Starting phenix.real_space_refine on Sat Feb 17 01:12:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smt_25208/02_2024/7smt_25208_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smt_25208/02_2024/7smt_25208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smt_25208/02_2024/7smt_25208.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smt_25208/02_2024/7smt_25208.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smt_25208/02_2024/7smt_25208_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smt_25208/02_2024/7smt_25208_updated.pdb" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 85 5.16 5 C 11156 2.51 5 N 2648 2.21 5 O 3122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17016 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3140 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 366} Chain breaks: 1 Chain: "B" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3456 Classifications: {'peptide': 425} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 397} Chain breaks: 1 Chain: "C" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3294 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 382} Chain breaks: 1 Chain: "D" Number of atoms: 3204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3204 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 374} Chain breaks: 1 Chain: "E" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3317 Classifications: {'peptide': 409} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 386} Chain breaks: 1 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {'CCE': 1, 'CLR': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {'DD9': 1, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'CLR': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 108 Unusual residues: {'CLR': 1, 'POV': 1, 'TC9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" C1 CLR A 602 " occ=0.80 ... (26 atoms not shown) pdb=" O1 CLR A 602 " occ=0.80 residue: pdb=" N POV A 603 " occ=0.75 ... (38 atoms not shown) pdb="C215 POV A 603 " occ=0.75 residue: pdb=" N POV B 602 " occ=0.75 ... (35 atoms not shown) pdb="C311 POV B 602 " occ=0.75 residue: pdb=" N POV C 501 " occ=0.75 ... (33 atoms not shown) pdb="C311 POV C 501 " occ=0.75 residue: pdb=" N POV C 502 " occ=0.75 ... (30 atoms not shown) pdb=" P POV C 502 " occ=0.75 residue: pdb=" C1 CLR C 503 " occ=0.89 ... (26 atoms not shown) pdb=" O1 CLR C 503 " occ=0.89 residue: pdb=" C1 CLR D 602 " occ=0.75 ... (26 atoms not shown) pdb=" O1 CLR D 602 " occ=0.75 residue: pdb=" N POV D 603 " occ=0.75 ... (33 atoms not shown) pdb="C311 POV D 603 " occ=0.75 Time building chain proxies: 9.49, per 1000 atoms: 0.56 Number of scatterers: 17016 At special positions: 0 Unit cell: (103.732, 164.688, 124.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 P 5 15.00 O 3122 8.00 N 2648 7.00 C 11156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 193 " distance=2.04 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.02 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 193 " distance=2.04 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 5 " " BMA I 3 " - " MAN I 4 " " MAN I 4 " - " MAN I 5 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " 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 J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG B 601 " - " ASN B 208 " " NAG E 501 " - " ASN E 68 " " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN B 143 " " NAG H 1 " - " ASN C 141 " " NAG I 1 " - " ASN D 141 " " NAG J 1 " - " ASN E 141 " Time building additional restraints: 7.16 Conformation dependent library (CDL) restraints added in 3.0 seconds 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3906 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 22 sheets defined 39.7% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 69 through 72 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 219 through 234 removed outlier: 3.514A pdb=" N LEU A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 229 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR A 234 " --> pdb=" O GLY 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 242 through 263 removed outlier: 3.702A pdb=" N LEU A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 299 Processing helix chain 'A' and resid 310 through 316 removed outlier: 3.883A pdb=" N ILE A 315 " --> pdb=" O TRP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 425 Processing helix chain 'B' and resid 3 through 12 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 233 through 248 removed outlier: 3.657A pdb=" N ALA B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N TYR B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 277 removed outlier: 3.650A pdb=" N ARG B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 313 