dependent library (CDL) restraints added in 3.6 seconds 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4016 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 30 sheets defined 27.8% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.20 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 219 through 225 Processing helix chain 'A' and resid 227 through 240 removed outlier: 4.322A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 271 removed outlier: 3.689A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR A 271 " --> pdb=" O HIS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 304 Processing helix chain 'A' and resid 310 through 319 removed outlier: 3.674A pdb=" N ALA A 314 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ILE A 316 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 339 Processing helix chain 'B' and resid 12 through 22 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 224 through 246 removed outlier: 3.585A pdb=" N ILE B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix removed outlier: 4.022A pdb=" N SER B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TRP B 246 " --> pdb=" O GLN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 276 removed outlier: 3.628A pdb=" N ARG B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 310 Processing helix chain 'B' and resid 315 through 345 removed outlier: 4.436A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix Processing helix chain 'C' and resid 8 through 20 Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 219 through 224 Processing helix chain 'C' and resid 226 through 240 removed outlier: 3.565A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 271 Processing helix chain 'C' and resid 280 through 304 Processing helix chain 'C' and resid 310 through 338 Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 224 through 245 removed outlier: 4.531A pdb=" N LEU D 232 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Proline residue: D 233 - end of helix removed outlier: 4.466A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 274 Processing helix chain 'D' and resid 285 through 310 removed outlier: 3.665A pdb=" N ILE D 302 " --> pdb=" O PHE D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 345 removed outlier: 4.016A pdb=" N ILE D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) Proline residue: D 330 - end of helix Processing helix chain 'E' and resid 27 through 34 Processing helix chain 'E' and resid 235 through 239 Processing helix chain 'E' and resid 241 through 255 removed outlier: 3.912A pdb=" N SER E 254 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE E 255 " --> pdb=" O SER E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 286 Processing helix chain 'E' and resid 296 through 323 removed outlier: 3.906A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 356 removed outlier: 3.944A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE E 337 " --> pdb=" O SER E 333 " (cutoff:3.500A) Proline residue: E 340 - end of helix Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing sheet with id= A, first strand: chain 'A' and resid 164 through 168 removed outlier: 6.433A pdb=" N VAL A 36 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N TYR A 167 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL A 38 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 130 through 132 Processing sheet with id= C, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= D, first strand: chain 'A' and resid 191 through 199 Processing sheet with id= E, first strand: chain 'B' and resid 167 through 171 removed outlier: 6.249A pdb=" N THR B 39 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLU B 170 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL B 41 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU B 119 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 179 through 181 removed outlier: 6.504A pdb=" N ILE B 45 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 99 through 101 Processing sheet with id= H, first strand: chain 'B' and resid 150 through 154 removed outlier: 3.794A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU B 193 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.491A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.854A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 39 through 43 Processing sheet with id= L, first strand: chain 'D' and resid 179 through 181 removed outlier: 6.604A pdb=" N ILE D 45 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 84 through 86 removed outlier: 4.218A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= O, first