Starting phenix.real_space_refine on Sat Feb 17 16:28:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi4_32521/02_2024/7wi4_32521_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi4_32521/02_2024/7wi4_32521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi4_32521/02_2024/7wi4_32521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi4_32521/02_2024/7wi4_32521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi4_32521/02_2024/7wi4_32521_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi4_32521/02_2024/7wi4_32521_updated.pdb" } resolution = 3.4 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= 0.004 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 18 5.49 5 Mg 6 5.21 5 S 120 5.16 5 C 12036 2.51 5 N 3462 2.21 5 O 3636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 312": "NH1" <-> "NH2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "D PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "D ASP 345": "OD1" <-> "OD2" Residue "D ARG 374": "NH1" <-> "NH2" Residue "D ARG 378": "NH1" <-> "NH2" Residue "D ASP 390": "OD1" <-> "OD2" Residue "D GLU 405": "OE1" <-> "OE2" Residue "D PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 477": "OE1" <-> "OE2" Residue "D ARG 543": "NH1" <-> "NH2" Residue "D GLU 548": "OE1" <-> "OE2" Residue "D TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 599": "NH1" <-> "NH2" Residue "E TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 286": "OE1" <-> "OE2" Residue "E ARG 312": "NH1" <-> "NH2" Residue "E ARG 325": "NH1" <-> "NH2" Residue "E PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 374": "NH1" <-> "NH2" Residue "E ARG 378": "NH1" <-> "NH2" Residue "E PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 492": "OD1" <-> "OD2" Residue "E ARG 543": "NH1" <-> "NH2" Residue "E ARG 599": "NH1" <-> "NH2" Residue "F TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 283": "OD1" <-> "OD2" Residue "F GLU 289": "OE1" <-> "OE2" Residue "F ARG 312": "NH1" <-> "NH2" Residue "F ARG 325": "NH1" <-> "NH2" Residue "F PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 374": "NH1" <-> "NH2" Residue "F ARG 378": "NH1" <-> "NH2" Residue "F PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 543": "NH1" <-> "NH2" Residue "F GLU 548": "OE1" <-> "OE2" Residue "F ARG 599": "NH1" <-> "NH2" Residue "B PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B ARG 312": "NH1" <-> "NH2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B ASP 345": "OD1" <-> "OD2" Residue "B ARG 374": "NH1" <-> "NH2" Residue "B ARG 378": "NH1" <-> "NH2" Residue "B PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 543": "NH1" <-> "NH2" Residue "B ARG 599": "NH1" <-> "NH2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 312": "NH1" <-> "NH2" Residue "C ARG 325": "NH1" <-> "NH2" Residue "C PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 374": "NH1" <-> "NH2" Residue "C ARG 378": "NH1" <-> "NH2" Residue "C PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 427": "OE1" <-> "OE2" Residue "C PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 492": "OD1" <-> "OD2" Residue "C ARG 543": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19284 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3181 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 bond proxies already assigned to first conformer: 3205 Chain: "D" Number of atoms: 3181 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 bond proxies already assigned to first conformer: 3205 Chain: "E" Number of atoms: 3181 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 bond proxies already assigned to first conformer: 3205 Chain: "F" Number of atoms: 3181 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 bond proxies already assigned to first conformer: 3205 Chain: "B" Number of atoms: 3181 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 bond proxies already assigned to first conformer: 3205 Chain: "C" Number of atoms: 3181 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 410, 3169 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 20, 'TRANS': 389} Chain breaks: 4 bond proxies already assigned to first conformer: 3205 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 18.84, per 1000 atoms: 0.98 Number of scatterers: 19284 At special positions: 0 Unit cell: (137.28, 140.026, 90.6048, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 120 16.00 P 18 15.00 Mg 6 11.99 O 3636 8.00 N 3462 7.00 C 12036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.10 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 418 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 414 " pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 418 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 414 " pdb=" ZN C 702 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 414 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 418 " pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 418 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 414 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 414 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 418 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" NE2 HIS F 418 " pdb="ZN ZN F 702 " - pdb=" NE2 HIS F 414 " 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4536 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 10 sheets defined 49.2% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.92 Creating SS restraints... Processing helix chain 'A' and resid 158 through 171 removed outlier: 5.000A pdb=" N LEU A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 200 through 210 removed outlier: 4.027A pdb=" N LYS A 203 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA A 204 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 205 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 206 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA A 209 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.752A pdb=" N GLN A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 374 Processing helix chain 'A' and resid 382 through 393 removed outlier: 3.836A pdb=" N LYS A 387 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 418 removed outlier: 3.656A pdb=" N SER A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N HIS A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN A 415 " --> pdb=" O THR A 411 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLY A 417 " --> pdb=" O TYR A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 422 No H-bonds generated for 'chain 'A' and resid 420 through 422' Processing helix chain 'A' and resid 459 through 480 removed outlier: 3.554A pdb=" N TYR A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLY A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 474 " --> pdb=" O TYR A 470 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 506 removed outlier: 3.853A pdb=" N VAL A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 566 removed outlier: 3.554A pdb=" N ARG A 543 " --> pdb=" O ASP A 539 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP A 566 " --> pdb=" O GLN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 580 removed outlier: 3.516A pdb=" N HIS A 572 " --> pdb=" O MET A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 594 Processing helix chain 'D' and resid 158 through 171 Processing helix chain 'D' and resid 174 through 176 No H-bonds generated for 'chain 'D' and resid 174 through 176' Processing helix chain 'D' and resid 200 through 210 removed outlier: 4.980A pdb=" N ALA D 209 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LYS D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 239 Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 324 through 337 removed outlier: 3.831A pdb=" N ARG D 336 " --> pdb=" O LYS D 332 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ARG D 337 " --> pdb=" O VAL D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 351 Processing helix chain 'D' and resid 358 through 375 removed outlier: 3.619A pdb=" N GLY D 375 " --> pdb=" O PHE D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 393 Processing helix chain 'D' and resid 405 through 415 Processing helix chain 'D' and resid 418 through 424 removed outlier: 3.953A pdb=" N LEU D 424 " --> pdb=" O ILE D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 480 removed outlier: 3.852A pdb=" N ILE D 466 " --> pdb=" O LEU D 462 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER D 467 " --> pdb=" O GLU D 463 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY D 471 " --> pdb=" O SER D 467 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY D 472 " --> pdb=" O THR D 468 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ARG D 473 " --> pdb=" O LEU D 469 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE D 479 " --> pdb=" O ALA D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 506 removed outlier: 3.514A pdb=" N ALA D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 504 " --> pdb=" O ALA D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 566 removed outlier: 3.764A pdb=" N ASP D 546 " --> pdb=" O ALA D 542 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP D 566 " --> pdb=" O GLN D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 580 removed outlier: 3.542A pdb=" N MET D 579 " --> pdb=" O LYS D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 593 Processing helix chain 'E' and resid 158 through 171 removed outlier: 4.494A pdb=" N LEU E 167 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 176 No H-bonds generated for 'chain 'E' and resid 174 through 176' Processing helix chain 'E' and resid 200 through 206 removed outlier: 3.550A pdb=" N ILE E 205 " --> pdb=" O ALA E 202 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA E 206 " --> pdb=" O LYS E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 210 No H-bonds generated for 'chain 'E' and resid 208 through 210' Processing helix chain 'E' and resid 233 through 237 Processing helix chain 'E' and resid 274 through 285 removed outlier: 4.329A pdb=" N VAL E 280 " --> pdb=" O ASN E 276 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU E 281 " --> pdb=" O GLN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 333 removed outlier: 4.164A pdb=" N GLU E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN E 329 " --> pdb=" O ARG E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 Processing helix chain 'E' and resid 358 through 375 removed outlier: 3.739A pdb=" N GLY E 375 " --> pdb=" O PHE E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 393 removed outlier: 3.993A pdb=" N LYS E 387 " --> pdb=" O VAL E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 424 removed outlier: 3.622A pdb=" N SER E 410 " --> pdb=" O ALA E 406 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY E 417 " --> pdb=" O TYR E 413 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS E 418 " --> pdb=" O HIS E 414 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE E 420 " --> pdb=" O ALA E 416 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG E 423 " --> pdb=" O ALA E 419 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU E 424 " --> pdb=" O ILE E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 480 removed outlier: 3.928A pdb=" N TYR E 470 " --> pdb=" O ILE E 466 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY E 471 " --> pdb=" O SER E 467 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLY E 472 " --> pdb=" O THR E 468 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG E 473 " --> pdb=" O LEU E 469 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU E 474 " --> pdb=" O TYR E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 487 through 505 removed outlier: 3.553A pdb=" N