Processing helix chain 'B' and resid 324 through 331 Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 417 through 475 Proline residue: B 463 - end of helix Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 69 through 72 Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 218 through 239 removed outlier: 4.703A pdb=" N ILE C 226 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Proline residue: C 227 - end of helix removed outlier: 4.690A pdb=" N PHE C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 245 No H-bonds generated for 'chain 'C' and resid 243 through 245' Processing helix chain 'C' and resid 248 through 268 removed outlier: 3.947A pdb=" N ASP C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 305 Processing helix chain 'C' and resid 316 through 322 Processing helix chain 'C' and resid 326 through 330 Processing helix chain 'C' and resid 399 through 459 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 69 through 72 Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 212 through 234 removed outlier: 4.442A pdb=" N ILE D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Proline residue: D 221 - end of helix removed outlier: 4.152A pdb=" N GLY D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N PHE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TYR D 234 " --> pdb=" O GLY D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 239 No H-bonds generated for 'chain 'D' and resid 237 through 239' Processing helix chain 'D' and resid 242 through 263 Processing helix chain 'D' and resid 273 through 299 Processing helix chain 'D' and resid 310 through 317 Processing helix chain 'D' and resid 320 through 323 No H-bonds generated for 'chain 'D' and resid 320 through 323' Processing helix chain 'D' and resid 371 through 423 Processing helix chain 'D' and resid 426 through 432 removed outlier: 6.042A pdb=" N LEU D 430 " --> pdb=" O ALA D 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 69 through 72 Processing helix chain 'E' and resid 82 through 84 No H-bonds generated for 'chain 'E' and resid 82 through 84' Processing helix chain 'E' and resid 220 through 241 removed outlier: 4.479A pdb=" N ALA E 228 " --> pdb=" O ILE E 224 " (cutoff:3.500A) Proline residue: E 229 - end of helix removed outlier: 3.884A pdb=" N LEU E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL E 237 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU E 239 " --> pdb=" O SER E 235 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR E 241 " --> pdb=" O VAL E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 271 removed outlier: 3.502A pdb=" N GLN E 271 " --> pdb=" O PHE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 308 Processing helix chain 'E' and resid 319 through 327 Processing helix chain 'E' and resid 412 through 471 removed outlier: 3.621A pdb=" N LEU E 457 " --> pdb=" O TRP E 453 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 156 through 160 removed outlier: 5.931A pdb=" N VAL A 29 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N SER A 159 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE A 31 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP A 30 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE A 61 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN A 53 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU A 40 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLU A 51 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 42 through 44 Processing sheet with id= C, first strand: chain 'A' and resid 77 through 81 Processing sheet with id= D, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.036A pdb=" N CYS A 142 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 205 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N MET A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 158 through 162 removed outlier: 6.388A pdb=" N VAL B 31 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ASP B 161 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE B 33 " --> pdb=" O ASP B 161 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASN B 32 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR B 63 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN B 55 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 44 through 46 Processing sheet with id= G, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.003A pdb=" N ALA B 150 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLN B 213 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 164 through 166 Processing sheet with id= I, first strand: chain 'B' and resid 190 through 194 removed outlier: 6.763A pdb=" N ILE B 220 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 156 through 160 removed outlier: 6.550A pdb=" N VAL C 29 