strand: chain 'D' and resid 152 through 154 removed outlier: 3.830A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 179 through 183 removed outlier: 5.928A pdb=" N THR E 51 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLN E 182 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE E 53 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 111 through 113 removed outlier: 3.562A pdb=" N PHE E 227 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 116 through 121 removed outlier: 7.006A pdb=" N ASP E 148 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 4 through 7 Processing sheet with id= T, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.925A pdb=" N LYS I 102 " --> pdb=" O MET I 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'I' and resid 85 through 90 removed outlier: 6.010A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 3 through 6 Processing sheet with id= W, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.502A pdb=" N TRP J 36 " --> pdb=" O GLY J 49 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N LYS J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N TRP J 47 " --> pdb=" O LYS J 38 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 68 through 73 Processing sheet with id= Y, first strand: chain 'L' and resid 4 through 7 Processing sheet with id= Z, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.981A pdb=" N LYS L 102 " --> pdb=" O MET L 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'L' and resid 85 through 90 removed outlier: 6.086A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.560A pdb=" N VAL K 18 " --> pdb=" O LEU K 83 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'K' and resid 11 through 13 removed outlier: 5.902A pdb=" N THR K 115 " --> pdb=" O VAL K 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'K' and resid 58 through 60 removed outlier: 6.868A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N TYR K 33 " --> pdb=" O LYS K 99 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS K 99 " --> pdb=" O TYR K 33 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 693 hydrogen bonds defined for protein. 1995 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: 13.16 Time building geometry restraints manager: 28.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 16924 1.00 - 1.21: 32 1.21 - 1.42: 7519 1.42 - 1.62: 10172 1.62 - 1.83: 167 Bond restraints: 34814 Sorted by residual: bond pdb=" C13 Y4B A 402 " pdb=" C16 Y4B A 402 " ideal model delta sigma weight residual 1.734 1.544 0.190 2.00e-02 2.50e+03 9.05e+01 bond pdb=" C13 Y4B C 403 " pdb=" C16 Y4B C 403 " ideal model delta sigma weight residual 1.734 1.554 0.180 2.00e-02 2.50e+03 8.12e+01 bond pdb=" N ARG A 269 " pdb=" H ARG A 269 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" N GLN D 242 " pdb=" H GLN D 242 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.74e+01 bond pdb=" NE2 GLN D 242 " pdb="HE22 GLN D 242 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.10e+01 ... (remaining 34809 not shown) Histogram of bond angle deviations from ideal: 86.81 - 100.80: 41 100.80 - 114.79: 42808 114.79 - 128.78: 19561 128.78 - 142.77: 154 142.77 - 156.76: 2 Bond angle restraints: 62566 Sorted by residual: angle pdb=" CD GLN A 309 " pdb=" NE2 GLN A 309 " pdb="HE22 GLN A 309 " ideal model delta sigma weight residual 120.00 156.76 -36.76 3.00e+00 1.11e-01 1.50e+02 angle pdb="HE21 GLN A 309 " pdb=" NE2 GLN A 309 " pdb="HE22 GLN A 309 " ideal model delta sigma weight residual 120.00 86.81 33.19 3.00e+00 1.11e-01 1.22e+02 angle pdb=" CD GLN A 309 " pdb=" NE2 GLN A 309 " pdb="HE21 GLN A 309 " ideal model delta sigma weight residual 120.00 91.85 28.15 3.00e+00 1.11e-01 8.81e+01 angle pdb=" CG ASN E 347 " pdb=" ND2 ASN E 347 " pdb="HD22 ASN E 347 " ideal model delta sigma weight residual 120.00 147.24 -27.24 3.00e+00 1.11e-01 8.24e+01 angle pdb="HD21 ASN E 347 " pdb=" ND2 ASN E 347 " pdb="HD22 ASN E 347 " ideal model delta sigma weight residual 120.00 94.78 25.22 3.00e+00 1.11e-01 7.07e+01 ... (remaining 62561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.80: 15762 21.80 - 43.60: 841 43.60 - 65.39: 200 65.39 - 87.19: 46 87.19 - 108.99: 16 Dihedral angle restraints: 16865 sinusoidal: 9183 harmonic: 7682 Sorted by residual: 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 -86.00 -19.11 -66.89 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CB CYS A 136 " pdb=" SG CYS A 136 " pdb=" SG CYS A 150 " pdb=" CB CYS A 150 " ideal model delta sinusoidal sigma weight residual -86.00 -27.42 -58.58 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CD