Starting phenix.real_space_refine on Fri Apr 12 15:22:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6usf_20863/04_2024/6usf_20863_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6usf_20863/04_2024/6usf_20863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6usf_20863/04_2024/6usf_20863.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6usf_20863/04_2024/6usf_20863.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6usf_20863/04_2024/6usf_20863_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6usf_20863/04_2024/6usf_20863_updated.pdb" } resolution = 3.87 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3066 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 14903 2.51 5 N 3726 2.21 5 O 4276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 7": "NH1" <-> "NH2" Residue "A GLU 12": "OE1" <-> "OE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "D ARG 7": "NH1" <-> "NH2" Residue "D GLU 11": "OE1" <-> "OE2" Residue "E TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 157": "OE1" <-> "OE2" Residue "E GLU 189": "OE1" <-> "OE2" Residue "H TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 163": "OE1" <-> "OE2" Residue "L GLU 197": "OE1" <-> "OE2" Residue "L PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 108": "OE1" <-> "OE2" Residue "K TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 163": "OE1" <-> "OE2" Residue "M GLU 167": "OE1" <-> "OE2" Residue "M GLU 197": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 23022 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3764 Classifications: {'peptide': 464} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 441} Chain breaks: 2 Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2917 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 337} Chain breaks: 1 Chain: "C" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2908 Classifications: {'peptide': 357} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 336} Chain breaks: 1 Chain: "D" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3764 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 22, 'TRANS': 441} Chain breaks: 2 Chain: "E" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2908 Classifications: {'peptide': 357} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 336} Chain breaks: 1 Chain: "H" Number of atoms: 1655 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 219, 1649 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 205} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 219, 1649 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 205} Chain breaks: 1 bond proxies already assigned to first conformer: 1689 Chain: "L" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1602 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 198} Chain breaks: 1 Chain: "K" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1700 Classifications: {'peptide': 227} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 213} Chain: "M" Number of atoms: 1627 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 213, 1626 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 213, 1626 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1658 Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 1, 'QMR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 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 Chain: "C" 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 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 1, 'QMR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'BMA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.55, per 1000 atoms: 0.59 Number of scatterers: 23022 At special positions: 0 Unit cell: (214.968, 145.517, 177.486, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 4276 8.00 N 3726 7.00 C 14903 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.05 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 200 " distance=2.65 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.05 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 144 " distance=2.06 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=2.05 Simple disulfide: pdb=" SG CYS E 130 " - pdb=" SG CYS E 144 " distance=2.05 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.05 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.46 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 Simple disulfide: pdb=" SG CYS K 25 " - pdb=" SG CYS K 99 " distance=2.04 Simple disulfide: pdb=" SG CYS K 154 " - pdb=" SG CYS K 210 " distance=2.03 Simple disulfide: pdb=" SG CYS M 24 " - pdb=" SG CYS M 89 " distance=2.04 Simple disulfide: pdb=" SG CYS M 136 " - pdb=" SG CYS M 196 " distance=2.07 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 Atom "HETATM22965 O5 NAG B 401 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " BMA F 2 " " NAG F 1 " - " NAG B 401 " " NAG G 1 " - " BMA G 2 " " NAG G 1 " - " NAG C 401 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA E 403 " NAG-ASN " NAG A 501 " - " ASN A 148 " " NAG B 401 " - " ASN B 143 " " NAG C 401 " - " ASN C 143 " " NAG D 501 " - " ASN D 148 " " NAG I 1 " - " ASN E 143 " Time building additional restraints: 9.24 Conformation dependent library (CDL) restraints added in 4.8 seconds 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5498 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 39 sheets defined 25.2% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.19 Creating SS restraints... Processing helix chain 'A' and resid 7 through 18 Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'A' and resid 233 through 240 removed outlier: 4.233A pdb=" N VAL A 236 " --> pdb=" O CYS A 233 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU A 237 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL A 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 239 " --> pdb=" O VAL A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 268 removed outlier: 5.489A pdb=" N GLU A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 305 removed outlier: 3.641A pdb=" N TYR A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 325 Processing helix chain 'A' and resid 346 through 349 No H-bonds generated for 'chain 'A' and resid 346 through 349' Processing helix chain 'A' and resid 351 through 354 No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 356 through 360 Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.615A pdb=" N LYS A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 369' Processing helix chain 'A' and resid 371 through 381 removed outlier: 3.589A pdb=" N LEU A 380 " --> pdb=" O ARG A 376 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 421 removed outlier: 3.656A pdb=" N PHE A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 407 " --> pdb=" O PHE A 403 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE A 409 " --> pdb=" O HIS A 405 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 