SER E 490 " --> pdb=" O THR E 487 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASN E 491 " --> pdb=" O GLY E 488 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE E 493 " --> pdb=" O SER E 490 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS E 494 " --> pdb=" O ASN E 491 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL E 495 " --> pdb=" O ASP E 492 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA E 500 " --> pdb=" O THR E 497 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET E 503 " --> pdb=" O ALA E 500 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL E 504 " --> pdb=" O ARG E 501 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR E 505 " --> pdb=" O ASN E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 566 removed outlier: 3.864A pdb=" N ASP E 546 " --> pdb=" O ALA E 542 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP E 566 " --> pdb=" O GLN E 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 568 through 580 removed outlier: 3.508A pdb=" N HIS E 572 " --> pdb=" O MET E 568 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA E 577 " --> pdb=" O ALA E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 586 through 593 removed outlier: 3.745A pdb=" N ASP E 590 " --> pdb=" O ALA E 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 171 removed outlier: 4.943A pdb=" N LEU F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL F 168 " --> pdb=" O VAL F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 176 No H-bonds generated for 'chain 'F' and resid 174 through 176' Processing helix chain 'F' and resid 201 through 210 removed outlier: 4.690A pdb=" N ALA F 209 " --> pdb=" O ILE F 205 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS F 210 " --> pdb=" O ALA F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 239 removed outlier: 3.709A pdb=" N GLU F 238 " --> pdb=" O ARG F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 283 removed outlier: 4.410A pdb=" N ASN F 276 " --> pdb=" O GLN F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 337 removed outlier: 3.818A pdb=" N GLN F 329 " --> pdb=" O ARG F 325 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS F 334 " --> pdb=" O ILE F 330 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG F 336 " --> pdb=" O LYS F 332 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ARG F 337 " --> pdb=" O VAL F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 352 Processing helix chain 'F' and resid 358 through 375 removed outlier: 3.820A pdb=" N GLY F 375 " --> pdb=" O PHE F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 393 removed outlier: 3.607A pdb=" N LYS F 387 " --> pdb=" O VAL F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 418 removed outlier: 4.001A pdb=" N SER F 410 " --> pdb=" O ALA F 406 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS F 414 " --> pdb=" O SER F 410 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN F 415 " --> pdb=" O THR F 411 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA F 416 " --> pdb=" O ALA F 412 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLY F 417 " --> pdb=" O TYR F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 removed outlier: 3.693A pdb=" N LEU F 424 " --> pdb=" O ILE F 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 420 through 424' Processing helix chain 'F' and resid 459 through 480 removed outlier: 4.005A pdb=" N GLY F 472 " --> pdb=" O THR F 468 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ARG F 473 " --> pdb=" O LEU F 469 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU F 474 " --> pdb=" O TYR F 470 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA F 475 " --> pdb=" O GLY F 471 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU F 476 " --> pdb=" O GLY F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 484 No H-bonds generated for 'chain 'F' and resid 482 through 484' Processing helix chain 'F' and resid 494 through 505 removed outlier: 3.753A pdb=" N VAL F 504 " --> pdb=" O ALA F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 566 removed outlier: 3.558A pdb=" N ILE F 545 " --> pdb=" O THR F 541 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU F 564 " --> pdb=" O ALA F 560 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP F 566 " --> pdb=" O GLN F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 568 through 580 removed outlier: 3.582A pdb=" N HIS F 572 " --> pdb=" O MET F 568 " (cutoff:3.500A) Processing helix chain 'F' and resid 586 through 594 Processing helix chain 'B' and resid 158 through 171 removed outlier: 4.604A pdb=" N LEU B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 198 through 210 removed outlier: 4.257A pdb=" N ALA B 202 " --> pdb=" O LYS B 198 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA B 206 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY B 207 " --> pdb=" O LYS B 203 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ALA B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 273 through 285 Processing helix chain 'B' and resid 324 through 337 removed outlier: 3.804A pdb=" N ARG B 336 " --> pdb=" O LYS B 332 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG B 337 " --> pdb=" O VAL B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 358 through 374 Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 405 through 418 removed outlier: 3.696A pdb=" N ALA B 412 " --> pdb=" O LYS B 408 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY B 417 " --> pdb=" O TYR B 413 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS B 418 " --> pdb=" O HIS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 424 removed outlier: 3.510A pdb=" N LEU B 424 " --> pdb=" O ILE B 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 420 through 424' Processing helix chain 'B' and resid 459 through 480 removed outlier: 3.992A