ARG E 232 " pdb=" NE ARG E 232 " pdb=" CZ ARG E 232 " pdb=" NH1 ARG E 232 " ideal model delta sinusoidal sigma weight residual 0.00 -53.72 53.72 1 1.00e+01 1.00e-02 3.92e+01 ... (remaining 16862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2671 0.100 - 0.201: 133 0.201 - 0.301: 13 0.301 - 0.401: 2 0.401 - 0.501: 2 Chirality restraints: 2821 Sorted by residual: chirality pdb=" C06 Y4B A 402 " pdb=" C05 Y4B A 402 " pdb=" C10 Y4B A 402 " pdb=" C12 Y4B A 402 " both_signs ideal model delta sigma weight residual False 2.46 2.96 -0.50 2.00e-01 2.50e+01 6.28e+00 chirality pdb=" C06 Y4B C 403 " pdb=" C05 Y4B C 403 " pdb=" C10 Y4B C 403 " pdb=" C12 Y4B C 403 " both_signs ideal model delta sigma weight residual False 2.46 2.96 -0.50 2.00e-01 2.50e+01 6.13e+00 chirality pdb=" C12 Y4B C 403 " pdb=" C06 Y4B C 403 " pdb=" C16 Y4B C 403 " pdb=" C22 Y4B C 403 " both_signs ideal model delta sigma weight residual False 2.87 2.54 0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 2818 not shown) Planarity restraints: 5010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 321 " -0.436 9.50e-02 1.11e+02 2.19e-01 6.21e+02 pdb=" NE ARG A 321 " -0.191 2.00e-02 2.50e+03 pdb=" CZ ARG A 321 " -0.052 2.00e-02 2.50e+03 pdb=" NH1 ARG A 321 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 321 " 0.031 2.00e-02 2.50e+03 pdb="HH11 ARG A 321 " 0.322 2.00e-02 2.50e+03 pdb="HH12 ARG A 321 " -0.231 2.00e-02 2.50e+03 pdb="HH21 ARG A 321 " 0.195 2.00e-02 2.50e+03 pdb="HH22 ARG A 321 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 232 " 0.910 9.50e-02 1.11e+02 3.09e-01 1.71e+02 pdb=" NE ARG E 232 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG E 232 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG E 232 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG E 232 " -0.011 2.00e-02 2.50e+03 pdb="HH11 ARG E 232 " -0.091 2.00e-02 2.50e+03 pdb="HH12 ARG E 232 " 0.113 2.00e-02 2.50e+03 pdb="HH21 ARG E 232 " 0.052 2.00e-02 2.50e+03 pdb="HH22 ARG E 232 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 231 " 0.635 9.50e-02 1.11e+02 2.24e-01 1.67e+02 pdb=" NE ARG E 231 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG E 231 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG E 231 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG E 231 " -0.018 2.00e-02 2.50e+03 pdb="HH11 ARG E 231 " -0.154 2.00e-02 2.50e+03 pdb="HH12 ARG E 231 " 0.145 2.00e-02 2.50e+03 pdb="HH21 ARG E 231 " -0.009 2.00e-02 2.50e+03 pdb="HH22 ARG E 231 " -0.047 2.00e-02 2.50e+03 ... (remaining 5007 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 1013 2.13 - 2.74: 62929 2.74 - 3.36: 94276 3.36 - 3.98: 127621 3.98 - 4.60: 200482 Nonbonded interactions: 486321 Sorted by model distance: nonbonded pdb=" HE2 HIS C 107 " pdb=" OG1 THR C 131 " model vdw 1.507 1.850 nonbonded pdb=" OE2 GLU C 270 " pdb="HE22 GLN D 229 " model vdw 1.512 1.850 nonbonded pdb=" OE1 GLU C 155 " pdb="HH21 ARG C 207 " model vdw 1.513 1.850 nonbonded pdb=" H GLY K 100 " pdb=" O ALA K 104 " model vdw 1.547 1.850 nonbonded pdb=" OG1 THR B 207 " pdb=" HH TYR B 210 " model vdw 1.563 1.850 ... (remaining 486316 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' and (resid 7 through 340 or resid 401)) selection = (chain 'C' and (resid 7 through 340 or resid 401)) } ncs_group { reference = (chain 'B' and resid 11 through 347) selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'I' selection = (chain 'L' and resid 1 through 105) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 2 through 117) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.470 Extract box with map and model: 6.790 Check model and map are aligned: 0.480 Set scattering table: 0.320 Process input model: 107.540 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 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 : 0.006 0.190 17860 Z= 0.413 Angle : 0.715 8.952 24300 Z= 0.377 Chirality : 0.051 0.501 2821 Planarity : 0.010 0.387 2980 Dihedral : 14.296 108.991 6795 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.43 % Favored : 95.53 % Rotamer: Outliers : 0.05 % Allowed : 0.11 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.16), residues: 2101 helix: -1.01 (0.20), residues: 582 sheet: -2.51 (0.17), residues: 668 loop : -2.36 (0.18), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 134 HIS 0.005 0.001 HIS B 110 PHE 0.017 0.002 PHE D 226 TYR 0.019 0.002 TYR D 129 ARG 0.010 0.001 ARG E 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 413 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LEU cc_start: 0.9108 (mt) cc_final: 0.8896 (tt) REVERT: A 299 TYR cc_start: 0.8390 (t80) cc_final: 