429 No H-bonds generated for 'chain 'A' and resid 426 through 429' Processing helix chain 'A' and resid 436 through 443 removed outlier: 4.106A pdb=" N ALA A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 473 removed outlier: 3.703A pdb=" N ASP A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE A 461 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TRP A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE A 467 " --> pdb=" O TRP A 463 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL A 468 " --> pdb=" O MET A 464 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 473 " --> pdb=" O CYS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 480 No H-bonds generated for 'chain 'A' and resid 477 through 480' Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 210 through 216 Processing helix chain 'B' and resid 218 through 226 removed outlier: 4.792A pdb=" N LEU B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 241 through 261 Processing helix chain 'B' and resid 271 through 297 Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'B' and resid 318 through 320 No H-bonds generated for 'chain 'B' and resid 318 through 320' Processing helix chain 'B' and resid 337 through 351 removed outlier: 3.679A pdb=" N VAL B 344 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP B 346 " --> pdb=" O ALA B 342 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG B 347 " --> pdb=" O MET B 343 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP B 351 " --> pdb=" O ARG B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 359 No H-bonds generated for 'chain 'B' and resid 356 through 359' Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 210 through 216 Processing helix chain 'C' and resid 218 through 226 removed outlier: 4.913A pdb=" N LEU C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) 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 314 Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 334 through 341 removed outlier: 3.872A pdb=" N TRP C 338 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS C 339 " --> pdb=" O SER C 335 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 349 Processing helix chain 'C' and resid 351 through 360 removed outlier: 3.519A pdb=" N PHE C 355 " --> pdb=" O TRP C 351 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 356 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE C 359 " --> pdb=" O PHE C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'D' and resid 7 through 18 Processing helix chain 'D' and resid 218 through 223 Processing helix chain 'D' and resid 225 through 234 removed outlier: 3.905A pdb=" N CYS D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 269 removed outlier: 4.834A pdb=" N GLU D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 305 removed outlier: 3.784A pdb=" N TYR D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 325 Processing helix chain 'D' and resid 345 through 352 removed outlier: 3.521A pdb=" N THR D 351 " --> pdb=" O ASP D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.901A pdb=" N ALA D 371 " --> pdb=" O GLN D 367 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA D 379 " --> pdb=" O MET D 375 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP D 381 " --> pdb=" O ALA D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 390 No H-bonds generated for 'chain 'D' and resid 388 through 390' Processing helix chain 'D' and resid 398 through 404 Processing helix chain 'D' and resid 408 through 414 Processing helix chain 'D' and resid 416 through 419 No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 426 through 432 removed outlier: 4.276A pdb=" N GLN D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 441 removed outlier: 3.567A pdb=" N ASN D 441 " --> pdb=" O LYS D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 477 removed outlier: 4.431A pdb=" N ASP D 458 " --> pdb=" O ALA D 454 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE D 460 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE D 461 " --> pdb=" O ILE D 457 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU D 462 " --> pdb=" O ASP D 458 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE D 466 " --> pdb=" O LEU D 462 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE D 467 " --> pdb=" O TRP D 463 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR D 473 " --> pdb=" O CYS D 469 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 210 through 226 removed outlier: 4.916A pdb=" N ILE E 218 " --> pdb=" O ILE E 214 " (cutoff:3.500A) Proline residue: E 219 - end of helix removed outlier: 4.243A pdb=" N LEU E 226 " --> pdb=" O LEU E 222 " (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 removed outlier: 3.526A pdb=" N TYR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 314 Processing helix chain 'E' and resid 318 through 320 No H-bonds generated for 'chain 'E' and resid 318 through 320' Processing helix chain 'E' and resid 341 through 357 removed outlier: 4.328A pdb=" N ASP E 346 " --> pdb=" O ALA E 342 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG E 347 " --> pdb=" O MET E 343 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TRP E 351 " --> pdb=" O ARG E 347 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE E 352 " --> pdb=" O LEU E 348 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL E 356 " --> pdb=" O ILE E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 362 No H-bonds generated for 'chain 'E' and resid 359 through 362' Processing helix chain 'H' and resid 108 through 111 No H-bonds generated for 'chain 'H' and resid 108 through 111' Processing helix chain 'H' and resid 169 through 171 No H-bonds generated for 'chain 'H' and resid 169 through 171' Processing helix chain 'H' and resid 200 through 202 No H-bonds generated for 'chain 'H' and resid 200 through 202' Processing helix chain 'L' and resid 95 through 97 No H-bonds generated for 'chain 'L' and resid 95 through 97' Processing helix chain 'L' and resid 124 through 129 removed outlier: 3.697A pdb=" N SER L 129 " --> pdb=" O SER L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 189 Processing helix chain 'K' and resid 32 through 34 No H-bonds generated for 'chain 'K' and resid 32 through 34' Processing helix chain 'K' and resid 91 through 93 No H-bonds generated for 'chain 'K' and resid 91 through 93' Processing helix chain 'K' and resid 108 through 111 No H-bonds generated for 'chain 'K' and resid 108 through 111' Processing helix chain 'K' and resid 169 through 171 No H-bonds generated for 'chain 'K' and resid 169 through 171' Processing helix chain 'K' and resid 200 through 202 No H-bonds generated for 'chain 'K' and resid 200 through 202' Processing helix chain 'M' and resid 124 through 127 No H-bonds generated for 'chain 'M' and resid 124 through 127' Processing helix chain 'M' and