Starting phenix.real_space_refine on Wed Apr 17 08:45:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st1_40754/04_2024/8st1_40754_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st1_40754/04_2024/8st1_40754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st1_40754/04_2024/8st1_40754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st1_40754/04_2024/8st1_40754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st1_40754/04_2024/8st1_40754_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st1_40754/04_2024/8st1_40754_trim_updated.pdb" } resolution = 3.41 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= 0.001 sd= 0.006 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 S 120 5.16 5 Na 1 4.78 5 C 14329 2.51 5 N 3569 2.21 5 O 4067 1.98 5 H 21833 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "D TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "G TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "K GLU 90": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 43923 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 6195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 6195 Classifications: {'peptide': 375} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 355} Chain: "B" Number of atoms: 6195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 6195 Classifications: {'peptide': 375} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 355} Chain: "C" Number of atoms: 5978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 5978 Classifications: {'peptide': 365} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 342} Chain breaks: 1 Chain: "D" Number of atoms: 6195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 6195 Classifications: {'peptide': 375} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 355} Chain: "E" Number of atoms: 5978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 5978 Classifications: {'peptide': 365} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 342} Chain breaks: 1 Chain: "F" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3325 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "G" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3265 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 202} Chain: "J" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3325 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "K" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3265 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 202} 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: "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: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 40 Unusual residues: {' CA': 2, 'ACH': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 39 Unusual residues: {' CA': 1, 'ACH': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 39 Unusual residues: {' CA': 1, 'ACH': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 19.31, per 1000 atoms: 0.44 Number of scatterers: 43923 At special positions: 0 Unit cell: (137.953, 182.867, 146.508, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 120 16.00 Na 1 11.00 O 4067 8.00 N 3569 7.00 C 14329 6.00 H 21833 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 200 " distance=2.04 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 200 " distance=2.04 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 144 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 199 " - pdb=" SG CYS D 200 " distance=2.04 Simple disulfide: pdb=" SG CYS E 130 " - pdb=" SG CYS E 144 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 93 " distance=2.03 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 199 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 147 " - pdb=" SG CYS G 202 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 93 " distance=2.03 Simple disulfide: pdb=" SG CYS J 139 " - pdb=" SG CYS J 199 " distance=2.24 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 97 " distance=2.03 Simple disulfide: pdb=" SG CYS K 147 " - pdb=" SG CYS K 202 " 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 BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A 701 " - " ASN A 31 " " NAG A 702 " - " ASN A 148 " " NAG B 701 " - " ASN B 31 " " NAG B 702 " - " ASN B 148 " " NAG D 701 " - " ASN D 31 " " NAG D 702 " - " ASN D 148 " " NAG H 1 " - " ASN C 143 " " NAG I 1 " - " ASN E 143 " Time building additional restraints: 35.36 Conformation dependent library (CDL) restraints added in 4.6 seconds 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5220 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 41 sheets defined 27.0% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.63 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 218 through 234 removed outlier: 4.403A pdb=" N ILE A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Proline residue: A 227 - end of helix removed outlier: 3.745A