Starting phenix.real_space_refine on Sat Feb 24 13:47:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st2_40755/02_2024/8st2_40755_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st2_40755/02_2024/8st2_40755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st2_40755/02_2024/8st2_40755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st2_40755/02_2024/8st2_40755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st2_40755/02_2024/8st2_40755_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st2_40755/02_2024/8st2_40755_trim_updated.pdb" } resolution = 2.94 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= 0.007 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: 6 Type Number sf(0) Gaussians S 120 5.16 5 Na 1 4.78 5 C 14419 2.51 5 N 3599 2.21 5 O 4108 1.98 5 H 21937 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 198": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "F GLU 39": "OE1" <-> "OE2" Residue "F TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 86": "OE1" <-> "OE2" Residue "G GLU 198": "OE1" <-> "OE2" Residue "J GLU 39": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 44184 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 6257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 6257 Classifications: {'peptide': 379} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 359} Chain: "B" Number of atoms: 6257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 6257 Classifications: {'peptide': 379} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 359} Chain: "C" Number of atoms: 5995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 5995 Classifications: {'peptide': 366} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 343} Chain breaks: 1 Chain: "D" Number of atoms: 6257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 6257 Classifications: {'peptide': 379} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 359} Chain: "E" Number of atoms: 5995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 5995 Classifications: {'peptide': 366} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 343} 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: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {'ACH': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {'ACH': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {'ACH': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" 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: 19.36, per 1000 atoms: 0.44 Number of scatterers: 44184 At special positions: 0 Unit cell: (125.12, 203.186, 145.438, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 120 16.00 Na 1 11.00 O 4108 8.00 N 3599 7.00 C 14419 6.00 H 21937 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=2.04 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 200 " distance=2.05 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.04 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=2.03 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 81 " " NAG A 703 " - " ASN A 148 " " NAG B 701 " - " ASN B 31 " " NAG B 702 " - " ASN B 81 " " NAG B 703 " - " ASN B 148 " " NAG D 701 " - " ASN D 31 " " NAG D 702 " - " ASN D 81 " " NAG D 703 " - " ASN D 148 " " NAG H 1 " - " ASN C 143 " " NAG I 1 " - " ASN E 143 " Time building additional restraints: 39.53 Conformation dependent library (CDL) restraints added in 4.8 seconds 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5248 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 43 sheets defined 27.5% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.24 Creating SS restraints... Processing helix chain 'A' and resid 7 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 223 Processing helix chain 'A' and resid 225 through 234 removed outlier: 3.747A 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: 5.587A 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 removed outlier: 3.575A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET A 355 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Proline residue: A 379 - end of helix Processing helix chain 'B' and resid 7 through 18 removed outlier: 4.017A pdb=" N GLU B 12 " --> pdb=" O ALA B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 219 through 223 Processing helix chain 'B' and resid 225 through 235 removed outlier: 3.722A pdb=" N LEU B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR B 235 " --> pdb=" O ILE B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' 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 321 Processing helix chain 'B' and resid 325 through 329 Processing helix chain 'B' and resid 345 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: 4.364A pdb=" N ILE C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Proline residue: C 219 - end of helix removed outlier: 3.685A pdb=" N LEU C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 231 Processing helix chain 'C' and