0.8170 (t80) REVERT: B 314 GLN cc_start: 0.7373 (mt0) cc_final: 0.7152 (tm-30) REVERT: C 283 MET cc_start: 0.8587 (tpp) cc_final: 0.8344 (tpp) REVERT: D 114 MET cc_start: 0.8446 (mmm) cc_final: 0.8205 (mmp) REVERT: E 152 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7354 (mm-40) REVERT: E 162 GLU cc_start: 0.8355 (tt0) cc_final: 0.7800 (tm-30) REVERT: E 317 LEU cc_start: 0.8575 (tt) cc_final: 0.8356 (tt) REVERT: E 331 MET cc_start: 0.7038 (ttm) cc_final: 0.6557 (ttm) REVERT: J 67 LYS cc_start: 0.8546 (tttt) cc_final: 0.8291 (ttmt) REVERT: J 89 GLU cc_start: 0.7989 (pp20) cc_final: 0.7612 (pp20) REVERT: L 56 THR cc_start: 0.9239 (m) cc_final: 0.9010 (p) REVERT: L 105 LEU cc_start: 0.8862 (tp) cc_final: 0.8620 (tp) outliers start: 1 outliers final: 0 residues processed: 413 average time/residue: 2.6814 time to fit residues: 1248.3072 Evaluate side-chains 257 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.6980 chunk 156 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 309 GLN C 267 HIS D 88 ASN K 110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17860 Z= 0.324 Angle : 0.589 8.051 24300 Z= 0.301 Chirality : 0.043 0.246 2821 Planarity : 0.004 0.055 2980 Dihedral : 7.829 64.275 2859 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.97 % Allowed : 12.60 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -1.77 (0.17), residues: 2101 helix: 0.65 (0.21), residues: 586 sheet: -1.91 (0.18), residues: 671 loop : -1.74 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 134 HIS 0.005 0.001 HIS C 267 PHE 0.017 0.001 PHE E 346 TYR 0.015 0.001 TYR D 129 ARG 0.008 0.000 ARG E 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 264 time to evaluate : 2.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.7853 (mmm) cc_final: 0.7625 (mmm) REVERT: A 247 SER cc_start: 0.7920 (m) cc_final: 0.7666 (p) REVERT: B 40 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7405 (tm-30) REVERT: B 314 GLN cc_start: 0.7251 (mt0) cc_final: 0.6910 (tm-30) REVERT: C 250 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6985 (mtm180) REVERT: C 283 MET cc_start: 0.8579 (tpp) cc_final: 0.8283 (tpp) REVERT: E 162 GLU cc_start: 0.8333 (tt0) cc_final: 0.7785 (tm-30) REVERT: L 105 LEU cc_start: 0.8617 (tp) cc_final: 0.8413 (tp) outliers start: 37 outliers final: 13 residues processed: 280 average time/residue: 2.6627 time to fit residues: 841.8337 Evaluate side-chains 256 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 241 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 344 CYS Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain K residue 55 ASN Chi-restraints excluded: chain K residue 84 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 203 optimal weight: 0.6980 chunk 167 optimal weight: 0.7980 chunk 186 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 151 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 267 HIS D 88 ASN K 110 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17860 Z= 0.190 Angle : 0.532 6.887 24300 Z= 0.270 Chirality : 0.042 0.168 2821 Planarity : 0.004 0.053 2980 Dihedral : 6.188 59.729 2859 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.70 % Allowed : 13.77 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.95 (0.18), residues: 2101 helix: 1.57 (0.22), residues: 574 sheet: -1.58 (0.18), residues: 701 loop : -1.21 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 67 HIS 0.006 0.001 HIS C 267 PHE 0.018 0.001 PHE C 307 TYR 0.013 0.001 TYR D 294 ARG 0.004 0.000 ARG C 312 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 252 time to evaluate : 2.762 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 224 GLN cc_start: 0.8705 (tp40) cc_final: 0.8422 (mm-40) REVERT: A 235 LEU cc_start: 0.9095 (tt) cc_final: 0.8828 (tt) REVERT: A 247 SER cc_start: 0.7985 (m) cc_final: 0.7772 (p) REVERT: B 40 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7387 (tm-30) REVERT: B 314 GLN cc_start: 0.7216 (mt0) cc_final: 0.6917 (tm-30) REVERT: C 250 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.6972 (mtm180) REVERT: C 283 MET cc_start: 0.8566 (tpp) cc_final: 0.8269 (tpp) REVERT: E 162 GLU cc_start: 0.8285 (tt0) cc_final: 0.7751 (tm-30) REVERT: E 178 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8395 (mt-10) outliers start: 32 outliers final: 10 residues processed: 265 average time/residue: 2.6219 time to fit residues: 787.2891 Evaluate side-chains 252 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 240 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain K residue 55 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 0.4980 chunk 141 