pdb=" N LEU A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 248 through 268 Processing helix chain 'A' and resid 279 through 305 Processing helix chain 'A' and resid 316 through 329 removed outlier: 5.551A pdb=" N VAL A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing helix chain 'A' and resid 342 through 381 Proline residue: A 379 - end of helix Processing helix chain 'B' and resid 9 through 18 Processing helix chain 'B' and resid 76 through 79 Processing helix chain 'B' and resid 218 through 223 Processing helix chain 'B' and resid 225 through 234 removed outlier: 3.868A pdb=" N LEU B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 240 Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 248 through 268 Processing helix chain 'B' and resid 279 through 305 Processing helix chain 'B' and resid 316 through 329 removed outlier: 3.541A pdb=" N VAL B 321 " --> pdb=" O TRP B 317 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N VAL B 326 " --> pdb=" O PHE B 322 " (cutoff:3.500A) Proline residue: B 327 - end of helix Processing helix chain 'B' and resid 342 through 381 Proline residue: B 379 - end of helix Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 84 through 86 No H-bonds generated for 'chain 'C' and resid 84 through 86' Processing helix chain 'C' and resid 210 through 226 removed outlier: 4.313A pdb=" N ILE C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Proline residue: C 219 - end of helix removed outlier: 3.691A pdb=" N LEU C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 240 through 261 Processing helix chain 'C' and resid 271 through 297 Processing helix chain 'C' and resid 308 through 322 removed outlier: 5.793A pdb=" N LEU C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Proline residue: C 319 - end of helix Processing helix chain 'C' and resid 338 through 367 removed outlier: 4.561A pdb=" N THR C 365 " --> pdb=" O CYS C 361 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE C 366 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY C 367 " --> pdb=" O PHE C 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 18 Processing helix chain 'D' and resid 76 through 79 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 218 through 234 removed outlier: 4.480A pdb=" N ILE D 226 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Proline residue: D 227 - end of helix removed outlier: 3.924A pdb=" N LEU D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 240 No H-bonds generated for 'chain 'D' and resid 237 through 240' Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'D' and resid 248 through 267 Processing helix chain 'D' and resid 279 through 305 Processing helix chain 'D' and resid 316 through 329 removed outlier: 5.543A pdb=" N VAL D 326 " --> pdb=" O PHE D 322 " (cutoff:3.500A) Proline residue: D 327 - end of helix Processing helix chain 'D' and resid 342 through 381 Proline residue: D 379 - end of helix Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 65 through 67 No H-bonds generated for 'chain 'E' and resid 65 through 67' Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 210 through 215 Processing helix chain 'E' and resid 217 through 232 removed outlier: 3.759A pdb=" N LEU E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA E 227 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE E 228 " --> pdb=" O THR E 224 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LEU E 229 " --> pdb=" O SER E 225 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL E 230 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N PHE E 231 " --> pdb=" O ALA E 227 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR E 232 " --> pdb=" O ILE E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 237 No H-bonds generated for 'chain 'E' and resid 235 through 237' Processing helix chain 'E' and resid 240 through 261 Processing helix chain 'E' and resid 271 through 297 Processing helix chain 'E' and resid 308 through 314 Processing helix chain 'E' and resid 317 through 321 Processing helix chain 'E' and resid 338 through 369 removed outlier: 3.556A pdb=" N CYS E 361 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR E 365 " --> pdb=" O CYS E 361 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE E 366 " --> pdb=" O VAL E 362 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY E 367 " --> pdb=" O PHE E 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 132 Processing helix chain 'F' and resid 188 through 191 No H-bonds generated for 'chain 'F' and resid 188 through 191' Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'G' and resid 89 through 91 No H-bonds generated for 'chain 'G' and resid 89 through 91' Processing helix chain 'G' and resid 192 through 195 No H-bonds generated for 'chain 'G' and resid 192 through 195' Processing helix chain 'G' and resid 207 through 209 No H-bonds generated for 'chain 'G' and