resid 235 through 237 No H-bonds generated for 'chain 'C' and resid 235 through 237' 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: 5.853A 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: 4.380A pdb=" N THR C 365 " --> pdb=" O CYS C 361 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE C 366 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY C 367 " --> pdb=" O PHE C 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 18 Processing helix chain 'D' and resid 76 through 78 No H-bonds generated for 'chain 'D' and resid 76 through 78' 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: 4.573A pdb=" N ILE D 226 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Proline residue: D 227 - end of helix removed outlier: 3.781A pdb=" N LEU D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix 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 268 removed outlier: 3.562A pdb=" N GLU D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 305 Processing helix chain 'D' and resid 316 through 329 removed outlier: 5.505A 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: 3.853A pdb=" N LEU E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA E 227 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE E 228 " --> pdb=" O THR E 224 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU E 229 " --> pdb=" O SER E 225 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL E 230 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N PHE E 231 " --> pdb=" O ALA E 227 " (cutoff:3.500A) removed outlier: 4.137A 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: 3.832A pdb=" N THR E 365 " --> pdb=" O CYS E 361 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE E 366 " --> pdb=" O VAL E 362 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY E 367 " --> pdb=" O PHE E 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 87 No H-bonds generated for 'chain 'F' and resid 85 through 87' Processing helix chain 'F' and resid 127 through 132 Processing helix chain 'F' and resid 155 through 157 No H-bonds generated for 'chain 'F' and resid 155 through 157' 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 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' 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 63 through 65 No H-bonds generated for 'chain 'K' and resid 63 through 65' Processing helix chain 'K' and resid 162 through 164 No H-bonds generated for 'chain 'K' and resid 162 through 164' Processing helix chain 'K' and resid 192 through 195 No H-bonds generated for 'chain 'K' and resid 192 through 195' Processing helix chain 'K' and resid 207 through 209 No H-bonds generated for 'chain 'K' and resid 207 through 209' Processing sheet with id= A, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.134A pdb=" N VAL A 36 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL A 166 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL A 38 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU A 37 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N HIS A 68 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.948A 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: 4.333A pdb=" N SER A 155 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 189 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG A 214 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.479A 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 122 through 134 removed outlier: 6.323A pdb=" N TRP B 62 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ILE B 44 " --> pdb=" O TRP B 62 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS B 64 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU B 42 " --> pdb=" O LYS B 64 " (cutoff:3.500A) 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: 4.340A pdb=" N SER B 155 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 189 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ARG B 214 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ILE B 185 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 158 through 162 removed outlier: 6.680A pdb=" N VAL C 31 " --> pdb=" O ASP C 159 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL C 161 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL C 33 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN C 55 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU C 42 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR C 53 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 44 through 46 Processing sheet with id= K, first strand: chain 'C' and resid 79 through 83 Processing sheet with id= L, first strand: chain 'C' and resid 92 through 94 removed outlier: 5.190A pdb=" N SER C 150 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL C 197 " --> pdb=" O SER C 150 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 178 through 182 removed outlier: 6.802A pdb=" N ILE C 204 