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 188 optimal weight: 0.3980 chunk 200 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN C 267 HIS D 88 ASN K 110 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17860 Z= 0.160 Angle : 0.512 6.420 24300 Z= 0.258 Chirality : 0.042 0.203 2821 Planarity : 0.004 0.052 2980 Dihedral : 5.392 50.912 2859 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.59 % Allowed : 14.94 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.51 (0.19), residues: 2101 helix: 1.88 (0.22), residues: 573 sheet: -1.35 (0.18), residues: 702 loop : -0.87 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 67 HIS 0.006 0.001 HIS C 267 PHE 0.018 0.001 PHE E 346 TYR 0.011 0.001 TYR E 314 ARG 0.009 0.000 ARG C 312 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 253 time to evaluate : 2.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.8602 (tp40) cc_final: 0.8347 (mm-40) REVERT: B 314 GLN cc_start: 0.7184 (mt0) cc_final: 0.6886 (tm-30) REVERT: C 224 GLN cc_start: 0.8523 (tp40) cc_final: 0.8259 (tm-30) REVERT: C 250 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6970 (mtm180) REVERT: C 283 MET cc_start: 0.8561 (tpp) cc_final: 0.8262 (tpp) REVERT: D 131 MET cc_start: 0.8829 (mtp) cc_final: 0.8586 (mtp) REVERT: E 162 GLU cc_start: 0.8246 (tt0) cc_final: 0.7751 (tm-30) REVERT: E 238 ILE cc_start: 0.9200 (pp) cc_final: 0.8805 (tt) outliers start: 30 outliers final: 15 residues processed: 268 average time/residue: 2.5992 time to fit residues: 788.3343 Evaluate side-chains 257 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 241 time to evaluate : 4.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain K residue 55 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 170 optimal weight: 0.2980 chunk 138 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN K 110 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17860 Z= 0.270 Angle : 0.531 7.584 24300 Z= 0.270 Chirality : 0.042 0.213 2821 Planarity : 0.004 0.062 2980 Dihedral : 5.241 47.659 2859 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.81 % Allowed : 15.58 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.19), residues: 2101 helix: 1.98 (0.21), residues: 587 sheet: -1.17 (0.19), residues: 710 loop : -0.74 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 134 HIS 0.006 0.001 HIS C 267 PHE 0.018 0.001 PHE E 236 TYR 0.012 0.001 TYR E 172 ARG 0.008 0.000 ARG E 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 245 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7328 (tm-30) REVERT: B 131 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8272 (mtp) REVERT: C 224 GLN cc_start: 0.8549 (tp40) cc_final: 0.7953 (tp-100) REVERT: C 250 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6995 (mtm180) REVERT: C 283 MET cc_start: 0.8561 (tpp) cc_final: 0.8225 (tpp) REVERT: D 112 MET cc_start: 0.8490 (tpp) cc_final: 0.8265 (tpp) REVERT: D 131 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8605 (mtp) REVERT: D 338 LEU cc_start: 0.8636 (mm) cc_final: 0.8363 (tm) REVERT: E 162 GLU cc_start: 0.8222 (tt0) cc_final: 0.7778 (tm-30) REVERT: E 178 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8386 (mt-10) REVERT: K 10 GLU cc_start: 0.7979 (mp0) cc_final: 0.7709 (mp0) outliers start: 34 outliers final: 11 residues processed: 260 average time/residue: 2.5997 time to fit residues: 766.2490 Evaluate side-chains 256 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 241 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain K residue 55 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN K 110 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17860 Z= 0.217 Angle : 0.521 7.246 24300 Z= 0.264 Chirality : 0.042 0.220 2821 Planarity : 0.004 0.061 2980 Dihedral : 5.019 43.782 2859 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.65 % Allowed : 16.21 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2101 helix: 2.06 (0.21), residues: 587 sheet: -0.98 (0.19), residues: 698 loop : -0.62 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 237 HIS 0.006 0.001 HIS C 267 PHE 0.018 0.001 PHE E 346 TYR 0.012 0.001 TYR E 314 ARG 0.009 0.000 ARG C 312 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 246 time to evaluate : 2.