resid 207 through 209' Processing helix chain 'J' and resid 85 through 87 No H-bonds generated for 'chain 'J' and resid 85 through 87' Processing helix chain 'J' and resid 127 through 132 Processing helix chain 'J' and resid 188 through 191 No H-bonds generated for 'chain 'J' and resid 188 through 191' Processing helix chain 'K' and resid 30 through 32 No H-bonds generated for 'chain 'K' and resid 30 through 32' Processing helix chain 'K' and resid 192 through 195 No H-bonds generated for 'chain 'K' and resid 192 through 195' Processing sheet with id= A, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.126A pdb=" N VAL A 36 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL A 166 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL A 38 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 37 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS A 68 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR A 58 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 49 through 51 Processing sheet with id= C, first strand: chain 'A' and resid 84 through 88 Processing sheet with id= D, first strand: chain 'A' and resid 97 through 99 removed outlier: 4.238A pdb=" N SER A 155 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 189 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG A 214 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ILE A 185 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 36 through 40 Processing sheet with id= F, first strand: chain 'B' and resid 49 through 51 Processing sheet with id= G, first strand: chain 'B' and resid 84 through 87 Processing sheet with id= H, first strand: chain 'B' and resid 97 through 99 removed outlier: 4.497A pdb=" N SER B 155 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 204 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 189 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG B 214 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE B 185 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 41 through 47 removed outlier: 6.810A pdb=" N ASN B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 158 through 162 removed outlier: 6.687A pdb=" N VAL C 31 " --> pdb=" O ASP C 159 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL C 161 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL C 33 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASN C 55 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU C 42 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR C 53 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 44 through 46 Processing sheet with id= L, first strand: chain 'C' and resid 79 through 83 Processing sheet with id= M, first strand: chain 'C' and resid 92 through 94 removed outlier: 5.071A pdb=" N SER C 150 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL C 197 " --> pdb=" O SER C 150 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 178 through 182 removed outlier: 6.898A pdb=" N ILE C 204 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 36 through 40 Processing sheet with id= P, first strand: chain 'D' and resid 49 through 51 Processing sheet with id= Q, first strand: chain 'D' and resid 84 through 88 Processing sheet with id= R, first strand: chain 'D' and resid 97 through 99 removed outlier: 4.293A pdb=" N SER D 155 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL D 189 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG D 214 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ILE D 185 " --> pdb=" O ARG D 214 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 42 through 46 removed outlier: 6.697A pdb=" N ASN D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 158 through 162 removed outlier: 6.508A pdb=" N VAL E 31 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL E 161 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL E 33 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR E 32 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU E 63 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASN E 55 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU E 42 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N THR E 53 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 44 through 46 Processing sheet with id= V, first strand: chain 'E' and resid 79 through 83 Processing sheet with id= W, first strand: chain 'E' and resid 92 through 94 removed outlier: 5.099A pdb=" N SER E 150 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL E 197 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ARG E 206 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE E 180 " --> pdb=" O ARG E 206 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.526A pdb=" N THR F 7 " --> pdb=" O SER F 22 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 10 through 12 removed outlier: 7.119A pdb=" N LYS F 108 " --> pdb=" O LEU F 