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N GLN C 159 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 31 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N THR C 30 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR C 61 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN C 53 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LEU C 40 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N THR C 51 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 42 through 44 Processing sheet with id= L, first strand: chain 'C' and resid 77 through 80 Processing sheet with id= M, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.502A pdb=" N GLN C 214 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ILE C 188 " --> pdb=" O GLN C 214 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 193 through 198 removed outlier: 4.341A pdb=" N ARG C 198 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N TYR C 204 " --> pdb=" O ARG C 198 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 156 through 160 removed outlier: 6.058A pdb=" N VAL D 29 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N SER D 159 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE D 31 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASP D 30 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE D 61 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASN D 53 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LEU D 40 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLU D 51 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 42 through 44 Processing sheet with id= Q, first strand: chain 'D' and resid 77 through 81 Processing sheet with id= R, first strand: chain 'D' and resid 90 through 92 removed outlier: 3.693A pdb=" N CYS D 142 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE D 205 " --> pdb=" O CYS D 142 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP D 180 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLN D 208 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N MET D 178 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 156 through 160 removed outlier: 6.664A pdb=" N ILE E 29 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN E 159 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL E 31 " --> pdb=" O GLN E 159 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASP E 30 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASN E 61 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN E 53 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU E 40 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU E 119 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN E 107 " --> pdb=" O LEU E 119 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 42 through 44 Processing sheet with id= U, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.259A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 184 through 188 removed outlier: 6.926A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) 788 hydrogen bonds defined for protein. 2295 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: 4.97 Time building geometry restraints manager: 7.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2646 1.31 - 1.44: 4800 1.44 - 1.58: 9870 1.58 - 1.71: 11 1.71 - 1.84: 139 Bond restraints: 17466 Sorted by residual: bond pdb=" C19 TC9 D 601 " pdb=" C24 TC9 D 601 " ideal model delta sigma weight residual 1.519 1.394 0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C19 TC9 D 601 " pdb=" N20 TC9 D 601 " ideal model delta sigma weight residual 1.540 1.483 0.057 2.00e-02 2.50e+03 8.11e+00 bond pdb=" N POV B 602 " pdb=" C12 POV B 602 " ideal model delta sigma weight residual 1.508 1.451 0.057 2.00e-02 2.50e+03 8.01e+00 bond pdb=" N POV D 603 " pdb=" C12 POV D 603 " ideal model delta sigma weight residual 1.508 1.452 0.056 2.00e-02 2.50e+03 7.81e+00 bond pdb=" N POV A 603 " pdb=" C12 POV A 603 " ideal model delta sigma weight residual 1.508 1.452 0.056 2.00e-02 2.50e+03 7.74e+00 ... (remaining 17461 not shown) Histogram of bond angle deviations from ideal: 99.16 - 106.15: 473 106.15 - 113.13: 10035 113.13 - 120.12: 5940 120.12 - 127.10: 7118 127.10 - 134.08: 261 Bond angle restraints: 23827 Sorted by residual: angle pdb=" O11 POV C 502 " pdb=" P POV C 502 " pdb=" O12 POV C 502 " ideal model delta sigma weight residual 97.67 109.59 -11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O13 POV D 603 " pdb=" P POV D 603 " pdb=" O14 POV D 603 " ideal model delta sigma weight residual 121.11 109.41 11.70 3.00e+00 1.11e-01 1.52e+01 angle pdb=" O13 POV B 602 " pdb=" P POV B 602 " pdb=" O14 POV B 602 " ideal model delta sigma weight residual 121.11 109.48 11.63 3.00e+00 1.11e-01 1.50e+01 angle pdb=" O13 POV C 501 " pdb=" P POV C 501 " pdb=" O14 POV C 501 " ideal model delta