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ASN cc_start: 0.7711 (OUTLIER) cc_final: 0.7283 (t0) REVERT: B 40 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: B 131 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8259 (mtp) REVERT: C 224 GLN cc_start: 0.8509 (tp40) cc_final: 0.7962 (tp-100) REVERT: C 250 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7016 (mtm180) REVERT: C 283 MET cc_start: 0.8552 (tpp) cc_final: 0.8215 (tpp) REVERT: D 131 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8553 (mtp) REVERT: D 294 TYR cc_start: 0.8339 (t80) cc_final: 0.8059 (t80) REVERT: D 338 LEU cc_start: 0.8632 (mm) cc_final: 0.8367 (tm) REVERT: E 162 GLU cc_start: 0.8266 (tt0) cc_final: 0.7816 (tm-30) REVERT: E 238 ILE cc_start: 0.9227 (pp) cc_final: 0.8837 (tt) outliers start: 31 outliers final: 16 residues processed: 258 average time/residue: 2.5842 time to fit residues: 756.4783 Evaluate side-chains 260 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 239 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain K residue 55 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN K 110 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17860 Z= 0.209 Angle : 0.519 7.175 24300 Z= 0.262 Chirality : 0.041 0.221 2821 Planarity : 0.004 0.067 2980 Dihedral : 4.825 39.611 2859 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.75 % Allowed : 16.11 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.14 (0.19), residues: 2101 helix: 2.25 (0.21), residues: 587 sheet: -0.87 (0.19), residues: 698 loop : -0.49 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 237 HIS 0.005 0.001 HIS C 267 PHE 0.021 0.001 PHE C 307 TYR 0.012 0.001 TYR E 314 ARG 0.009 0.000 ARG E 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 240 time to evaluate : 2.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ASN cc_start: 0.7704 (OUTLIER) cc_final: 0.7256 (t0) REVERT: B 40 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7332 (tm-30) REVERT: B 131 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8289 (mtp) REVERT: C 224 GLN cc_start: 0.8486 (tp40) cc_final: 0.7976 (tp-100) REVERT: C 250 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7016 (mtm180) REVERT: C 283 MET cc_start: 0.8551 (tpp) cc_final: 0.8212 (tpp) REVERT: D 131 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8584 (mtp) REVERT: D 294 TYR cc_start: 0.8299 (t80) cc_final: 0.8014 (t80) REVERT: D 338 LEU cc_start: 0.8526 (mm) cc_final: 0.8272 (tm) REVERT: E 162 GLU cc_start: 0.8274 (tt0) cc_final: 0.7819 (tm-30) outliers start: 33 outliers final: 13 residues processed: 251 average time/residue: 2.6161 time to fit residues: 743.6572 Evaluate side-chains 250 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 232 time to evaluate : 3.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain K residue 55 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 2.9990 chunk 79 optimal weight: 0.0970 chunk 119 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 126 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN K 110 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17860 Z= 0.220 Angle : 0.523 7.423 24300 Z= 0.264 Chirality : 0.042 0.222 2821 Planarity : 0.004 0.071 2980 Dihedral : 4.745 36.799 2859 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.59 % Allowed : 16.32 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.27 (0.19), residues: 2101 helix: 2.35 (0.21), residues: 587 sheet: -0.78 (0.20), residues: 684 loop : -0.44 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 237 HIS 0.005 0.001 HIS C 267 PHE 0.012 0.001 PHE E 346 TYR 0.012 0.001 TYR E 314 ARG 0.011 0.000 ARG C 312 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 240 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ASN cc_start: 0.7708 (OUTLIER) cc_final: 0.7272 (t0) REVERT: B 40 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7355 (tm-30) REVERT: B 131 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8293 (mtp) REVERT: B 247 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8541 (tt) REVERT: C 224 GLN cc_start: 0.8487 (tp40) cc_final: 0.7988 (tp-100) REVERT: C 250 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7005 (mtm180) REVERT: C 283 MET cc_start: 0.8551 (tpp) cc_final: 0.8210 (tpp) REVERT: D 131 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8579 (mtp) REVERT: D 338 LEU cc_start: 0.8524 (mm) cc_final: 0.8274 (tm) REVERT: E 162 GLU cc_start: 0.8261 (tt0) cc_final: 0.7806 (tm-30) REVERT: J 11 LEU cc_start: 0.8414 (tp) cc_final: 0.8174 (tm) outliers start: 30 outliers final: 14 residues processed: 252 average time/residue: 2.5648 time to fit residues: 736.5838 Evaluate side-chains 253 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 233 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain L residue 104 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 174 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 168 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN K 110 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17860 Z= 0.267 Angle : 0.535 7.133 24300 Z= 0.271 Chirality : 0.042 0.227 2821 Planarity : 0.004 0.075 2980 Dihedral : 4.802 37.105 2859 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.28 % Allowed : 17.01 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.36 (0.19), residues: 2101 helix: 2.38 (0.21), residues: 587 sheet: -0.67 (0.20), residues: 682 loop : -0.41 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 237 HIS 0.005 0.001 HIS C 267 PHE 0.022 0.001 PHE E 346 TYR 0.012 0.001 TYR E 314 ARG 0.011 0.000 ARG C 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 236 time to evaluate : 3.