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'F' and resid 90 through 95 removed outlier: 6.068A pdb=" N LEU F 42 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU F 51 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 119 through 123 removed outlier: 3.594A pdb=" N VAL F 138 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR F 178 " --> pdb=" O ASN F 143 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER F 179 " --> pdb=" O THR F 169 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 150 through 152 removed outlier: 3.520A pdb=" N LYS F 212 " --> pdb=" O CYS F 199 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.770A pdb=" N THR G 79 " --> pdb=" O ASP G 74 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 11 through 13 removed outlier: 3.568A pdb=" N ILE G 52 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY G 50 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS G 39 " --> pdb=" O ARG G 48 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ARG G 48 " --> pdb=" O LYS G 39 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 127 through 130 removed outlier: 3.714A pdb=" N GLY G 151 " --> pdb=" O TYR G 182 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR G 182 " --> pdb=" O GLY G 151 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 158 through 161 Processing sheet with id= AG, first strand: chain 'J' and resid 4 through 7 Processing sheet with id= AH, first strand: chain 'J' and resid 107 through 109 removed outlier: 4.126A pdb=" N GLY J 89 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU J 42 " --> pdb=" O LEU J 51 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU J 51 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'J' and resid 119 through 123 removed outlier: 6.153A pdb=" N TYR J 178 " --> pdb=" O ASN J 143 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'J' and resid 149 through 153 removed outlier: 3.526A pdb=" N LYS J 212 " --> pdb=" O CYS J 199 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'K' and resid 4 through 7 Processing sheet with id= AL, first strand: chain 'K' and resid 11 through 13 removed outlier: 3.712A pdb=" N ILE K 52 " --> pdb=" O ILE K 35 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY K 50 " --> pdb=" O TRP K 37 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS K 39 " --> pdb=" O ARG K 48 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ARG K 48 " --> pdb=" O LYS K 39 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ARG K 41 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU K 46 " --> pdb=" O ARG K 41 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'K' and resid 142 through 144 Processing sheet with id= AN, first strand: chain 'K' and resid 170 through 172 Processing sheet with id= AO, first strand: chain 'K' and resid 203 through 206 862 hydrogen bonds defined for protein. 2445 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: 15.78 Time building geometry restraints manager: 36.80 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: 21808 1.03 - 1.23: 847 1.23 - 1.43: 8955 1.43 - 1.63: 12717 1.63 - 1.83: 183 Bond restraints: 44510 Sorted by residual: bond pdb=" C ARG D 171 " pdb=" N VAL D 172 " ideal model delta sigma weight residual 1.334 1.368 -0.033 1.26e-02 6.30e+03 6.96e+00 bond pdb=" C ALA A 210 " pdb=" N PHE A 211 " ideal model delta sigma weight residual 1.331 1.363 -0.032 1.43e-02 4.89e+03 5.11e+00 bond pdb=" N ASP F 1 " pdb=" CA ASP F 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N ASP J 1 " pdb=" CA ASP J 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 bond pdb=" CG ARG F 216 " pdb=" CD ARG F 216 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.30e+00 ... (remaining 44505 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.03: 536 106.03 - 113.04: 52370 113.04 - 120.06: 13225 120.06 - 127.07: 13973 127.07 - 134.08: 379 Bond angle restraints: 80483 Sorted by residual: angle pdb=" CB ARG F 216 " pdb=" CG ARG F 216 " pdb=" CD ARG F 216 " ideal model delta sigma weight residual 111.30 119.07 -7.77 2.30e+00 1.89e-01 1.14e+01 angle pdb=" CA ARG F 216 " pdb=" CB ARG F 216 " pdb=" CG ARG F 216 " ideal model delta sigma weight residual 114.10 119.77 -5.67 2.00e+00 2.50e-01 8.04e+00 angle pdb=" CG ARG F 216 " pdb=" CD ARG F 216 " pdb=" NE ARG F 216 " ideal model delta sigma weight residual 112.00 117.90 -5.90 2.20e+00 2.07e-01 7.19e+00 angle pdb=" C ASP C 193 " pdb=" N SER C 194 " pdb=" CA SER C 194 " ideal model delta sigma weight residual 121.54 126.51 -4.97 1.91e+00 2.74e-01 6.78e+00 angle pdb=" N SER K 179 " pdb=" CA SER K 179 " pdb=" C SER K 179 " ideal model delta sigma weight residual 112.93 109.95 2.98 1.33e+00 5.65e-01 5.03e+00 ... (remaining 80478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.90: 19849 21.90 - 43.80: 1176 43.80 - 65.70: 217 65.70 - 87.60: 49 87.60 - 109.50: 11 Dihedral angle restraints: 21302 sinusoidal: 