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 163 through 167 removed outlier: 5.983A pdb=" N VAL D 36 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL D 166 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL D 38 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU D 37 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N HIS D 68 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASN D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR D 58 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 49 through 51 Processing sheet with id= P, first strand: chain 'D' and resid 84 through 88 Processing sheet with id= Q, first strand: chain 'D' and resid 97 through 99 removed outlier: 4.454A pdb=" N SER D 155 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG D 195 " --> pdb=" O TYR D 204 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL D 189 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG D 214 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE D 185 " --> pdb=" O ARG D 214 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 158 through 162 removed outlier: 6.530A pdb=" N VAL E 31 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL E 161 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL E 33 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR E 32 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU E 63 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN E 55 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU E 42 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR E 53 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 44 through 46 Processing sheet with id= T, first strand: chain 'E' and resid 79 through 83 Processing sheet with id= U, first strand: chain 'E' and resid 92 through 94 removed outlier: 5.157A pdb=" N SER E 150 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL E 197 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ARG E 206 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE E 180 " --> pdb=" O ARG E 206 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 4 through 7 Processing sheet with id= W, first strand: chain 'F' and resid 10 through 12 removed outlier: 7.414A pdb=" N LYS F 108 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY F 89 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU F 42 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU F 51 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 119 through 123 Processing sheet with id= Y, first strand: chain 'F' and resid 149 through 152 removed outlier: 3.573A pdb=" N LYS F 152 " --> pdb=" O GLU F 200 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 153 through 155 removed outlier: 3.951A pdb=" N TRP F 153 " --> pdb=" O ARG F 160 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 4 through 7 Processing sheet with id= AB, first strand: chain 'G' and resid 11 through 13 removed outlier: 3.651A pdb=" N GLY G 50 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LYS G 39 " --> pdb=" O ARG G 48 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ARG G 48 " --> pdb=" O LYS G 39 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 142 through 144 Processing sheet with id= AD, first strand: chain 'G' and resid 170 through 172 Processing sheet with id= AE, first strand: chain 'G' and resid 203 through 206 removed outlier: 3.512A pdb=" N VAL G 204 " --> pdb=" O VAL G 213 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'J' and resid 4 through 7 Processing sheet with id= AG, first strand: chain 'J' and resid 10 through 12 removed outlier: 7.138A pdb=" N LYS J 108 " --> pdb=" O LEU J 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'J' and resid 90 through 95 removed outlier: 3.510A pdb=" N ILE J 53 " --> pdb=" O TRP J 40 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU J 42 " --> pdb=" O LEU J 51 " (cutoff:3.500A) removed outlier: 5.427A 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: 3.587A pdb=" N ASN J 142 " --> pdb=" O THR J 119 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL J 138 " --> pdb=" O PHE J 123 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'J' and resid 149 through 152 Processing sheet with id= AK, first strand: chain 'J' and resid 167 through 169 removed outlier: 3.740A pdb=" N SER J 179 " --> pdb=" O THR J 169 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'J' and resid 196 through 198 Processing sheet with id= AM, first strand: chain 'K' and resid 4 through 7 Processing sheet with id= AN, first strand: chain 'K' and resid 11 through 13 removed outlier: 3.634A pdb=" N GLY K 50 " --> pdb=" O TRP K 37 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LYS K 39 " --> pdb=" O ARG K 48 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ARG K 48 " --> pdb=" O LYS K 39 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'K' and resid 142 through 144 removed outlier: 4.022A pdb=" N VAL K 143 " --> pdb=" O VAL K 190 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL K 190 " --> pdb=" O VAL K 143 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'K' and resid 158 through 161 Processing sheet with id= AQ, first strand: chain 'K' and resid 147 through 152 removed outlier: 6.290A pdb=" N TYR K 182 " --> pdb=" O GLY K 151 " (cutoff:3.500A) 842 hydrogen bonds defined for protein. 