resid 185 through 189 Processing sheet with id= A, first strand: chain 'A' and resid 165 through 167 removed outlier: 6.438A pdb=" N VAL A 38 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 49 through 51 removed outlier: 3.588A pdb=" N ASP A 49 " --> pdb=" O THR A 58 " (cutoff:3.500A) 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: 4.169A pdb=" N SER A 155 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG A 214 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE A 185 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 44 through 47 removed outlier: 7.020A pdb=" N ASN A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 158 through 161 removed outlier: 6.974A pdb=" N VAL B 31 " --> pdb=" O ASP B 159 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL B 161 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 33 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N THR B 32 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU B 63 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASN B 55 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 58 " --> pdb=" O PRO B 122 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B 113 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU B 121 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASN B 109 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 44 through 46 Processing sheet with id= H, first strand: chain 'B' and resid 92 through 94 removed outlier: 3.645A pdb=" N ARG B 149 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER B 150 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL B 197 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 178 through 182 removed outlier: 7.151A pdb=" N ILE B 204 " --> pdb=" O VAL B 181 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 158 through 162 removed outlier: 6.129A pdb=" N VAL C 31 " --> pdb=" O ASP C 159 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL C 161 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL C 33 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR C 32 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU C 63 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASN C 55 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU C 42 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR C 53 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 58 " --> pdb=" O PRO C 122 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 44 through 46 Processing sheet with id= L, first strand: chain 'C' and resid 79 through 82 Processing sheet with id= M, first strand: chain 'C' and resid 92 through 94 removed outlier: 4.918A pdb=" N SER C 150 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL C 197 " --> pdb=" O SER C 150 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 178 through 182 removed outlier: 6.924A pdb=" N ILE C 204 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 163 through 167 removed outlier: 6.565A pdb=" N VAL D 36 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL D 166 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL D 38 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LEU D 37 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N HIS D 68 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 49 through 51 removed outlier: 3.560A pdb=" N ASP D 49 " --> pdb=" O THR D 58 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 85 through 87 Processing sheet with id= R, first strand: chain 'D' and resid 97 through 99 removed outlier: 4.379A pdb=" N SER D 155 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG D 214 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ILE D 185 " --> pdb=" O ARG D 214 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 44 through 47 removed outlier: 7.118A pdb=" N ASN D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 158 through 162 removed outlier: 6.402A pdb=" N VAL E 31 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL E 161 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL E 33 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N THR E 32 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLU E 63 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASN E 55 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LEU E 42 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N THR E 53 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 44 through 46 Processing sheet with id= V, first strand: chain 'E' and resid 141 through 149 removed outlier: 3.735A pdb=" N ALA E 182 " --> pdb=" O ILE E 204 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ARG E 206 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE E 180 " --> pdb=" O ARG E 206 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 6 through 10 Processing sheet with id= X, first strand: chain 'H' and resid 95 through 102 removed outlier: 6.103A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.399A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 165 through 168 removed outlier: 4.393A pdb=" N TYR H 208 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'L' and resid 5 through 8 Processing sheet with id= AB, first strand: chain 'L' and resid 11 through 13 removed outlier: 5.743A pdb=" N LYS L 105 " --> pdb=" O LEU L 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'L' and resid 116 through 120 removed outlier: 6.079A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'L' and resid 147 through 152 Processing sheet with id= AE, first strand: chain 'L' and resid 36 through 38 removed outlier: 6.218A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 6 through 10 Processing sheet with id= AG, first strand: chain 'K' and resid 121 through 123 removed outlier: 5.367A pdb=" N ARG K 41 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N TRP K 50 " --> pdb=" O ARG K 41 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA K 43 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU K 48 " --> pdb=" O ALA K 43 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'K' and resid 134 through 138 removed outlier: 6.206A pdb=" N TYR K 190 " --> pdb=" O ASP K 158 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'K' and resid 164 through 168 removed outlier: 4.413A pdb=" N TYR K 208 " --> pdb=" O VAL K 225 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'M' and resid 5 through 8 Processing sheet with id= AK, first strand: chain 'M' and resid 34 through 39 Processing sheet with id= AL, first strand: chain 'M' and resid 116 through 120 Processing sheet with id= AM, first strand: chain 'M' and resid 146 through 152 806 hydrogen bonds defined for protein. 2288 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: 7.71 Time building geometry restraints manager: 9.