11498 harmonic: 9804 Sorted by residual: dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 93 " pdb=" CB CYS J 93 " ideal model delta sinusoidal sigma weight residual -86.00 -169.54 83.54 1 1.00e+01 1.00e-02 8.52e+01 dihedral pdb=" CB CYS J 139 " pdb=" SG CYS J 139 " pdb=" SG CYS J 199 " pdb=" CB CYS J 199 " ideal model delta sinusoidal sigma weight residual 93.00 167.66 -74.66 1 1.00e+01 1.00e-02 7.06e+01 dihedral pdb=" CB CYS D 135 " pdb=" SG CYS D 135 " pdb=" SG CYS D 149 " pdb=" CB CYS D 149 " ideal model delta sinusoidal sigma weight residual 93.00 33.27 59.73 1 1.00e+01 1.00e-02 4.76e+01 ... (remaining 21299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2980 0.053 - 0.106: 501 0.106 - 0.159: 108 0.159 - 0.212: 0 0.212 - 0.265: 2 Chirality restraints: 3591 Sorted by residual: chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.76e+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 -2.52 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ILE A 277 " pdb=" N ILE A 277 " pdb=" C ILE A 277 " pdb=" CB ILE A 277 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 3588 not shown) Planarity restraints: 6379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 307 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO C 308 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 308 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 308 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 313 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C VAL E 313 " 0.027 2.00e-02 2.50e+03 pdb=" O VAL E 313 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE E 314 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 213 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" C THR C 213 " 0.027 2.00e-02 2.50e+03 pdb=" O THR C 213 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE C 214 " -0.009 2.00e-02 2.50e+03 ... (remaining 6376 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.07: 579 2.07 - 2.70: 70016 2.70 - 3.33: 127433 3.33 - 3.97: 166710 3.97 - 4.60: 260417 Nonbonded interactions: 625155 Sorted by model distance: nonbonded pdb="HG13 VAL B 299 " pdb="HD13 LEU C 233 " model vdw 1.433 2.440 nonbonded pdb=" OE1 GLU F 86 " pdb=" H GLU F 86 " model vdw 1.446 1.850 nonbonded pdb=" OE1 GLU K 90 " pdb=" H GLU K 90 " model vdw 1.478 1.850 nonbonded pdb=" H ASP J 156 " pdb=" O SER J 196 " model vdw 1.545 1.850 nonbonded pdb=" OD2 ASP B 145 " pdb="HE21 GLN B 147 " model vdw 1.562 1.850 ... (remaining 625150 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 8 through 382 or resid 701 through 704)) selection = chain 'B' selection = chain 'D' } ncs_group { reference = (chain 'C' and resid 1 through 372) selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'I' } 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: 2.040 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: 0.630 Extract box with map and model: 9.120 Check model and map are aligned: 0.600 Set scattering table: 0.450 Process input model: 136.300 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 0.004 0.045 22677 Z= 0.290 Angle : 0.526 7.769 30940 Z= 0.266 Chirality : 0.043 0.265 3591 Planarity : 0.003 0.056 3808 Dihedral : 15.268 109.502 8335 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.16), residues: 2705 helix: 1.67 (0.21), residues: 646 sheet: -0.66 (0.18), residues: 801 loop : -0.55 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 101 HIS 0.003 0.001 HIS F 31 PHE 0.010 0.001 PHE D 219 TYR 0.019 0.001 TYR K 182 ARG 0.006 0.000 ARG C 155 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 3.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 PHE cc_start: 0.7145 (m-80) cc_final: 0.6604 (m-10) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.9543 time to fit residues: 200.5429 Evaluate side-chains 132 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 225 optimal weight: 6.9990 chunk 202 optimal weight: 20.0000 chunk 112 optimal weight: 0.0970 chunk 69 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 209 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 155 optimal weight: 0.3980 chunk 242 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.0539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22677 Z= 0.209 Angle : 0.498 6.671 30940 Z= 0.262 Chirality : 0.043 0.160 3591 Planarity : 0.004 0.044 3808 Dihedral : 6.596 70.643 3205 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.52 % Allowed : 10.69 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2705 helix: 2.16 (0.20), residues: 651 sheet: -0.72 (0.18), residues: 804 loop : -0.50 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 101 HIS 0.003 0.001 HIS A 305 PHE 0.009 0.001 PHE E 369 TYR 0.019 0.001 TYR K 182 ARG 0.004 0.000 ARG C 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 4.079 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: 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: C 241 MET cc_start: 0.8260 (mmp) cc_final: 0.7990 (mmp) REVERT: D 169 HIS cc_start: 0.7621 (OUTLIER) cc_final: 0.7281 (p-80) REVERT: J 82 ARG cc_start: 0.7067 (ttp80) cc_final: 0.6652 (ttp80) REVERT: K 142 MET cc_start: 0.7161 (mmm) cc_final: 0.6856 (mmm) outliers start: 13 outliers final: 5 residues processed: 151 average time/residue: 1.0082 time to fit residues: 231.9753 Evaluate side-chains 137 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 3.