2382 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: 18.57 Time building geometry restraints manager: 40.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 21912 1.04 - 1.24: 2939 1.24 - 1.45: 7032 1.45 - 1.65: 12708 1.65 - 1.85: 183 Bond restraints: 44774 Sorted by residual: bond pdb=" C VAL A 189 " pdb=" N GLY A 190 " ideal model delta sigma weight residual 1.332 1.344 -0.012 6.60e-03 2.30e+04 3.07e+00 bond pdb=" N ASP F 1 " pdb=" CA ASP F 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N ASP J 1 " pdb=" CA ASP J 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.72e+00 bond pdb=" N ASP J 1 " pdb=" H ASP J 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" N ASP F 1 " pdb=" H ASP F 1 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.17e+00 ... (remaining 44769 not shown) Histogram of bond angle deviations from ideal: 98.49 - 105.60: 512 105.60 - 112.71: 52329 112.71 - 119.83: 11392 119.83 - 126.94: 16285 126.94 - 134.05: 417 Bond angle restraints: 80935 Sorted by residual: angle pdb=" CB ARG F 24 " pdb=" CG ARG F 24 " pdb=" CD ARG F 24 " ideal model delta sigma weight residual 111.30 119.04 -7.74 2.30e+00 1.89e-01 1.13e+01 angle pdb=" N PRO B 380 " pdb=" CD PRO B 380 " pdb=" CG PRO B 380 " ideal model delta sigma weight residual 103.20 98.49 4.71 1.50e+00 4.44e-01 9.86e+00 angle pdb=" N ASP G 180 " pdb=" CA ASP G 180 " pdb=" C ASP G 180 " ideal model delta sigma weight residual 114.39 110.24 4.15 1.45e+00 4.76e-01 8.20e+00 angle pdb=" CB MET E 241 " pdb=" CG MET E 241 " pdb=" SD MET E 241 " ideal model delta sigma weight residual 112.70 120.84 -8.14 3.00e+00 1.11e-01 7.36e+00 angle pdb=" CA PRO B 380 " pdb=" N PRO B 380 " pdb=" CD PRO B 380 " ideal model delta sigma weight residual 112.00 108.39 3.61 1.40e+00 5.10e-01 6.64e+00 ... (remaining 80930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.70: 19947 21.70 - 43.41: 1220 43.41 - 65.11: 245 65.11 - 86.81: 45 86.81 - 108.52: 10 Dihedral angle restraints: 21467 sinusoidal: 11615 harmonic: 9852 Sorted by residual: dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 93 " pdb=" CB CYS F 93 " ideal model delta sinusoidal sigma weight residual 93.00 160.46 -67.46 1 1.00e+01 1.00e-02 5.92e+01 dihedral pdb=" CB CYS C 130 " pdb=" SG CYS C 130 " pdb=" SG CYS C 144 " pdb=" CB CYS C 144 " ideal model delta sinusoidal sigma weight residual 93.00 38.10 54.90 1 1.00e+01 1.00e-02 4.08e+01 dihedral pdb=" CB CYS B 135 " pdb=" SG CYS B 135 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 38.30 54.70 1 1.00e+01 1.00e-02 4.05e+01 ... (remaining 21464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2929 0.052 - 0.105: 576 0.105 - 0.157: 115 0.157 - 0.210: 1 0.210 - 0.262: 2 Chirality restraints: 3623 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 0.26 2.00e-01 2.50e+01 1.72e+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 -2.53 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB ILE A 226 " pdb=" CA ILE A 226 " pdb=" CG1 ILE A 226 " pdb=" CG2 ILE A 226 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.77e-01 ... (remaining 3620 not shown) Planarity restraints: 6421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 379 " -0.047 5.00e-02 4.00e+02 7.00e-02 7.83e+00 pdb=" N PRO B 380 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 380 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 380 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 379 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO A 380 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 380 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 380 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 218 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C LEU A 218 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU A 218 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE A 219 " -0.010 2.00e-02 2.50e+03 ... (remaining 6418 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.79: 84 1.79 - 2.49: 31866 2.49 - 3.20: 133262 3.20 - 3.90: 180672 3.90 - 4.60: 285012 Nonbonded interactions: 630896 Sorted by model distance: nonbonded pdb=" O PRO B 242 " pdb=" HG CYS B 245 " model vdw 1.088 2.620 nonbonded pdb=" O PRO C 234 " pdb=" HG CYS C 237 " model vdw 1.249 2.620 nonbonded pdb=" OE1 GLU F 86 " pdb=" H GLU F 86 " model vdw 1.441 1.850 nonbonded pdb=" OD1 ASN F 142 " pdb="HD22 ASN F 143 " model vdw 1.442 1.850 nonbonded pdb=" O THR B 6 " pdb=" H ALA B 10 " model vdw 1.518 1.850 ... (remaining 630891 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = (chain 