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6599 1.34 - 1.47: 6548 1.47 - 1.59: 10287 1.59 - 1.72: 8 1.72 - 1.85: 178 Bond restraints: 23620 Sorted by residual: bond pdb=" N PRO A 480 " pdb=" CA PRO A 480 " ideal model delta sigma weight residual 1.473 1.707 -0.233 1.32e-02 5.74e+03 3.12e+02 bond pdb=" C04 QMR D 502 " pdb=" C05 QMR D 502 " ideal model delta sigma weight residual 1.536 1.240 0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C05 QMR D 502 " pdb=" C06 QMR D 502 " ideal model delta sigma weight residual 1.536 1.241 0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C04 QMR A 502 " pdb=" C05 QMR A 502 " ideal model delta sigma weight residual 1.536 1.243 0.293 2.00e-02 2.50e+03 2.15e+02 bond pdb=" C05 QMR A 502 " pdb=" C06 QMR A 502 " ideal model delta sigma weight residual 1.536 1.245 0.291 2.00e-02 2.50e+03 2.11e+02 ... (remaining 23615 not shown) Histogram of bond angle deviations from ideal: 93.33 - 103.31: 313 103.31 - 113.28: 13177 113.28 - 123.26: 17021 123.26 - 133.24: 1592 133.24 - 143.21: 102 Bond angle restraints: 32205 Sorted by residual: angle pdb=" N CYS A 200 " pdb=" CA CYS A 200 " pdb=" C CYS A 200 " ideal model delta sigma weight residual 109.96 143.21 -33.25 1.49e+00 4.50e-01 4.98e+02 angle pdb=" C PRO A 479 " pdb=" N PRO A 480 " pdb=" CA PRO A 480 " ideal model delta sigma weight residual 118.97 139.03 -20.06 1.04e+00 9.25e-01 3.72e+02 angle pdb=" C ALA B 307 " pdb=" N PRO B 308 " pdb=" CA PRO B 308 " ideal model delta sigma weight residual 118.97 137.39 -18.42 1.04e+00 9.25e-01 3.14e+02 angle pdb=" C LEU H 138 " pdb=" N ALA H 139 " pdb=" CA ALA H 139 " ideal model delta sigma weight residual 120.49 138.84 -18.35 1.42e+00 4.96e-01 1.67e+02 angle pdb=" N CYS A 200 " pdb=" CA CYS A 200 " pdb=" CB CYS A 200 " ideal model delta sigma weight residual 109.51 93.33 16.18 1.58e+00 4.01e-01 1.05e+02 ... (remaining 32200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.35: 12693 20.35 - 40.70: 1290 40.70 - 61.05: 170 61.05 - 81.40: 45 81.40 - 101.75: 15 Dihedral angle restraints: 14213 sinusoidal: 5745 harmonic: 8468 Sorted by residual: dihedral pdb=" CB CYS M 136 " pdb=" SG CYS M 136 " pdb=" SG CYS M 196 " pdb=" CB CYS M 196 " ideal model delta sinusoidal sigma weight residual -86.00 -5.32 -80.68 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CB CYS E 130 " pdb=" SG CYS E 130 " pdb=" SG CYS E 144 " pdb=" CB CYS E 144 " ideal model delta sinusoidal sigma weight residual 93.00 18.56 74.44 1 1.00e+01 1.00e-02 7.03e+01 dihedral pdb=" CB CYS A 135 " pdb=" SG CYS A 135 " pdb=" SG CYS A 149 " pdb=" CB CYS A 149 " ideal model delta sinusoidal sigma weight residual 93.00 32.04 60.96 1 1.00e+01 1.00e-02 4.94e+01 ... (remaining 14210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.659: 3737 0.659 - 1.317: 2 1.317 - 1.976: 1 1.976 - 2.634: 1 2.634 - 3.293: 1 Chirality restraints: 3742 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " pdb=" O4 NAG B 401 " both_signs ideal model delta sigma weight residual False -2.40 0.89 -3.29 2.00e-02 2.50e+03 2.71e+04 chirality pdb=" C1 BMA G 2 " pdb=" O4 NAG G 1 " pdb=" C2 BMA G 2 " pdb=" O5 BMA G 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-02 2.50e+03 1.17e+03 chirality pdb=" C1 BMA F 2 " pdb=" O4 NAG F 1 " pdb=" C2 BMA F 2 " pdb=" O5 BMA F 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.43e+02 ... (remaining 3739 not shown) Planarity restraints: 3983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 143 " -0.166 2.00e-02 2.50e+03 1.96e-01 4.82e+02 pdb=" CG ASN B 143 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN B 143 " 0.029 2.00e-02 2.50e+03 pdb=" ND2 ASN B 143 " 0.332 2.00e-02 2.50e+03 pdb=" C1 NAG B 401 " -0.230 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 143 " 0.141 2.00e-02 2.50e+03 1.48e-01 2.75e+02 pdb=" CG ASN C 143 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN C 143 " -0.061 2.00e-02 2.50e+03 pdb=" ND2 ASN C 143 " -0.233 2.00e-02 2.50e+03 pdb=" C1 NAG C 401 " 0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 304 " -0.032 2.00e-02 2.50e+03 6.69e-02 4.48e+01 pdb=" C HIS B 304 " 0.116 2.00e-02 2.50e+03 pdb=" O HIS B 304 " -0.044 2.00e-02 2.50e+03 pdb=" N THR B 305 " -0.039 2.00e-02 2.50e+03 ... (remaining 3980 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 254 2.58 - 3.16: 16203 3.16 - 3.74: 34151 3.74 - 4.32: 45039 4.32 - 4.90: 74920 Nonbonded interactions: 170567 Sorted by model distance: nonbonded pdb=" O PRO M 81 " pdb=" CD1 ILE M 108 " model vdw 2.004 3.460 nonbonded pdb=" O VAL B 197 " pdb=" OD1 ASP B 198 " model vdw 2.021 3.040 nonbonded pdb=" O GLN M 39 " pdb=" CB ALA M 85 " model vdw 2.048 3.460 nonbonded pdb=" CB SER E 84 " pdb=" O SER E 108 " model vdw 2.085 3.440 nonbonded pdb=" CB ASN D 102 " pdb=" CE1 PHE D 107 " model vdw 2.156 3.740 ... (remaining 170562 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 'D' } ncs_group { reference = (chain 'B' and (resid 2 through 325 or resid 333 through 365)) selection = (chain 'C' and resid 2 through 365) selection = (chain 'E' and resid 2 through 365) } ncs_group { reference = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) } ncs_group { reference = (chain 'H' and (resid 3 through 184 or resid 186 through 229)) selection = (chain 'K' and (resid 3 through 122 or resid 131 through 184 or resid 186 throug \ h 229)) } ncs_group { reference = (chain 'L' and (resid 2 through 23 or resid 25 through 214)) selection = (chain 'M' and (resid 2 through 23 or resid 25 through 108 or resid 113 through \ 214)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 13.790 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 62.630 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 : 0.014 0.296 23620 Z= 0.929 Angle : 1.546 33.255 32205 Z= 0.878 Chirality : 0.109 3.293 3742 Planarity : 0.011 0.109 3978 Dihedral : 16.343 101.747 8669 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.08 % Allowed : 13.81 % Favored : 86.11 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 9.33 % 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: -4.48 (0.13), residues: 2834 helix: -4.66 (0.08), residues: 710 sheet: -1.38 (0.18), residues: 819 loop : -2.98 (0.14), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP H 110 HIS 0.010 0.002 HIS K 38 PHE 0.045 0.004 PHE A 322 TYR 0.042 0.004 TYR B 340 ARG 0.010 0.001 ARG C 207 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 284 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8849 (mp0) REVERT: B 77 MET cc_start: 0.8751 (mtp) cc_final: 0.8302 (ttm) REVERT: B 324 MET cc_start: 0.6545 (ptp) cc_final: 0.6111 (ptt) REVERT: B 325 GLN cc_start: 0.6353 (mm110) cc_final: 0.6147 (tp40) REVERT: D 240 TYR cc_start: 0.8500 (t80) cc_final: 0.7894 (t80) REVERT: D 310 ARG cc_start: 0.6596 (tpt170) cc_final: 0.6266 (tpt90) REVERT: D 413 GLN cc_start: 0.8050 (mt0) cc_final: 0.7436 (mp10) REVERT: D 470 LEU cc_start: 0.8649 (tp) cc_final: 0.8375 (tp) REVERT: E 36 MET cc_start: 0.8320 (ppp) cc_final: 0.8028 (ppp) REVERT: H 23 LEU cc_start: 