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain K residue 214 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 134 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 201 optimal weight: 20.0000 chunk 165 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 242 optimal weight: 10.0000 chunk 262 optimal weight: 9.9990 chunk 216 optimal weight: 7.9990 chunk 240 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 371 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 22677 Z= 0.316 Angle : 0.505 5.024 30940 Z= 0.263 Chirality : 0.043 0.142 3591 Planarity : 0.004 0.038 3808 Dihedral : 5.145 46.275 3205 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.84 % Allowed : 11.53 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.16), residues: 2705 helix: 2.23 (0.20), residues: 651 sheet: -0.80 (0.18), residues: 807 loop : -0.59 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 161 HIS 0.004 0.001 HIS A 305 PHE 0.010 0.001 PHE A 142 TYR 0.009 0.001 TYR E 275 ARG 0.003 0.000 ARG C 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 3.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 PHE cc_start: 0.7172 (m-80) cc_final: 0.6635 (m-10) REVERT: B 371 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7473 (mt) REVERT: C 241 MET cc_start: 0.8296 (mmp) cc_final: 0.8055 (mmp) REVERT: D 169 HIS cc_start: 0.7719 (OUTLIER) cc_final: 0.7314 (p-80) outliers start: 21 outliers final: 11 residues processed: 152 average time/residue: 0.8745 time to fit residues: 201.7467 Evaluate side-chains 142 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 3.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain K residue 214 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 239 optimal weight: 20.0000 chunk 182 optimal weight: 0.9990 chunk 126 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 243 optimal weight: 20.0000 chunk 258 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 231 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22677 Z= 0.255 Angle : 0.480 4.509 30940 Z= 0.249 Chirality : 0.043 0.139 3591 Planarity : 0.004 0.051 3808 Dihedral : 4.510 40.400 3205 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.76 % Allowed : 12.17 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2705 helix: 2.32 (0.20), residues: 651 sheet: -0.75 (0.18), residues: 803 loop : -0.59 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 168 HIS 0.003 0.001 HIS E 297 PHE 0.010 0.001 PHE B 290 TYR 0.010 0.001 TYR K 105 ARG 0.002 0.000 ARG J 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 3.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 371 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7502 (mt) REVERT: C 241 MET cc_start: 0.8259 (mmp) cc_final: 0.8056 (mmp) REVERT: D 169 HIS cc_start: 0.7766 (OUTLIER) cc_final: 0.7387 (p-80) REVERT: E 77 MET cc_start: 0.8337 (mtm) cc_final: 0.8091 (mtm) outliers start: 19 outliers final: 13 residues processed: 154 average time/residue: 0.8752 time to fit residues: 204.5977 Evaluate side-chains 148 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain J residue 139 CYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain K residue 214 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 214 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 192 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 220 optimal weight: 40.0000 chunk 178 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 231 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 22677 Z= 0.401 Angle : 0.521 6.261 30940 Z= 0.272 Chirality : 0.044 0.144 3591 Planarity : 0.004 0.045 3808 Dihedral : 4.513 45.478 3205 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.16 % Allowed : 12.77 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2705 helix: 2.18 (0.20), residues: 651 sheet: -0.85 (0.17), residues: 807 loop : -0.66 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 101 HIS 0.004 0.001 HIS F 31 PHE 0.012 0.001 PHE D 219 TYR 0.011 0.001 TYR D 100 ARG 0.004 0.000 ARG J 82 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 135 time to evaluate : 3.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.9162 (tttt) cc_final: 0.8896 (tttp) REVERT: A 286 PHE cc_start: 0.7194 (m-80) cc_final: 0.6706 (m-10) REVERT: B 371 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7521 (mt) REVERT: D 169 HIS cc_start: 0.7794 (OUTLIER) cc_final: 0.7334 (p-80) REVERT: E 77 MET cc_start: 0.8387 (mtm) cc_final: 0.8174 (mtm) REVERT: J 41 TYR cc_start: 0.8616 (m-80) cc_final: 0.8262 (m-80) outliers start: 29 outliers final: 23 residues processed: 161 average time/residue: 0.8735 time to fit residues: 214.1860 Evaluate side-chains 154 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 3.