'E' and resid 1 through 372) } 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.640 Extract box with map and model: 8.290 Check model and map are aligned: 0.660 Set scattering table: 0.400 Process input model: 146.030 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.280 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:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 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 : 0.005 0.057 22837 Z= 0.317 Angle : 0.546 8.137 31156 Z= 0.275 Chirality : 0.044 0.262 3623 Planarity : 0.004 0.070 3833 Dihedral : 15.403 108.517 8443 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % 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: 0.11 (0.17), residues: 2719 helix: 1.43 (0.21), residues: 674 sheet: -0.24 (0.18), residues: 762 loop : -0.36 (0.18), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 317 HIS 0.006 0.001 HIS E 46 PHE 0.017 0.001 PHE A 290 TYR 0.021 0.001 TYR K 103 ARG 0.010 0.001 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 3.573 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: F 24 ARG cc_start: 0.7472 (mtp-110) cc_final: 0.7159 (ttp80) REVERT: J 9 LEU cc_start: 0.8784 (mm) cc_final: 0.8325 (tp) REVERT: J 24 ARG cc_start: 0.7367 (mtp-110) cc_final: 0.6916 (ttp-110) REVERT: J 66 ARG cc_start: 0.7484 (ptp-170) cc_final: 0.6927 (ptp-170) REVERT: J 215 ASN cc_start: 0.6637 (t0) cc_final: 0.6318 (t0) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 2.8227 time to fit residues: 748.4937 Evaluate side-chains 190 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 3.689 ------------------------------------------------------------------------------- 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: 8.9990 chunk 202 optimal weight: 30.0000 chunk 112 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 209 optimal weight: 0.1980 chunk 80 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 242 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22837 Z= 0.192 Angle : 0.512 5.772 31156 Z= 0.267 Chirality : 0.043 0.164 3623 Planarity : 0.004 0.043 3833 Dihedral : 6.403 67.598 3285 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.84 % Allowed : 13.67 % Favored : 85.49 % 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: 0.28 (0.17), residues: 2719 helix: 1.90 (0.21), residues: 669 sheet: -0.27 (0.18), residues: 771 loop : -0.37 (0.18), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 62 HIS 0.003 0.001 HIS E 297 PHE 0.016 0.001 PHE F 214 TYR 0.014 0.001 TYR J 145 ARG 0.006 0.000 ARG F 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 208 time to evaluate : 3.655 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: C 36 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8504 (tpt) REVERT: F 24 ARG cc_start: 0.7489 (mtp-110) cc_final: 0.7138 (ttp80) REVERT: J 9 LEU cc_start: 0.8756 (mm) cc_final: 0.8379 (tt) REVERT: J 24 ARG cc_start: 0.7216 (mtp-110) cc_final: 0.6803 (ttp-110) REVERT: J 66 ARG cc_start: 0.7496 (ptp-170) cc_final: 0.6953 (ptp-170) REVERT: J 215 ASN cc_start: 0.6726 (t0) cc_final: 0.6488 (t0) outliers start: 21 outliers final: 12 residues processed: 216 average time/residue: 2.6866 time to fit residues: 675.0858 Evaluate side-chains 209 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 196 time to evaluate : 3.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain C residue 1 THR Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 194 HIS 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: 2.9990 chunk 201 optimal weight: 20.0000 chunk 165 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 242 optimal weight: 10.0000 chunk 262 optimal weight: 20.0000 chunk 216 optimal weight: 3.9990 chunk 240 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 171 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 22837 Z= 0.334 Angle : 0.529 5.897 31156 Z= 0.276 Chirality : 0.044 0.157 3623 Planarity : 0.004 0.040 3833 Dihedral : 5.662 53.223 3285 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.24 % Allowed : 14.51 % Favored : 84.26 % 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: 0.20 (0.16), residues: 2719 helix: 1.85 (0.21), residues: 669 sheet: -0.26 (0.18), residues: 762 loop : -0.47 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 317 HIS 0.005 0.001 HIS B 111 PHE 0.018 0.001 PHE F 144 TYR 0.018 0.002 TYR G 105 ARG 0.004 0.000 ARG F 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 194 time to evaluate : 3.833 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 358 ASP cc_start: 0.8126 (t70) cc_final: 0.7846 (t0) REVERT: C 36 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8437 (tmm) REVERT: C 101 MET cc_start: 0.8745 (tpt) cc_final: 0.8475 (tpt) REVERT: E 241 MET cc_start: 0.9006 (mmp) cc_final: 0.8695 (mmp) REVERT: J 9 LEU cc_start: 0.8741 (mm) cc_final: 0.8389 (tt) REVERT: J 24 ARG cc_start: 0.7382 (mtp-110) cc_final: 0.6972 (ttp-110) REVERT: J 66 ARG cc_start: 0.7523 (ptp-170) cc_final: 0.6946 (ptp90) REVERT: J 215 ASN cc_start: 0.6849 (t0) cc_final: 0.6579 (t0) outliers start: 31 outliers final: 19 residues processed: 215 average time/residue: 2.5977 time to fit residues: 654.4397 Evaluate side-chains 207 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 187 time to evaluate : 3.