sigma weight residual 121.11 109.52 11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" O11 POV B 602 " pdb=" P POV B 602 " pdb=" O12 POV B 602 " ideal model delta sigma weight residual 97.67 109.25 -11.58 3.00e+00 1.11e-01 1.49e+01 ... (remaining 23822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.32: 10453 30.32 - 60.65: 296 60.65 - 90.97: 59 90.97 - 121.29: 21 121.29 - 151.62: 5 Dihedral angle restraints: 10834 sinusoidal: 4835 harmonic: 5999 Sorted by residual: dihedral pdb=" CA CYS A 142 " pdb=" C CYS A 142 " pdb=" N THR A 143 " pdb=" CA THR A 143 " ideal model delta harmonic sigma weight residual -180.00 -151.00 -29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA CYS D 142 " pdb=" C CYS D 142 " pdb=" N THR D 143 " pdb=" CA THR D 143 " ideal model delta harmonic sigma weight residual -180.00 -151.52 -28.48 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA CYS D 192 " pdb=" C CYS D 192 " pdb=" N CYS D 193 " pdb=" CA CYS D 193 " ideal model delta harmonic sigma weight residual -180.00 -155.20 -24.80 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 10831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2498 0.075 - 0.151: 290 0.151 - 0.226: 11 0.226 - 0.302: 7 0.302 - 0.377: 1 Chirality restraints: 2807 Sorted by residual: chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 208 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN D 141 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 2804 not shown) Planarity restraints: 2889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 223 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C ILE E 223 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE E 223 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE E 224 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C19 TC9 D 601 " -0.014 2.00e-02 2.50e+03 1.03e-02 2.91e+00 pdb=" C22 TC9 D 601 " 0.009 2.00e-02 2.50e+03 pdb=" C23 TC9 D 601 " -0.012 2.00e-02 2.50e+03 pdb=" C24 TC9 D 601 " 0.019 2.00e-02 2.50e+03 pdb=" C25 TC9 D 601 " 0.001 2.00e-02 2.50e+03 pdb=" C26 TC9 D 601 " -0.000 2.00e-02 2.50e+03 pdb=" C27 TC9 D 601 " -0.002 2.00e-02 2.50e+03 pdb=" C28 TC9 D 601 " -0.015 2.00e-02 2.50e+03 pdb=" O29 TC9 D 601 " 0.014 2.00e-02 2.50e+03 pdb=" O40 TC9 D 601 " 0.001 2.00e-02 2.50e+03 pdb=" O42 TC9 D 601 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 221 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C ILE C 221 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE C 221 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL C 222 " 0.010 2.00e-02 2.50e+03 ... (remaining 2886 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1309 2.74 - 3.28: 16553 3.28 - 3.82: 28767 3.82 - 4.36: 35261 4.36 - 4.90: 60431 Nonbonded interactions: 142321 Sorted by model distance: nonbonded pdb=" OG SER A 82 " pdb=" O THR A 106 " model vdw 2.198 2.440 nonbonded pdb=" OD2 ASP D 152 " pdb=" OG1 THR D 154 " model vdw 2.208 2.440 nonbonded pdb=" OD1 ASN B 98 " pdb=" OG SER B 129 " model vdw 2.217 2.440 nonbonded pdb=" OG SER B 494 " pdb=" OD1 ASP B 496 " model vdw 2.222 2.440 nonbonded pdb=" OE2 GLU D 45 " pdb=" NH2 ARG D 209 " model vdw 2.246 2.520 ... (remaining 142316 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 1 through 426 or resid 602 or (resid 603 and (name N or na \ me C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C3 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name \ C37 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or n \ ame O31 or name O32 or name P )))) selection = (chain 'D' and (resid 1 through 330 or resid 370 through 426 or resid 602 or (re \ sid 603 and (name N or name C1 or name C11 or name C12 or name C13 or name C14 o \ r name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or name C2 \ 5 or name C26 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or \ name O21 or name O22 or name O31 or name O32 or name P )))) } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'J' } 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=0.75 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: 1.350 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: 0.010 Extract box with map and model: 4.510 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 46.650 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 17466 Z= 0.377 Angle : 0.740 11.919 23827 Z= 0.331 Chirality : 0.049 0.377 2807 Planarity : 0.004 0.039 2882 Dihedral : 16.078 151.617 6907 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.12 (0.19), residues: 2002 helix: 2.44 (0.18), residues: 759 sheet: 0.24 (0.25), residues: 405 loop : -0.58 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 317 HIS 0.006 0.001 HIS C 312 PHE 0.018 0.002 PHE E 422 TYR 0.018 0.002 TYR D 93 ARG 0.004 0.000 ARG E 217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 