0.6835 (mt) cc_final: 0.6267 (mt) REVERT: H 73 ILE cc_start: 0.8409 (mt) cc_final: 0.8151 (mt) REVERT: H 108 GLU cc_start: 0.8462 (tt0) cc_final: 0.8209 (tm-30) REVERT: H 119 GLN cc_start: 0.8017 (pm20) cc_final: 0.6644 (mm110) REVERT: L 47 LEU cc_start: 0.7425 (tp) cc_final: 0.5418 (tt) REVERT: K 35 PHE cc_start: 0.7692 (m-80) cc_final: 0.7396 (m-80) REVERT: K 81 THR cc_start: 0.6921 (m) cc_final: 0.6631 (p) REVERT: K 83 TYR cc_start: 0.6443 (m-80) cc_final: 0.5998 (m-80) REVERT: M 87 TYR cc_start: 0.5856 (m-80) cc_final: 0.5307 (m-80) REVERT: M 92 TYR cc_start: 0.7867 (p90) cc_final: 0.7446 (p90) outliers start: 2 outliers final: 2 residues processed: 286 average time/residue: 0.3418 time to fit residues: 154.3632 Evaluate side-chains 206 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain E residue 86 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 237 optimal weight: 10.0000 chunk 212 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 143 optimal weight: 0.4980 chunk 113 optimal weight: 0.4980 chunk 220 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 133 optimal weight: 0.4980 chunk 163 optimal weight: 0.9980 chunk 255 optimal weight: 30.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 HIS A 405 HIS A 435 GLN B 60 GLN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 ASN C 109 ASN ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 HIS D 101 ASN D 119 HIS D 430 GLN D 445 GLN E 190 ASN H 185 GLN B L 91 GLN M 90 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 23620 Z= 0.214 Angle : 0.700 11.081 32205 Z= 0.362 Chirality : 0.046 0.314 3742 Planarity : 0.006 0.081 3978 Dihedral : 7.888 57.840 3343 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.59 % Allowed : 16.94 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.14), residues: 2834 helix: -2.39 (0.15), residues: 714 sheet: -1.03 (0.18), residues: 817 loop : -2.24 (0.15), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 110 HIS 0.008 0.001 HIS A 405 PHE 0.023 0.001 PHE B 359 TYR 0.026 0.001 TYR K 53 ARG 0.018 0.001 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 240 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 TRP cc_start: 0.7677 (t-100) cc_final: 0.6672 (t-100) REVERT: A 350 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8837 (mp0) REVERT: B 77 MET cc_start: 0.8659 (mtp) cc_final: 0.8226 (ttm) REVERT: B 324 MET cc_start: 0.6203 (ptp) cc_final: 0.5963 (ptt) REVERT: B 343 MET cc_start: 0.7992 (tpp) cc_final: 0.7629 (tpp) REVERT: C 21 ILE cc_start: 0.8725 (pt) cc_final: 0.8401 (mt) REVERT: D 11 GLU cc_start: 0.8139 (tt0) cc_final: 0.7917 (mt-10) REVERT: D 101 ASN cc_start: 0.9039 (OUTLIER) cc_final: 0.8657 (t0) REVERT: D 310 ARG cc_start: 0.6476 (tpt170) cc_final: 0.6270 (tpt90) REVERT: D 400 MET cc_start: 0.8126 (mtp) cc_final: 0.7850 (mmm) REVERT: D 481 TRP cc_start: 0.5840 (t-100) cc_final: 0.5600 (t-100) REVERT: E 95 TYR cc_start: 0.8997 (OUTLIER) cc_final: 0.8160 (m-80) REVERT: H 9 GLU cc_start: 0.6562 (mp0) cc_final: 0.6311 (mp0) REVERT: H 108 GLU cc_start: 0.8442 (tt0) cc_final: 0.8029 (tm-30) REVERT: H 112 LYS cc_start: 0.8273 (mttt) cc_final: 0.7329 (mttt) REVERT: H 119 GLN cc_start: 0.8195 (pm20) cc_final: 0.6522 (mm110) REVERT: L 86 THR cc_start: 0.6250 (m) cc_final: 0.5516 (t) REVERT: L 88 TYR cc_start: 0.6490 (m-10) cc_final: 0.6080 (m-10) REVERT: K 35 PHE cc_start: 0.7469 (m-80) cc_final: 0.7024 (m-10) REVERT: K 81 THR cc_start: 0.6762 (m) cc_final: 0.6377 (p) REVERT: K 108 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8210 (mm-30) REVERT: M 5 MET cc_start: 0.3177 (mmm) cc_final: 0.2218 (ttm) outliers start: 67 outliers final: 36 residues processed: 293 average time/residue: 0.3191 time to fit residues: 151.8556 Evaluate side-chains 245 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 207 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 135 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain M residue 34 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 141 optimal weight: 0.0070 chunk 79 optimal weight: 1.9990 chunk 212 optimal weight: 8.9990 chunk 173 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 255 optimal weight: 40.0000 chunk 276 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 253 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 ASN D 306 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 23620 Z= 0.240 Angle : 0.655 10.413 32205 Z= 0.335 Chirality : 0.045 0.233 3742 Planarity : 0.005 0.073 3978 Dihedral : 6.278 57.977 3339 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.63 % Favored : 95.34 % Rotamer: Outliers : 3.13 % Allowed : 19.03 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.15), residues: 2834 helix: -1.20 (0.18), residues: 725 sheet: -0.76 (0.18), residues: 798 loop : -1.88 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 110 HIS 0.004 0.001 HIS A 111 PHE 0.032 0.001 PHE A 286 TYR 0.018 0.001 TYR K 63 ARG 0.007 0.000 ARG K 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 223 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7899 (t70) REVERT: B 324 MET cc_start: 0.6037 (ptp) cc_final: 0.5740 (ptt) REVERT: B 343 MET cc_start: 0.8070 (tpp) cc_final: 0.7733 (tpp) REVERT: C 21 ILE cc_start: 0.8778 (pt) cc_final: 0.8533 (mt) REVERT: D 11 GLU cc_start: 0.8177 (tt0) cc_final: 0.7918 (mt-10) REVERT: D 222 ILE cc_start: 0.9483 (tp) cc_final: 0.9129 (tt) REVERT: E 95 TYR cc_start: 0.9033 (OUTLIER) cc_final: 0.8210 (m-80) REVERT: H 9 GLU cc_start: 0.6600 (mp0) cc_final: 0.6361 (mp0) REVERT: H 108 GLU cc_start: 0.8440 (tt0) cc_final: 0.8019 (tm-30) REVERT: H 112 LYS cc_start: 0.8283 (mttt) cc_final: 0.7316 (mttt) REVERT: H 119 GLN cc_start: 0.8170 (pm20) cc_final: 0.6370 (mm110) REVERT: L 86 THR cc_start: 0.6671 (m) cc_final: 0.6407 (t) REVERT: K 35 PHE cc_start: 0.7504 (m-80) cc_final: 0.7150 (m-10) outliers start: 81 outliers final: 58 residues processed: 282 average time/residue: 0.3164 time to fit residues: 146.6920 Evaluate side-chains 259 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 199 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 220 CYS Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 37 TYR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain M residue 34 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 252 optimal weight: 20.0000 chunk 192 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 171 optimal weight: 0.0470 chunk 256 optimal weight: 3.9990 chunk 271 optimal weight: 5.9990 chunk 134 optimal weight: 0.6980 chunk 243 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 ASN D 223 ASN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 23620 Z= 0.178 Angle : 0.600 12.088 32205 Z= 0.306 Chirality : 0.043 0.246 3742 Planarity : 0.005 0.063 3978 Dihedral : 5.595 57.027 3339 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.13 % Favored : 95.83 % Rotamer: Outliers : 3.68 % Allowed : 19.30 % Favored : 77.02 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 9.