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain C residue 1 THR Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 194 HIS Chi-restraints excluded: chain K residue 63 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 239 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 243 optimal weight: 20.0000 chunk 258 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 231 optimal weight: 7.9990 chunk 69 optimal weight: 0.2980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 ASN G 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 22837 Z= 0.255 Angle : 0.505 5.709 31156 Z= 0.262 Chirality : 0.043 0.153 3623 Planarity : 0.004 0.041 3833 Dihedral : 4.902 35.672 3285 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.43 % Allowed : 14.87 % Favored : 83.70 % 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: 0.23 (0.16), residues: 2719 helix: 1.89 (0.21), residues: 672 sheet: -0.26 (0.18), residues: 753 loop : -0.44 (0.18), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 317 HIS 0.004 0.001 HIS E 297 PHE 0.023 0.001 PHE F 144 TYR 0.015 0.001 TYR C 275 ARG 0.004 0.000 ARG J 216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 203 time to evaluate : 3.741 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 358 ASP cc_start: 0.8102 (t70) cc_final: 0.7825 (t0) REVERT: C 36 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8383 (tmm) REVERT: E 241 MET cc_start: 0.8952 (mmp) cc_final: 0.8536 (mmp) REVERT: J 9 LEU cc_start: 0.8780 (mm) cc_final: 0.8417 (tt) REVERT: J 24 ARG cc_start: 0.7285 (mtp-110) cc_final: 0.6842 (ttp-110) REVERT: J 66 ARG cc_start: 0.7486 (ptp-170) cc_final: 0.6894 (ptp90) outliers start: 36 outliers final: 27 residues processed: 227 average time/residue: 2.3624 time to fit residues: 634.4593 Evaluate side-chains 222 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 194 time to evaluate : 3.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain C residue 1 THR Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 202 CYS Chi-restraints excluded: chain J residue 1 ASP Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 139 CYS Chi-restraints excluded: chain J residue 194 HIS Chi-restraints excluded: chain K residue 63 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 214 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 192 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 220 optimal weight: 30.0000 chunk 178 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 22837 Z= 0.247 Angle : 0.497 5.599 31156 Z= 0.257 Chirality : 0.043 0.152 3623 Planarity : 0.004 0.042 3833 Dihedral : 4.594 35.427 3285 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.43 % Allowed : 15.11 % Favored : 83.46 % 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: 0.27 (0.16), residues: 2719 helix: 1.92 (0.21), residues: 675 sheet: -0.25 (0.18), residues: 753 loop : -0.42 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 317 HIS 0.004 0.001 HIS E 297 PHE 0.021 0.001 PHE F 214 TYR 0.016 0.001 TYR G 105 ARG 0.002 0.000 ARG F 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 200 time to evaluate : 3.411 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 358 ASP cc_start: 0.8096 (t70) cc_final: 0.7834 (t0) REVERT: C 36 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8373 (tmm) REVERT: F 18 GLN cc_start: 0.7680 (tm-30) cc_final: 0.7453 (tm-30) REVERT: J 9 LEU cc_start: 0.8814 (mm) cc_final: 0.8426 (tt) REVERT: J 24 ARG cc_start: 0.7278 (mtp-110) cc_final: 0.6837 (ttp-110) REVERT: J 66 ARG cc_start: 0.7516 (ptp-170) cc_final: 0.7153 (ptp90) outliers start: 36 outliers final: 28 residues processed: 224 average time/residue: 2.3639 time to fit residues: 627.0310 Evaluate side-chains 222 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 193 time to evaluate : 3.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain C residue 1 THR Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 202 CYS Chi-restraints excluded: chain J residue 1 ASP Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 139 CYS Chi-restraints excluded: chain J residue 194 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 0.8980 chunk 232 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 258 optimal weight: 10.0000 chunk 214 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22837 Z= 0.177 Angle : 0.475 6.145 31156 Z= 0.245 Chirality : 0.042 0.152 3623 Planarity : 0.004 0.042 3833 Dihedral : 4.323 23.918 3285 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.39 % Allowed : 15.23 % Favored : 83.38 % 