2.213 Fit side-chains REVERT: A 17 LYS cc_start: 0.9029 (pttt) cc_final: 0.8808 (pttp) REVERT: A 127 TYR cc_start: 0.8477 (t80) cc_final: 0.8120 (t80) REVERT: A 243 MET cc_start: 0.9035 (mmm) cc_final: 0.8744 (mmm) REVERT: A 278 MET cc_start: 0.8079 (mmm) cc_final: 0.7655 (mmm) REVERT: A 373 LYS cc_start: 0.8283 (pttp) cc_final: 0.7932 (mptt) REVERT: B 46 LYS cc_start: 0.8317 (mmtp) cc_final: 0.7914 (mtmt) REVERT: C 288 MET cc_start: 0.8572 (ttm) cc_final: 0.8313 (mtp) REVERT: D 97 ASP cc_start: 0.7567 (t0) cc_final: 0.7275 (t0) REVERT: D 178 MET cc_start: 0.8941 (mmp) cc_final: 0.8571 (tpp) REVERT: E 425 LYS cc_start: 0.8215 (ttmm) cc_final: 0.8014 (ttpp) outliers start: 0 outliers final: 2 residues processed: 209 average time/residue: 1.4056 time to fit residues: 325.6412 Evaluate side-chains 133 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain E residue 413 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 3.9990 chunk 150 optimal weight: 0.0970 chunk 83 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 276 GLN B 305 ASN D 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17466 Z= 0.192 Angle : 0.523 7.223 23827 Z= 0.262 Chirality : 0.043 0.293 2807 Planarity : 0.003 0.035 2882 Dihedral : 12.694 132.367 2989 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.66 % Allowed : 6.05 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.19), residues: 2002 helix: 2.68 (0.19), residues: 762 sheet: 0.27 (0.26), residues: 405 loop : -0.45 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 60 HIS 0.003 0.001 HIS A 204 PHE 0.014 0.001 PHE D 284 TYR 0.011 0.001 TYR C 124 ARG 0.004 0.000 ARG E 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 148 time to evaluate : 1.976 Fit side-chains revert: symmetry clash REVERT: A 127 TYR cc_start: 0.8429 (t80) cc_final: 0.8078 (t80) REVERT: A 397 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: B 46 LYS cc_start: 0.8236 (mmtp) cc_final: 0.7995 (mmtt) REVERT: B 420 LYS cc_start: 0.7737 (ttmt) cc_final: 0.7523 (ttpp) REVERT: C 288 MET cc_start: 0.8551 (ttm) cc_final: 0.8306 (mtp) REVERT: C 311 THR cc_start: 0.8316 (m) cc_final: 0.8075 (p) REVERT: D 97 ASP cc_start: 0.7405 (t0) cc_final: 0.7080 (t0) REVERT: D 278 MET cc_start: 0.7814 (tpp) cc_final: 0.7575 (tpp) REVERT: E 166 GLU cc_start: 0.7344 (pp20) cc_final: 0.7134 (pp20) REVERT: E 414 LYS cc_start: 0.6551 (OUTLIER) cc_final: 0.5718 (tptt) outliers start: 31 outliers final: 13 residues processed: 161 average time/residue: 1.2866 time to fit residues: 232.0865 Evaluate side-chains 147 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 414 LYS Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 100 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 150 optimal weight: 0.3980 chunk 123 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 181 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 chunk 161 optimal weight: 0.1980 chunk 179 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 28 ASN B 276 GLN B 432 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.087 17466 Z= 0.167 Angle : 0.487 7.114 23827 Z= 0.245 Chirality : 0.042 0.274 2807 Planarity : 0.003 0.034 2882 Dihedral : 11.199 122.206 2985 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.82 % Allowed : 8.03 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.19), residues: 2002 helix: 2.85 (0.19), residues: 761 sheet: 0.34 (0.26), residues: 404 loop : -0.43 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 60 HIS 0.004 0.000 HIS C 312 PHE 0.014 0.001 PHE D 284 TYR 0.010 0.001 TYR B 439 ARG 0.003 0.000 ARG E 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 146 time to evaluate : 2.181 Fit side-chains revert: symmetry clash REVERT: A 127 TYR cc_start: 0.8391 (t80) cc_final: 0.8045 (t80) REVERT: A 278 MET cc_start: 0.8052 (mmm) cc_final: 0.7842 (mmm) REVERT: A 387 LYS cc_start: 0.8439 (mmmm) cc_final: 0.8070 (tppt) REVERT: A 397 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: B 46 LYS cc_start: 0.8238 (mmtp) cc_final: 0.8005 (mmtt) REVERT: B 186 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6934 (tm-30) REVERT: B 432 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8216 (mm110) REVERT: C 288 MET cc_start: 0.8523 (ttm) cc_final: 0.8284 (mtp) REVERT: D 97 ASP cc_start: 0.7384 (t0) cc_final: 0.7078 (t0) REVERT: D 278 MET cc_start: 0.7870 (tpp) cc_final: 0.7615 (tpp) REVERT: E 166 GLU cc_start: 0.7427 (pp20) cc_final: 0.7111 (pp20) REVERT: E 292 PHE cc_start: 0.7974 (t80) cc_final: 0.7504 (m-80) REVERT: E 414 LYS cc_start: 0.6599 (OUTLIER) cc_final: 0.5764 (tptt) outliers start: 34 outliers final: 12 residues processed: 159 average time/residue: 1.3119 time to fit residues: 233.5736 Evaluate side-chains 145 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain E residue 414 LYS Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 178 optimal weight: 3.9990 chunk 136 optimal weight: 0.2980 chunk 93 optimal weight: 0.0770 chunk 20 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 276 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 17466 Z= 0.199 Angle : 0.503 8.275 23827 Z= 0.252 Chirality : 0.043 0.266 2807 Planarity : 0.003 0.034 2882 Dihedral : 10.022 117.489 2985 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.77 % Allowed : 8.94 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.19), residues: 2002 helix: 2.84 (0.19), residues: 768 sheet: 0.36 (0.26), residues: 404 loop : -0.40 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 187 HIS 0.003 0.001 HIS C 312 PHE 0.014 0.001 PHE D 284 TYR 0.010 0.001 TYR E 117 ARG 0.004 0.000 ARG E 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 140 time to evaluate : 1.951 Fit side-chains revert: symmetry clash REVERT: A 127 TYR cc_start: 0.8396 (t80) cc_final: 0.8050 (t80) REVERT: A 387 LYS cc_start: 0.8474 (mmmm) cc_final: 0.8063 (mttp) REVERT: A 397 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: B 46 LYS cc_start: 0.8240 (mmtp) cc_final: 0.8005 (mmtt) REVERT: B 186 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6903 (tm-30) REVERT: C 288 MET cc_start: 0.8498 (ttm) cc_final: 0.8289 (mtp) REVERT: D 97 ASP cc_start: 0.7404 (t0) cc_final: 0.7078 (t0) REVERT: E 166 GLU cc_start: 0.7510 (pp20) cc_final: 0.7295 (pp20) REVERT: E 292 PHE cc_start: 0.7981 (t80) cc_final: 0.7508 (m-80) outliers start: 33 outliers final: 17 residues processed: 156 average time/residue: 1.2643 time to fit residues: 221.4767 Evaluate side-chains 153 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 160 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 143 optimal weight: 0.0020 chunk 79 optimal weight: 0.0020 chunk 164 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 98 optimal weight: 0.0970 chunk 172 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.089 17466 Z= 0.145 Angle : 0.468 8.046 23827 Z= 0.236 Chirality : 0.042 0.259 2807 Planarity : 0.003 0.035 2882 Dihedral : 9.076 118.406 2985 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.71 % Allowed : 9.96 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.19), residues: 2002 helix: 2.99 (0.19), residues: 765 sheet: 0.40 (0.26), residues: 404 loop : -0.29 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 60 HIS 0.007 0.000 HIS C 312 PHE 0.015 0.001 PHE B 471 TYR 0.012 0.001 TYR E 117 ARG 0.005 0.000 ARG B 336 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 2.197 Fit side-chains revert: symmetry clash REVERT: A 127 TYR cc_start: 0.8340 (t80) cc_final: 0.8038 (t80) REVERT: A 387 LYS cc_start: 0.8445 (mmmm) cc_final: 0.8064 (mttp) REVERT: A 397 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: B 46 LYS cc_start: 0.8232 (mmtp) cc_final: 0.7996 (mmtt) REVERT: B 186 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6948 (tm-30) REVERT: C 171 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8759 (mttm) REVERT: C 288 MET cc_start: 0.8465 (ttm) cc_final: 0.8259 (mtp) REVERT: D 97 ASP cc_start: 0.7351 (t0) cc_final: 0.7032 (t0) REVERT: D 129 GLU cc_start: 0.7044 (pm20) cc_final: 0.6358 (pm20) REVERT: D 207 MET cc_start: 0.8339 (mtm) cc_final: 0.8049 (mtp) REVERT: D 227 PHE cc_start: 0.8152 (t80) cc_final: 0.7819 (m-80) REVERT: D 377 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: E 166 GLU cc_start: 0.7513 (pp20) cc_final: 0.7142 (pp20) REVERT: E 292 PHE cc_start: 0.7963 (t80) cc_final: 0.7543 (m-80) outliers start: 32 outliers final: 14 residues processed: 163 average time/residue: 1.2499 time to fit residues: 229.2086 Evaluate side-chains 153 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 377 GLU Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 64 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 192 optimal weight: 9.9990 chunk 159 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 267 GLN B 276 GLN B 432 GLN C 196 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 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 : 0.005 0.086 17466 Z= 0.325 Angle : 0.559 10.262 23827 Z= 0.280 Chirality : 0.045 0.255 2807 Planarity : 0.004 0.037 2882 Dihedral : 9.195 119.805 2985 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.71 % Allowed : 10.60 % Favored : 87.69 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.19), residues: 2002 helix: 2.82 (0.19), residues: 767 sheet: 0.33 (0.26), residues: 406 loop : -0.35 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 453 HIS 0.006 0.001 HIS B 60 PHE 0.017 0.001 PHE D 256 TYR 0.017 0.001 TYR D 93 ARG 0.006 0.000 ARG E 217 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 134 time to evaluate : 2.023 Fit