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain J residue 139 CYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain K residue 214 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 0.7980 chunk 232 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 258 optimal weight: 7.9990 chunk 214 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22677 Z= 0.205 Angle : 0.468 5.132 30940 Z= 0.242 Chirality : 0.042 0.138 3591 Planarity : 0.004 0.048 3808 Dihedral : 4.338 41.765 3205 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.28 % Allowed : 12.85 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.16), residues: 2705 helix: 2.35 (0.20), residues: 651 sheet: -0.82 (0.17), residues: 807 loop : -0.58 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 101 HIS 0.004 0.001 HIS E 297 PHE 0.009 0.001 PHE A 142 TYR 0.016 0.001 TYR K 182 ARG 0.004 0.000 ARG J 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 3.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.9112 (tttt) cc_final: 0.8854 (tttp) REVERT: B 371 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7487 (mt) REVERT: D 169 HIS cc_start: 0.7785 (OUTLIER) cc_final: 0.7332 (p-80) REVERT: E 77 MET cc_start: 0.8351 (mtm) cc_final: 0.8124 (mtm) REVERT: J 41 TYR cc_start: 0.8473 (m-80) cc_final: 0.8103 (m-80) outliers start: 32 outliers final: 25 residues processed: 162 average time/residue: 0.8778 time to fit residues: 217.8541 Evaluate side-chains 157 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 4.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 192 GLU Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 139 CYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain K residue 214 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 249 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 217 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 257 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 371 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22677 Z= 0.255 Angle : 0.477 6.336 30940 Z= 0.246 Chirality : 0.042 0.140 3591 Planarity : 0.004 0.057 3808 Dihedral : 4.293 41.268 3205 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.44 % Allowed : 12.85 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.17), residues: 2705 helix: 2.37 (0.20), residues: 651 sheet: -0.92 (0.17), residues: 849 loop : -0.51 (0.19), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 101 HIS 0.004 0.001 HIS E 297 PHE 0.010 0.001 PHE A 142 TYR 0.019 0.001 TYR K 182 ARG 0.004 0.000 ARG J 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 4.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.9107 (tttt) cc_final: 0.8768 (tttp) REVERT: D 169 HIS cc_start: 0.7883 (OUTLIER) cc_final: 0.7463 (p-80) REVERT: E 77 MET cc_start: 0.8358 (mtm) cc_final: 0.8155 (mtm) REVERT: J 41 TYR cc_start: 0.8484 (m-80) cc_final: 0.8107 (m-80) REVERT: J 82 ARG cc_start: 0.7259 (ttp80) cc_final: 0.6963 (ttp80) outliers start: 36 outliers final: 29 residues processed: 169 average time/residue: 0.9219 time to fit residues: 238.5186 Evaluate side-chains 161 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 131 time to evaluate : 4.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 192 GLU Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 139 CYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain K residue 214 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 159 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 163 optimal weight: 0.0370 chunk 175 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22677 Z= 0.184 Angle : 0.459 5.720 30940 Z= 0.236 Chirality : 0.042 0.137 3591 Planarity : 0.004 0.051 3808 Dihedral : 4.197 38.369 3205 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.12 % Allowed : 13.05 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.17), residues: 2705 helix: 2.47 (0.20), residues: 651 sheet: -0.89 (0.17), residues: 849 loop : -0.45 (0.19), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 161 HIS 0.004 0.001 HIS E 297 PHE 0.008 0.001 PHE A 361 TYR 0.014 0.001 TYR K 182 ARG 0.010 0.000 ARG C 155 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 3.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.9086 (tttt) cc_final: 0.8722 (tttp) REVERT: B 371 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7531 (mt) REVERT: D 169 HIS cc_start: 0.7819 (OUTLIER) cc_final: 0.7323 (p-80) REVERT: J 41 TYR cc_start: 0.8422 (m-80) cc_final: 0.8023 (m-80) REVERT: J 82 ARG cc_start: 0.7256 (ttp80) cc_final: 0.7001 (ttp80) outliers start: 28 outliers final: 23 residues processed: 161 average time/residue: 0.8529 time to fit residues: 210.7195 Evaluate side-chains 157 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 3.