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: 0.39 (0.17), residues: 2719 helix: 2.07 (0.21), residues: 675 sheet: -0.22 (0.18), residues: 753 loop : -0.34 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 161 HIS 0.003 0.000 HIS E 297 PHE 0.013 0.001 PHE F 214 TYR 0.016 0.001 TYR G 152 ARG 0.003 0.000 ARG F 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 202 time to evaluate : 3.663 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 358 ASP cc_start: 0.8080 (t70) cc_final: 0.7817 (t0) REVERT: F 18 GLN cc_start: 0.7643 (tm-30) cc_final: 0.7409 (tm-30) REVERT: J 66 ARG cc_start: 0.7571 (ptp-170) cc_final: 0.7161 (ptp-170) outliers start: 35 outliers final: 25 residues processed: 225 average time/residue: 2.4306 time to fit residues: 648.5297 Evaluate side-chains 218 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 193 time to evaluate : 3.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain C residue 1 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 202 CYS Chi-restraints excluded: chain J residue 1 ASP Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 139 CYS Chi-restraints excluded: chain J residue 194 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 249 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 217 optimal weight: 50.0000 chunk 144 optimal weight: 3.9990 chunk 257 optimal weight: 6.9990 chunk 161 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 HIS E 371 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22837 Z= 0.283 Angle : 0.506 6.574 31156 Z= 0.261 Chirality : 0.043 0.150 3623 Planarity : 0.004 0.041 3833 Dihedral : 4.395 25.083 3285 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.75 % Allowed : 15.11 % Favored : 83.14 % 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: 0.23 (0.16), residues: 2719 helix: 1.79 (0.21), residues: 693 sheet: -0.22 (0.18), residues: 753 loop : -0.47 (0.18), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 161 HIS 0.005 0.001 HIS E 297 PHE 0.023 0.001 PHE F 144 TYR 0.016 0.001 TYR G 105 ARG 0.003 0.000 ARG D 195 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 188 time to evaluate : 4.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ASP cc_start: 0.8094 (t70) cc_final: 0.7836 (t0) REVERT: E 16 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7071 (ptt90) REVERT: E 36 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8725 (ttt) REVERT: F 18 GLN cc_start: 0.7661 (tm-30) cc_final: 0.7416 (tm-30) REVERT: F 150 ASN cc_start: 0.7107 (t0) cc_final: 0.6884 (m-40) REVERT: J 128 GLU cc_start: 0.8978 (mp0) cc_final: 0.8616 (mp0) outliers start: 44 outliers final: 28 residues processed: 221 average time/residue: 2.5367 time to fit residues: 656.8713 Evaluate side-chains 214 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 184 time to evaluate : 3.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain C residue 1 THR Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 202 CYS Chi-restraints excluded: chain J residue 1 ASP Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 139 CYS Chi-restraints excluded: chain J residue 194 HIS Chi-restraints excluded: chain K residue 63 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 159 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 202 optimal weight: 40.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22837 Z= 0.174 Angle : 0.480 8.343 31156 Z= 0.246 Chirality : 0.042 0.153 3623 Planarity : 0.004 0.042 3833 Dihedral : 4.233 22.452 3285 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.28 % Allowed : 15.66 % Favored : 83.06 % 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: 0.31 (0.17), residues: 2719 helix: 1.85 (0.21), residues: 705 sheet: -0.22 (0.18), residues: 763 loop : -0.39 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 62 HIS 0.003 0.000 HIS E 297 PHE 0.014 0.001 PHE F 144 TYR 0.019 0.001 TYR J 145 ARG 0.003 0.000 ARG F 113 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 189 time to evaluate : 3.614 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: A 358 ASP cc_start: 0.8069 (t70) cc_final: 0.7827 (t0) REVERT: F 18 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7405 (tm-30) outliers start: 32 outliers final: 28 residues processed: 210 average time/residue: 2.4333 time to fit residues: 606.5487 Evaluate side-chains 213 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 185 time to evaluate : 3.