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.15), residues: 2834 helix: -0.50 (0.19), residues: 730 sheet: -0.57 (0.18), residues: 801 loop : -1.66 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 110 HIS 0.003 0.001 HIS A 111 PHE 0.027 0.001 PHE A 286 TYR 0.021 0.001 TYR K 53 ARG 0.005 0.000 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 224 time to evaluate : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: A 405 HIS cc_start: 0.8736 (m-70) cc_final: 0.8523 (m-70) REVERT: B 77 MET cc_start: 0.8695 (mtp) cc_final: 0.8350 (ttm) REVERT: B 324 MET cc_start: 0.5966 (ptp) cc_final: 0.5648 (ptt) REVERT: B 343 MET cc_start: 0.8146 (tpp) cc_final: 0.7806 (tpp) REVERT: C 21 ILE cc_start: 0.8731 (pt) cc_final: 0.8494 (mt) REVERT: C 95 TYR cc_start: 0.9061 (OUTLIER) cc_final: 0.8785 (m-10) REVERT: C 321 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8214 (mm) REVERT: D 11 GLU cc_start: 0.8105 (tt0) cc_final: 0.7891 (mt-10) REVERT: D 222 ILE cc_start: 0.9485 (tp) cc_final: 0.9169 (tt) REVERT: D 240 TYR cc_start: 0.8165 (t80) cc_final: 0.7571 (t80) REVERT: D 400 MET cc_start: 0.8441 (mmm) cc_final: 0.7889 (mmm) REVERT: E 95 TYR cc_start: 0.8980 (OUTLIER) cc_final: 0.8160 (m-80) REVERT: E 280 MET cc_start: 0.8401 (ttm) cc_final: 0.8052 (mtt) REVERT: H 108 GLU cc_start: 0.8454 (tt0) cc_final: 0.8006 (tm-30) REVERT: H 119 GLN cc_start: 0.8124 (pm20) cc_final: 0.6416 (mm110) REVERT: L 86 THR cc_start: 0.6673 (m) cc_final: 0.6096 (t) REVERT: L 88 TYR cc_start: 0.6390 (m-10) cc_final: 0.5700 (m-10) REVERT: K 35 PHE cc_start: 0.7485 (m-80) cc_final: 0.7045 (m-10) outliers start: 95 outliers final: 61 residues processed: 292 average time/residue: 0.3009 time to fit residues: 145.9772 Evaluate side-chains 274 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 209 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 220 CYS Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain D residue 481 TRP Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 37 TYR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 108 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 226 optimal weight: 0.0980 chunk 154 optimal weight: 6.9990 chunk 3 optimal weight: 0.5980 chunk 202 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 231 optimal weight: 9.9990 chunk 187 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 243 optimal weight: 10.0000 chunk 68 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 HIS ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23620 Z= 0.160 Angle : 0.575 10.192 32205 Z= 0.292 Chirality : 0.043 0.246 3742 Planarity : 0.004 0.061 3978 Dihedral : 5.267 57.175 3339 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.06 % Favored : 95.90 % Rotamer: Outliers : 3.79 % Allowed : 20.54 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.16), residues: 2834 helix: -0.06 (0.20), residues: 732 sheet: -0.46 (0.18), residues: 812 loop : -1.57 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 349 HIS 0.002 0.001 HIS D 68 PHE 0.027 0.001 PHE A 286 TYR 0.023 0.001 TYR K 63 ARG 0.005 0.000 ARG M 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 220 time to evaluate : 2.743 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: B 77 MET cc_start: 0.8714 (mtp) cc_final: 0.8393 (ttm) REVERT: B 324 MET cc_start: 0.5593 (ptp) cc_final: 0.5309 (ptt) REVERT: B 343 MET cc_start: 0.8025 (tpp) cc_final: 0.7698 (tpp) REVERT: C 95 TYR cc_start: 0.9075 (OUTLIER) cc_final: 0.8769 (m-10) REVERT: C 317 LYS cc_start: 0.8349 (tmtt) cc_final: 0.8088 (tmtt) REVERT: C 321 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8059 (mm) REVERT: D 11 GLU cc_start: 0.8129 (tt0) cc_final: 0.7909 (mt-10) REVERT: D 168 MET cc_start: 0.7791 (ptm) cc_final: 0.7540 (ptp) REVERT: D 240 TYR cc_start: 0.8155 (t80) cc_final: 0.7574 (t80) REVERT: D 400 MET cc_start: 0.8464 (mmm) cc_final: 0.8233 (tpp) REVERT: E 95 TYR cc_start: 0.8966 (OUTLIER) cc_final: 0.8177 (m-80) REVERT: H 108 GLU cc_start: 0.8494 (tt0) cc_final: 0.8051 (tm-30) REVERT: L 86 THR cc_start: 0.6318 (m) cc_final: 0.5611 (t) REVERT: L 88 TYR cc_start: 0.6011 (m-10) cc_final: 0.5450 (m-10) REVERT: K 35 PHE cc_start: 0.7530 (m-80) cc_final: 0.7145 (m-10) REVERT: K 101 ARG cc_start: 0.7466 (ptm-80) cc_final: 0.6948 (ptt-90) outliers start: 98 outliers final: 70 residues processed: 295 average time/residue: 0.3133 time to fit residues: 152.2037 Evaluate side-chains 283 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 210 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 220 CYS Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 481 TRP Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 37 TYR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 108 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 91 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 53 optimal weight: 0.0870 chunk 159 optimal weight: 2.9990 chunk 67 optimal weight: 0.1980 chunk 271 optimal weight: 6.9990 chunk 225 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 89 optimal weight: 0.0570 chunk 142 optimal weight: 0.9980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23620 Z= 0.146 Angle : 0.565 13.354 32205 Z= 0.285 Chirality : 0.042 0.248 3742 Planarity : 0.004 0.058 3978 Dihedral : 5.022 56.759 3339 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.95 % Favored : 96.01 % Rotamer: Outliers : 3.48 % Allowed : 20.93 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.33 % 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: -1.09 (0.16), residues: 2834 helix: 0.30 (0.20), residues: 724 sheet: -0.35 (0.18), residues: 812 loop : -1.53 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 349 HIS 0.002 0.001 HIS D 68 PHE 0.027 0.001 PHE K 71 TYR 0.023 0.001 TYR K 63 ARG 0.005 0.000 ARG K 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 229 time to evaluate : 2.