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 139 CYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain K residue 214 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 234 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 239 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 216 optimal weight: 10.0000 chunk 226 optimal weight: 5.9990 chunk 238 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 22677 Z= 0.369 Angle : 0.518 10.246 30940 Z= 0.268 Chirality : 0.043 0.144 3591 Planarity : 0.004 0.045 3808 Dihedral : 4.416 43.631 3205 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.32 % Allowed : 13.05 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.02 (0.16), residues: 2705 helix: 2.32 (0.20), residues: 651 sheet: -0.82 (0.18), residues: 801 loop : -0.65 (0.18), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 101 HIS 0.004 0.001 HIS B 9 PHE 0.013 0.001 PHE A 290 TYR 0.011 0.001 TYR D 100 ARG 0.005 0.000 ARG J 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 130 time to evaluate : 3.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.9139 (tttt) cc_final: 0.8777 (tttp) REVERT: A 286 PHE cc_start: 0.7113 (m-80) cc_final: 0.6619 (m-10) REVERT: B 371 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7543 (mt) REVERT: D 169 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.7429 (p-80) REVERT: J 41 TYR cc_start: 0.8486 (m-80) cc_final: 0.8167 (m-80) REVERT: J 82 ARG cc_start: 0.7264 (ttp80) cc_final: 0.6990 (ttp80) outliers start: 33 outliers final: 28 residues processed: 161 average time/residue: 0.8567 time to fit residues: 211.9451 Evaluate side-chains 157 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 3.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 139 CYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain K residue 214 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 157 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 266 optimal weight: 20.0000 chunk 244 optimal weight: 8.9990 chunk 211 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 22677 Z= 0.253 Angle : 0.487 11.902 30940 Z= 0.250 Chirality : 0.043 0.140 3591 Planarity : 0.004 0.049 3808 Dihedral : 4.375 42.396 3205 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.16 % Allowed : 13.09 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.17), residues: 2705 helix: 2.37 (0.20), residues: 651 sheet: -0.89 (0.17), residues: 845 loop : -0.51 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 101 HIS 0.004 0.001 HIS E 297 PHE 0.010 0.001 PHE A 142 TYR 0.013 0.001 TYR K 182 ARG 0.005 0.000 ARG J 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 135 time to evaluate : 3.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.9098 (tttt) cc_final: 0.8743 (tttp) REVERT: A 286 PHE cc_start: 0.7074 (m-80) cc_final: 0.6593 (m-10) REVERT: B 371 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7538 (mt) REVERT: C 241 MET cc_start: 0.8189 (mmp) cc_final: 0.7726 (mmp) REVERT: D 169 HIS cc_start: 0.7835 (OUTLIER) cc_final: 0.7339 (p-80) REVERT: J 82 ARG cc_start: 0.7267 (ttp80) cc_final: 0.6994 (ttp80) outliers start: 29 outliers final: 27 residues processed: 163 average time/residue: 0.8585 time to fit residues: 213.7912 Evaluate side-chains 160 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 131 time to evaluate : 3.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 139 CYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain K residue 214 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 168 optimal weight: 2.9990 chunk 225 optimal weight: 8.9990 chunk 64 optimal weight: 0.0570 chunk 195 optimal weight: 20.0000 chunk 31 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 212 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 217 optimal weight: 30.0000 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.103345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.072236 restraints weight = 122604.533| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.57 r_work: 0.2833 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.101 22677 Z= 0.147 Angle : 0.460 10.850 30940 Z= 0.236 Chirality : 0.042 0.138 3591 Planarity : 0.004 0.047 3808 Dihedral : 4.146 40.796 3205 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.80 % Allowed : 13.57 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.24 (0.17), residues: 2705 helix: 2.58 (0.20), residues: 651 sheet: -0.77 (0.17), residues: 819 loop : -0.41 (0.18), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 355 HIS 0.004 0.001 HIS E 297 PHE 0.009 0.001 PHE A 290 TYR 0.011 0.001 TYR K 182 ARG 0.006 0.000 ARG J 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7899.26 seconds wall clock time: 337 minutes 53.87 seconds (20273.87 seconds total)