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain C residue 1 THR Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 31 HIS Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain G residue 202 CYS Chi-restraints excluded: chain J residue 1 ASP Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 139 CYS Chi-restraints excluded: chain J residue 194 HIS Chi-restraints excluded: chain K residue 63 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 234 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 224 optimal weight: 20.0000 chunk 239 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 chunk 238 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 150 ASN ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 22837 Z= 0.404 Angle : 0.547 9.227 31156 Z= 0.282 Chirality : 0.045 0.152 3623 Planarity : 0.004 0.042 3833 Dihedral : 4.570 29.293 3285 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.55 % Allowed : 15.50 % Favored : 82.94 % 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: 0.08 (0.16), residues: 2719 helix: 1.61 (0.20), residues: 703 sheet: -0.27 (0.18), residues: 766 loop : -0.57 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 62 HIS 0.006 0.001 HIS B 111 PHE 0.018 0.002 PHE A 290 TYR 0.016 0.002 TYR C 275 ARG 0.005 0.000 ARG D 195 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 183 time to evaluate : 3.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ASP cc_start: 0.8134 (t70) cc_final: 0.7847 (t0) REVERT: D 370 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7903 (mp) REVERT: E 16 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7145 (ptt90) REVERT: F 18 GLN cc_start: 0.7740 (tm-30) cc_final: 0.7479 (tm-30) outliers start: 39 outliers final: 29 residues processed: 212 average time/residue: 2.4720 time to fit residues: 615.9100 Evaluate side-chains 212 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 4.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain C residue 1 THR Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 31 HIS Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 202 CYS Chi-restraints excluded: chain J residue 1 ASP Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 139 CYS Chi-restraints excluded: chain J residue 194 HIS Chi-restraints excluded: chain K residue 63 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 157 optimal weight: 0.9990 chunk 253 optimal weight: 3.9990 chunk 154 optimal weight: 0.0000 chunk 120 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 266 optimal weight: 0.9980 chunk 244 optimal weight: 40.0000 chunk 211 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22837 Z= 0.184 Angle : 0.487 9.644 31156 Z= 0.250 Chirality : 0.043 0.157 3623 Planarity : 0.004 0.042 3833 Dihedral : 4.341 25.811 3285 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.16 % Allowed : 15.78 % Favored : 83.06 % 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: 0.24 (0.16), residues: 2719 helix: 1.80 (0.20), residues: 703 sheet: -0.22 (0.18), residues: 763 loop : -0.47 (0.18), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 317 HIS 0.003 0.001 HIS E 297 PHE 0.017 0.001 PHE J 214 TYR 0.014 0.001 TYR C 275 ARG 0.002 0.000 ARG K 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 182 time to evaluate : 3.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ASP cc_start: 0.8092 (t70) cc_final: 0.7827 (t0) REVERT: D 370 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.7902 (mp) REVERT: F 18 GLN cc_start: 0.7686 (tm-30) cc_final: 0.7330 (tm-30) REVERT: K 90 GLU cc_start: 0.8203 (tp30) cc_final: 0.7972 (tp30) outliers start: 29 outliers final: 25 residues processed: 202 average time/residue: 2.5192 time to fit residues: 601.9901 Evaluate side-chains 206 residues out of total 2509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 180 time to evaluate : 3.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain C residue 1 THR Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 31 HIS Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 202 CYS Chi-restraints excluded: chain J residue 1 ASP Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 139 CYS Chi-restraints excluded: chain J residue 194 HIS Chi-restraints excluded: chain K residue 63 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 168 optimal weight: 0.5980 chunk 225 optimal weight: 8.9990 chunk 64 optimal weight: 0.5980 chunk 195 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 212 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.129997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.081960 restraints weight = 90234.911| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.92 r_work: 0.2845 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22837 Z= 0.205 Angle : 0.486 9.666 31156 Z= 0.248 Chirality : 0.042 0.157 3623 Planarity : 0.004 0.042 3833 Dihedral : 4.267 22.336 3285 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.04 % Allowed : 15.94 % Favored : 83.02 % 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: 0.30 (0.16), residues: 2719 helix: 1.89 (0.20), residues: 703 sheet: -0.20 (0.18), residues: 763 loop : -0.46 (0.18), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 317 HIS 0.004 0.001 HIS E 297 PHE 0.014 0.001 PHE J 214 TYR 0.013 0.001 TYR C 275 ARG 0.003 0.000 ARG A 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12438.65 seconds wall clock time: 222 minutes 17.50 seconds (13337.50 seconds total)