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ASN cc_start: 0.8877 (m-40) cc_final: 0.8510 (m110) REVERT: A 405 HIS cc_start: 0.8792 (m-70) cc_final: 0.8375 (t70) REVERT: B 77 MET cc_start: 0.8773 (mtp) cc_final: 0.8458 (ttm) REVERT: B 324 MET cc_start: 0.5849 (ptp) cc_final: 0.5361 (ptt) REVERT: B 343 MET cc_start: 0.8089 (tpp) cc_final: 0.7754 (tpp) REVERT: C 95 TYR cc_start: 0.9077 (OUTLIER) cc_final: 0.8682 (m-10) REVERT: C 317 LYS cc_start: 0.8270 (tmtt) cc_final: 0.7890 (tmtt) REVERT: C 321 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.7827 (mm) REVERT: D 11 GLU cc_start: 0.8043 (tt0) cc_final: 0.7840 (mt-10) REVERT: D 240 TYR cc_start: 0.8111 (t80) cc_final: 0.7593 (t80) REVERT: D 400 MET cc_start: 0.8363 (mmm) cc_final: 0.8097 (tpp) REVERT: E 95 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.8127 (m-80) REVERT: H 9 GLU cc_start: 0.5406 (mp0) cc_final: 0.4509 (pm20) REVERT: H 108 GLU cc_start: 0.8538 (tt0) cc_final: 0.8096 (tm-30) REVERT: L 88 TYR cc_start: 0.6129 (m-80) cc_final: 0.5905 (m-10) REVERT: K 35 PHE cc_start: 0.7866 (m-80) cc_final: 0.7381 (m-10) REVERT: K 53 TYR cc_start: 0.7023 (p90) cc_final: 0.6453 (p90) REVERT: K 54 ILE cc_start: 0.8648 (tp) cc_final: 0.8163 (mp) REVERT: K 101 ARG cc_start: 0.7399 (ptm-80) cc_final: 0.6851 (ptt-90) outliers start: 90 outliers final: 64 residues processed: 296 average time/residue: 0.3167 time to fit residues: 152.1676 Evaluate side-chains 277 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 210 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 220 CYS Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 481 TRP Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 37 TYR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 108 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 262 optimal weight: 7.9990 chunk 30 optimal weight: 0.0670 chunk 154 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 228 optimal weight: 9.9990 chunk 151 optimal weight: 0.7980 chunk 270 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 125 optimal weight: 0.4980 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23620 Z= 0.252 Angle : 0.605 9.542 32205 Z= 0.308 Chirality : 0.044 0.246 3742 Planarity : 0.005 0.061 3978 Dihedral : 5.195 64.779 3339 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.59 % Favored : 95.37 % Rotamer: Outliers : 3.98 % Allowed : 21.04 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.16), residues: 2834 helix: 0.39 (0.20), residues: 732 sheet: -0.32 (0.18), residues: 796 loop : -1.48 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 349 HIS 0.004 0.001 HIS A 111 PHE 0.024 0.001 PHE A 286 TYR 0.021 0.001 TYR K 53 ARG 0.006 0.000 ARG C 299 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 211 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ASN cc_start: 0.8955 (m-40) cc_final: 0.8619 (m110) REVERT: A 405 HIS cc_start: 0.8522 (m-70) cc_final: 0.8171 (t70) REVERT: B 77 MET cc_start: 0.8746 (mtp) cc_final: 0.8412 (ttm) REVERT: B 324 MET cc_start: 0.5731 (ptp) cc_final: 0.5409 (ptt) REVERT: B 343 MET cc_start: 0.8019 (tpp) cc_final: 0.7740 (tpp) REVERT: C 317 LYS cc_start: 0.8423 (tmtt) cc_final: 0.8188 (tmtt) REVERT: C 321 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8113 (mm) REVERT: D 222 ILE cc_start: 0.9435 (tp) cc_final: 0.9201 (tt) REVERT: D 240 TYR cc_start: 0.8188 (t80) cc_final: 0.7656 (t80) REVERT: D 329 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8712 (mt) REVERT: D 400 MET cc_start: 0.8412 (mmm) cc_final: 0.8167 (tpp) REVERT: E 95 TYR cc_start: 0.8925 (OUTLIER) cc_final: 0.8297 (m-80) REVERT: E 357 CYS cc_start: 0.7941 (t) cc_final: 0.7591 (t) REVERT: H 9 GLU cc_start: 0.5532 (mp0) cc_final: 0.4424 (pm20) REVERT: H 108 GLU cc_start: 0.8540 (tt0) cc_final: 0.8119 (tm-30) REVERT: L 88 TYR cc_start: 0.6174 (m-80) cc_final: 0.5757 (m-10) REVERT: K 35 PHE cc_start: 0.7500 (m-80) cc_final: 0.6990 (m-10) REVERT: K 53 TYR cc_start: 0.7099 (p90) cc_final: 0.6585 (p90) REVERT: K 54 ILE cc_start: 0.8656 (tp) cc_final: 0.8154 (mp) outliers start: 103 outliers final: 81 residues processed: 291 average time/residue: 0.3182 time to fit residues: 153.1910 Evaluate side-chains 286 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 202 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 85 LYS Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 220 CYS Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 481 TRP Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 324 MET Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 37 TYR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 86 MET Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 108 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 167 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 53 optimal weight: 0.0870 chunk 52 optimal weight: 0.5980 chunk 172 optimal weight: 0.5980 chunk 184 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 212 optimal weight: 8.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 23620 Z= 0.177 Angle : 0.571 10.611 32205 Z= 0.289 Chirality : 0.043 0.249 3742 Planarity : 0.004 0.059 3978 Dihedral : 5.062 65.553 3339 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.06 % Favored : 95.90 % Rotamer: Outliers : 3.68 % Allowed : 21.35 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.16), residues: 2834 helix: 0.56 (0.20), residues: 728 sheet: -0.25 (0.18), residues: 807 loop : -1.39 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 349 HIS 0.012 0.001 HIS C 304 PHE 0.022 0.001 PHE A 286 TYR 0.020 0.001 TYR K 53 ARG 0.006 0.000 ARG C 299 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 207 time to evaluate : 2.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 HIS cc_start: 0.8712 (m-70) cc_final: 0.8384 (t70) REVERT: B 324 MET cc_start: 0.5773 (ptp) cc_final: 0.5375 (ptt) REVERT: B 343 MET cc_start: 0.7984 (tpp) cc_final: 0.7738 (tpp) REVERT: C 95 TYR cc_start: 0.9047 (OUTLIER) cc_final: 0.8763 (m-10) REVERT: C 321 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8045 (mm) REVERT: D 222 ILE cc_start: 0.9413 (tp) cc_final: 0.9209 (tt) REVERT: D 240 TYR cc_start: 0.8144 (t80) cc_final: 0.7651 (t80) REVERT: D 329 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8738 (mt) REVERT: D 400 MET cc_start: 0.8373 (mmm) cc_final: 0.8100 (tpp) REVERT: E 95 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.8148 (m-80) REVERT: E 357 CYS cc_start: 0.7904 (t) cc_final: 0.7607 (t) REVERT: H 9 GLU cc_start: 0.5547 (mp0) cc_final: 0.4577 (pm20) REVERT: H 108 GLU cc_start: 0.8546 (tt0) cc_final: 0.8014 (tm-30) REVERT: H 112 LYS cc_start: 0.8442 (mttt) cc_final: 0.7485 (mttt) REVERT: L 86 THR cc_start: 0.5649 (m) cc_final: 0.5176 (t) REVERT: L 88 TYR cc_start: 0.6151 (m-80) cc_final: 0.5434 (m-10) REVERT: K 35 PHE cc_start: 0.7850 (m-80) cc_final: 0.7228 (m-10) REVERT: K 53 TYR cc_start: 0.7203 (p90) cc_final: 0.6745 (p90) REVERT: K 54 ILE cc_start: 0.8642 (tp) cc_final: 0.8070 (mp) outliers start: 95 outliers final: 77 residues processed: 282 average time/residue: 0.2955 time to fit residues: 138.8012 Evaluate side-chains 280 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 199 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 220 CYS Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 481 TRP Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 37 TYR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 108 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 246 optimal weight: 8.9990 chunk 259 optimal weight: 6.9990 chunk 236 optimal weight: 50.0000 chunk 252 optimal weight: 20.0000 chunk 151 optimal weight: 0.0980 chunk 109 optimal weight: 0.7980 chunk 198 optimal weight: 6.9990 chunk 77 optimal weight: 0.4980 chunk 228 optimal weight: 7.9990 chunk 238 optimal weight: 8.9990 chunk 251 optimal weight: 50.0000 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 HIS D 422 ASN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.078 23620 Z= 0.646 Angle : 0.866 10.339 32205 Z= 0.437 Chirality : 0.051 0.250 3742 Planarity : 0.006 0.071 3978 Dihedral : 5.946 65.195 3339 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.57 % Favored : 93.40 % Rotamer: Outliers : 4.06 % Allowed : 21.04 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.16), residues: 2834 helix: -0.10 (0.19), residues: 749 sheet: -0.43 (0.19), residues: 783 loop : -1.56 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP D 349 HIS 0.006 0.002 HIS C 298 PHE 0.030 0.002 PHE E 172 TYR 0.035 0.002 TYR M 94 ARG 0.009 0.001 ARG C 155 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 188 time to evaluate : 2.