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ASN cc_start: 0.7701 (OUTLIER) cc_final: 0.7268 (t0) REVERT: B 40 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7360 (tm-30) REVERT: B 131 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8311 (mtp) REVERT: C 224 GLN cc_start: 0.8536 (tp40) cc_final: 0.8037 (tp-100) REVERT: C 250 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7036 (mtm180) REVERT: C 283 MET cc_start: 0.8561 (tpp) cc_final: 0.8214 (tpp) REVERT: D 131 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8566 (mtp) REVERT: D 338 LEU cc_start: 0.8527 (mm) cc_final: 0.8278 (tm) REVERT: E 162 GLU cc_start: 0.8262 (tt0) cc_final: 0.7827 (tm-30) REVERT: J 11 LEU cc_start: 0.8430 (tp) cc_final: 0.8203 (tm) outliers start: 24 outliers final: 14 residues processed: 246 average time/residue: 2.6287 time to fit residues: 733.4374 Evaluate side-chains 250 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 231 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain L residue 104 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 206 optimal weight: 0.6980 chunk 189 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN K 110 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17860 Z= 0.239 Angle : 0.535 8.420 24300 Z= 0.270 Chirality : 0.042 0.224 2821 Planarity : 0.004 0.077 2980 Dihedral : 4.762 35.927 2859 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.06 % Allowed : 17.54 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.45 (0.19), residues: 2101 helix: 2.44 (0.21), residues: 587 sheet: -0.62 (0.20), residues: 678 loop : -0.34 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 237 HIS 0.005 0.001 HIS C 267 PHE 0.011 0.001 PHE E 346 TYR 0.012 0.001 TYR E 314 ARG 0.014 0.001 ARG C 312 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 232 time to evaluate : 3.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ASN cc_start: 0.7709 (OUTLIER) cc_final: 0.7296 (t0) REVERT: B 40 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7378 (tm-30) REVERT: B 131 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8298 (mtp) REVERT: C 224 GLN cc_start: 0.8520 (tp40) cc_final: 0.8116 (tp-100) REVERT: C 250 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7022 (mtm180) REVERT: C 283 MET cc_start: 0.8556 (tpp) cc_final: 0.8206 (tpp) REVERT: D 131 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8575 (mtp) REVERT: D 338 LEU cc_start: 0.8470 (mm) cc_final: 0.8224 (tm) REVERT: E 162 GLU cc_start: 0.8287 (tt0) cc_final: 0.7830 (tm-30) REVERT: I 13 MET cc_start: 0.6908 (pp-130) cc_final: 0.6648 (pp-130) REVERT: J 11 LEU cc_start: 0.8445 (tp) cc_final: 0.8225 (tm) outliers start: 20 outliers final: 11 residues processed: 242 average time/residue: 2.6529 time to fit residues: 728.1312 Evaluate side-chains 247 residues out of total 1881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 231 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain L residue 104 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN K 110 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.092630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.063265 restraints weight = 100637.262| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.62 r_work: 0.2710 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17860 Z= 0.194 Angle : 0.527 8.610 24300 Z= 0.265 Chirality : 0.042 0.215 2821 Planarity : 0.004 0.076 2980 Dihedral : 4.635 34.399 2859 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.90 % Allowed : 17.92 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.56 (0.19), residues: 2101 helix: 2.55 (0.21), residues: 585 sheet: -0.58 (0.20), residues: 678 loop : -0.27 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 237 HIS 0.005 0.001 HIS C 267 PHE 0.020 0.001 PHE C 307 TYR 0.011 0.001 TYR E 314 ARG 0.015 0.000 ARG C 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13201.05 seconds wall clock time: 234 minutes 1.10 seconds (14041.10 seconds total)