side-chains revert: symmetry clash REVERT: A 127 TYR cc_start: 0.8361 (t80) cc_final: 0.8021 (t80) REVERT: A 387 LYS cc_start: 0.8535 (mmmm) cc_final: 0.8156 (mttp) REVERT: A 397 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: B 46 LYS cc_start: 0.8261 (mmtp) cc_final: 0.8014 (mmtt) REVERT: B 186 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7056 (tm-30) REVERT: D 97 ASP cc_start: 0.7567 (t0) cc_final: 0.7246 (t0) REVERT: D 377 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: E 166 GLU cc_start: 0.7588 (pp20) cc_final: 0.7314 (pp20) outliers start: 32 outliers final: 17 residues processed: 150 average time/residue: 1.3098 time to fit residues: 220.0025 Evaluate side-chains 150 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain D residue 377 GLU Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 185 optimal weight: 0.9990 chunk 21 optimal weight: 0.0040 chunk 109 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 108 optimal weight: 0.1980 chunk 162 optimal weight: 1.9990 chunk 107 optimal weight: 0.2980 chunk 191 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 276 GLN C 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.118 17466 Z= 0.168 Angle : 0.487 11.287 23827 Z= 0.247 Chirality : 0.042 0.267 2807 Planarity : 0.003 0.034 2882 Dihedral : 8.637 119.301 2985 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.34 % Allowed : 10.97 % Favored : 87.69 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.19), residues: 2002 helix: 2.96 (0.19), residues: 766 sheet: 0.39 (0.26), residues: 404 loop : -0.25 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 60 HIS 0.004 0.000 HIS C 312 PHE 0.012 0.001 PHE D 284 TYR 0.012 0.001 TYR E 117 ARG 0.006 0.000 ARG B 336 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 1.892 Fit side-chains revert: symmetry clash REVERT: A 127 TYR cc_start: 0.8350 (t80) cc_final: 0.8007 (t80) REVERT: A 387 LYS cc_start: 0.8507 (mmmm) cc_final: 0.8103 (mtmm) REVERT: A 397 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: B 46 LYS cc_start: 0.8238 (mmtp) cc_final: 0.8002 (mmtt) REVERT: B 186 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6919 (tm-30) REVERT: B 336 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7840 (ptp-110) REVERT: D 97 ASP cc_start: 0.7404 (t0) cc_final: 0.7085 (t0) REVERT: D 227 PHE cc_start: 0.8125 (t80) cc_final: 0.7819 (m-80) REVERT: D 377 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: E 166 GLU cc_start: 0.7659 (pp20) cc_final: 0.7393 (pp20) REVERT: E 292 PHE cc_start: 0.7978 (t80) cc_final: 0.7503 (m-80) outliers start: 25 outliers final: 13 residues processed: 145 average time/residue: 1.3205 time to fit residues: 214.2062 Evaluate side-chains 146 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 377 GLU Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 118 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 121 optimal weight: 0.1980 chunk 130 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 276 GLN C 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.142 17466 Z= 0.198 Angle : 0.497 13.577 23827 Z= 0.250 Chirality : 0.043 0.277 2807 Planarity : 0.003 0.034 2882 Dihedral : 8.293 120.066 2985 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.66 % Allowed : 11.19 % Favored : 87.15 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.19), residues: 2002 helix: 2.97 (0.19), residues: 768 sheet: 0.42 (0.26), residues: 404 loop : -0.24 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 311 HIS 0.003 0.001 HIS C 312 PHE 0.014 0.001 PHE B 471 TYR 0.010 0.001 TYR E 117 ARG 0.005 0.000 ARG B 336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 1.804 Fit side-chains revert: symmetry clash REVERT: A 127 TYR cc_start: 0.8344 (t80) cc_final: 0.8033 (t80) REVERT: A 387 LYS cc_start: 0.8499 (mmmm) cc_final: 0.8123 (mtmm) REVERT: A 397 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: B 46 LYS cc_start: 0.8265 (mmtp) cc_final: 0.8028 (mmtt) REVERT: B 186 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6943 (tm-30) REVERT: D 97 ASP cc_start: 0.7416 (t0) cc_final: 0.7092 (t0) REVERT: D 207 MET cc_start: 0.8372 (mtm) cc_final: 0.8120 (mtp) REVERT: D 227 PHE cc_start: 0.8129 (t80) cc_final: 0.7825 (m-80) REVERT: D 377 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: E 166 GLU cc_start: 0.7615 (pp20) cc_final: 0.7320 (pp20) REVERT: E 292 PHE cc_start: 0.7976 (t80) cc_final: 0.7502 (m-80) outliers start: 31 outliers final: 17 residues processed: 152 average time/residue: 1.2903 time to fit residues: 220.8618 Evaluate side-chains 148 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 377 GLU Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 183 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 161 optimal weight: 0.2980 chunk 169 