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 324 MET cc_start: 0.5923 (ptp) cc_final: 0.5425 (ptt) REVERT: B 343 MET cc_start: 0.8191 (tpp) cc_final: 0.7951 (tpp) REVERT: C 277 MET cc_start: 0.7216 (tmm) cc_final: 0.7005 (tmm) REVERT: C 321 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8411 (mm) REVERT: D 163 ILE cc_start: 0.9627 (OUTLIER) cc_final: 0.9423 (mt) REVERT: D 222 ILE cc_start: 0.9454 (tp) cc_final: 0.9208 (tt) REVERT: D 400 MET cc_start: 0.8451 (mmm) cc_final: 0.8166 (tpp) REVERT: E 95 TYR cc_start: 0.9150 (OUTLIER) cc_final: 0.8432 (m-80) REVERT: E 268 ASP cc_start: 0.8226 (t0) cc_final: 0.8010 (t0) REVERT: E 357 CYS cc_start: 0.8162 (t) cc_final: 0.7792 (t) REVERT: H 108 GLU cc_start: 0.8547 (tt0) cc_final: 0.8273 (tm-30) REVERT: L 88 TYR cc_start: 0.6613 (m-80) cc_final: 0.6045 (m-10) REVERT: K 35 PHE cc_start: 0.7312 (m-80) cc_final: 0.6815 (m-80) REVERT: K 53 TYR cc_start: 0.7275 (p90) cc_final: 0.6723 (p90) REVERT: K 54 ILE cc_start: 0.8674 (tp) cc_final: 0.8095 (mp) REVERT: M 63 PHE cc_start: 0.3912 (OUTLIER) cc_final: 0.2455 (m-80) outliers start: 105 outliers final: 82 residues processed: 275 average time/residue: 0.2848 time to fit residues: 131.2765 Evaluate side-chains 270 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 184 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 220 CYS Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 481 TRP Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 37 TYR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 63 PHE Chi-restraints excluded: chain M residue 108 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 165 optimal weight: 0.9980 chunk 266 optimal weight: 0.7980 chunk 162 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 185 optimal weight: 0.1980 chunk 279 optimal weight: 20.0000 chunk 257 optimal weight: 40.0000 chunk 222 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 172 optimal weight: 0.9980 chunk 136 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 HIS ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN L 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 23620 Z= 0.196 Angle : 0.614 13.482 32205 Z= 0.311 Chirality : 0.044 0.238 3742 Planarity : 0.004 0.063 3978 Dihedral : 5.384 66.203 3339 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 2.75 % Allowed : 22.59 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.16), residues: 2834 helix: 0.51 (0.20), residues: 730 sheet: -0.26 (0.19), residues: 793 loop : -1.33 (0.18), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 349 HIS 0.003 0.001 HIS A 111 PHE 0.022 0.001 PHE A 286 TYR 0.030 0.001 TYR M 94 ARG 0.004 0.000 ARG C 155 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5668 Ramachandran restraints generated. 2834 Oldfield, 0 Emsley, 2834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 197 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8464 (ptp) REVERT: A 349 TRP cc_start: 0.7835 (t-100) cc_final: 0.6384 (t-100) REVERT: B 324 MET cc_start: 0.5338 (ptp) cc_final: 0.4764 (ptt) REVERT: B 343 MET cc_start: 0.8124 (tpp) cc_final: 0.7921 (tpp) REVERT: C 95 TYR cc_start: 0.9058 (OUTLIER) cc_final: 0.8834 (m-10) REVERT: D 222 ILE cc_start: 0.9407 (tp) cc_final: 0.9177 (tt) REVERT: D 240 TYR cc_start: 0.8330 (t80) cc_final: 0.7803 (t80) REVERT: D 400 MET cc_start: 0.8435 (mmm) cc_final: 0.8128 (tpp) REVERT: E 95 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.8121 (m-80) REVERT: E 268 ASP cc_start: 0.8094 (t0) cc_final: 0.7872 (t0) REVERT: E 357 CYS cc_start: 0.8116 (t) cc_final: 0.7847 (t) REVERT: H 9 GLU cc_start: 0.5350 (mp0) cc_final: 0.4212 (pm20) REVERT: H 108 GLU cc_start: 0.8542 (tt0) cc_final: 0.7998 (tm-30) REVERT: H 112 LYS cc_start: 0.8460 (mttt) cc_final: 0.7588 (mttt) REVERT: L 105 LYS cc_start: 0.6453 (tppt) cc_final: 0.5926 (mtmt) REVERT: K 53 TYR cc_start: 0.6853 (p90) cc_final: 0.6387 (p90) REVERT: K 54 ILE cc_start: 0.8655 (tp) cc_final: 0.8257 (mp) outliers start: 71 outliers final: 61 residues processed: 258 average time/residue: 0.3150 time to fit residues: 135.7295 Evaluate side-chains 255 residues out of total 2583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 191 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 220 CYS Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 309 TRP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 68 HIS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 252 CYS Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 481 TRP Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 37 TYR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 59 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 177 optimal weight: 0.7980 chunk 237 optimal weight: 50.0000 chunk 68 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 223 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 229 optimal weight: 50.0000 chunk 28 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 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 = 0.4006 r_free = 0.4006 target = 0.146967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.111966 restraints weight = 59708.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.106727 restraints weight = 43174.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.107579 restraints weight = 37555.855| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 23620 Z= 0.212 Angle : 0.601 9.576 32205 Z= 0.304 Chirality : 0.043 0.256 3742 Planarity : 0.004 0.062 3978 Dihedral : 5.226 66.394 3339 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.70 % Favored : 95.27 % Rotamer: Outliers : 2.82 % Allowed : 22.48 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.16), residues: 2834 helix: 0.67 (0.20), residues: 726 sheet: -0.27 (0.19), residues: 800 loop : -1.31 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 349 HIS 0.007 0.001 HIS B 46 PHE 0.023 0.001 PHE A 286 TYR 0.028 0.001 TYR M 94 ARG 0.004 0.000 ARG C 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4216.21 seconds wall clock time: 78 minutes 23.98 seconds (4703.98 seconds total)