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 276 GLN C 310 ASN ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.177 17466 Z= 0.221 Angle : 0.508 15.575 23827 Z= 0.256 Chirality : 0.042 0.283 2807 Planarity : 0.003 0.034 2882 Dihedral : 8.113 120.307 2985 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.55 % Allowed : 11.46 % Favored : 86.99 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.19), residues: 2002 helix: 2.98 (0.19), residues: 766 sheet: 0.41 (0.26), residues: 404 loop : -0.22 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 311 HIS 0.003 0.001 HIS B 60 PHE 0.013 0.001 PHE D 256 TYR 0.010 0.001 TYR E 117 ARG 0.009 0.000 ARG B 336 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 2.041 Fit side-chains revert: symmetry clash REVERT: A 127 TYR cc_start: 0.8336 (t80) cc_final: 0.8026 (t80) REVERT: A 387 LYS cc_start: 0.8495 (mmmm) cc_final: 0.8164 (mtmm) REVERT: A 397 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: B 46 LYS cc_start: 0.8224 (mmtp) cc_final: 0.7992 (mmtt) REVERT: B 186 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6942 (tm-30) REVERT: D 97 ASP cc_start: 0.7416 (t0) cc_final: 0.7092 (t0) REVERT: D 207 MET cc_start: 0.8370 (mtm) cc_final: 0.8114 (mtp) REVERT: D 227 PHE cc_start: 0.8128 (t80) cc_final: 0.7823 (m-80) REVERT: D 325 PHE cc_start: 0.6577 (m-80) cc_final: 0.6328 (m-80) REVERT: D 377 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: E 166 GLU cc_start: 0.7665 (pp20) cc_final: 0.7388 (pp20) REVERT: E 292 PHE cc_start: 0.7978 (t80) cc_final: 0.7502 (m-80) outliers start: 29 outliers final: 18 residues processed: 146 average time/residue: 1.2934 time to fit residues: 211.6233 Evaluate side-chains 149 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 377 GLU Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 115 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 182 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 121 optimal weight: 0.0050 chunk 96 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 276 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.187 17466 Z= 0.284 Angle : 0.562 20.571 23827 Z= 0.283 Chirality : 0.043 0.279 2807 Planarity : 0.003 0.039 2882 Dihedral : 8.100 120.421 2985 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.45 % Allowed : 11.56 % Favored : 86.99 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.19), residues: 2002 helix: 2.94 (0.19), residues: 768 sheet: 0.40 (0.26), residues: 406 loop : -0.21 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 311 HIS 0.004 0.001 HIS C 312 PHE 0.013 0.001 PHE D 256 TYR 0.010 0.001 TYR E 117 ARG 0.009 0.000 ARG B 336 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 132 time to evaluate : 2.081 Fit side-chains revert: symmetry clash REVERT: A 127 TYR cc_start: 0.8340 (t80) cc_final: 0.8028 (t80) REVERT: A 387 LYS cc_start: 0.8484 (mmmm) cc_final: 0.8144 (mtmm) REVERT: A 397 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: B 46 LYS cc_start: 0.8229 (mmtp) cc_final: 0.7996 (mmtt) REVERT: B 186 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6932 (tm-30) REVERT: D 97 ASP cc_start: 0.7414 (t0) cc_final: 0.7088 (t0) REVERT: D 227 PHE cc_start: 0.8132 (t80) cc_final: 0.7826 (m-80) REVERT: D 377 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: E 166 GLU cc_start: 0.7707 (pp20) cc_final: 0.7441 (pp20) outliers start: 27 outliers final: 19 residues processed: 148 average time/residue: 1.2520 time to fit residues: 208.8353 Evaluate side-chains 150 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 128 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 377 GLU Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 48 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 23 optimal weight: 0.0770 chunk 43 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 276 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.089731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.068657 restraints weight = 28552.236| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.16 r_work: 0.2778 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.199 17466 Z= 0.272 Angle : 0.543 21.191 23827 Z= 0.274 Chirality : 0.043 0.276 2807 Planarity : 0.003 0.037 2882 Dihedral : 7.945 120.474 2985 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.45 % Allowed : 11.51 % Favored : 87.04 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.19), residues: 2002 helix: 2.99 (0.19), residues: 765 sheet: 0.41 (0.26), residues: 406 loop : -0.18 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 311 HIS 0.003 0.001 HIS C 312 PHE 0.017 0.001 PHE B 471 TYR 0.010 0.001 TYR E 117 ARG 0.009 0.000 ARG B 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5221.24 seconds wall clock time: 94 minutes 8.97 seconds (5648.97 seconds total)