pdb=" N ILE B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER B 467 " --> pdb=" O GLU B 463 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY B 471 " --> pdb=" O SER B 467 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLY B 472 " --> pdb=" O THR B 468 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ARG B 473 " --> pdb=" O LEU B 469 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU B 474 " --> pdb=" O TYR B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 505 removed outlier: 3.773A pdb=" N ASN B 502 " --> pdb=" O ASN B 498 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 504 " --> pdb=" O ALA B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 566 removed outlier: 3.864A pdb=" N ASP B 546 " --> pdb=" O ALA B 542 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 580 Processing helix chain 'B' and resid 586 through 593 Processing helix chain 'C' and resid 158 through 171 removed outlier: 3.764A pdb=" N LEU C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 200 through 210 removed outlier: 5.080A pdb=" N ALA C 209 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LYS C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 239 Processing helix chain 'C' and resid 274 through 285 Processing helix chain 'C' and resid 324 through 336 removed outlier: 4.130A pdb=" N GLU C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN C 329 " --> pdb=" O ARG C 325 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 358 through 375 removed outlier: 4.025A pdb=" N GLY C 375 " --> pdb=" O PHE C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 393 removed outlier: 3.660A pdb=" N LYS C 387 " --> pdb=" O VAL C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 424 removed outlier: 3.656A pdb=" N SER C 410 " --> pdb=" O ALA C 406 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY C 417 " --> pdb=" O TYR C 413 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS C 418 " --> pdb=" O HIS C 414 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 423 " --> pdb=" O ALA C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 479 removed outlier: 3.979A pdb=" N TYR C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY C 471 " --> pdb=" O SER C 467 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLY C 472 " --> pdb=" O THR C 468 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ARG C 473 " --> pdb=" O LEU C 469 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 474 " --> pdb=" O TYR C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 505 removed outlier: 3.515A pdb=" N SER C 490 " --> pdb=" O THR C 487 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASN C 491 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 493 " --> pdb=" O SER C 490 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS C 494 " --> pdb=" O ASN C 491 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL C 495 " --> pdb=" O ASP C 492 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA C 500 " --> pdb=" O THR C 497 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN C 502 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET C 503 " --> pdb=" O ALA C 500 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 504 " --> pdb=" O ARG C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 566 removed outlier: 3.573A pdb=" N ASP C 546 " --> pdb=" O ALA C 542 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP C 566 " --> pdb=" O GLN C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 580 removed outlier: 3.569A pdb=" N ALA C 577 " --> pdb=" O ALA C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 593 removed outlier: 3.621A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 188 through 190 Processing sheet with id= B, first strand: chain 'D' and resid 247 through 249 removed outlier: 5.798A pdb=" N ILE D 292 " --> pdb=" O ILE D 248 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'E' and resid 188 through 190 removed outlier: 6.256A pdb=" N ARG E 315 " --> pdb=" O LEU E 189 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'E' and resid 248 through 250 removed outlier: 3.623A pdb=" N ILE E 250 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 430 through 434 removed outlier: 6.831A pdb=" N PHE E 447 " --> pdb=" O HIS E 432 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 248 through 250 removed outlier: 3.512A pdb=" N ILE F 250 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 430 through 435 removed outlier: 6.629A pdb=" N PHE F 447 " --> pdb=" O HIS F 432 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL F 434 " --> pdb=" O VAL F 445 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL F 445 " --> pdb=" O VAL F 434 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 294 through 296 removed outlier: 6.213A pdb=" N VAL B 188 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG B 315 " --> pdb=" O LEU B 189 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 430 through 435 removed outlier: 6.648A pdb=" N PHE B 447 " --> pdb=" O HIS B 432 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL B 434 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL B 445 " --> pdb=" O VAL B 434 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 293 through 296 removed outlier: 3.946A pdb=" N VAL C 188 " --> pdb=" O VAL C 293 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 295 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ARG C 315 " --> pdb=" O LEU C 189 " (cutoff:3.500A) 694 hydrogen bonds defined for protein. 1989 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.94 Time building geometry restraints manager: 7.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6306 1.33 - 1.46: 3212 1.46 - 1.58: 9817 1.58 - 1.70: 15 1.70 - 1.82: 222 Bond restraints: 19572 Sorted by residual: bond pdb=" O3A ANP F 701 " pdb=" PB ANP F 701 " ideal model delta sigma weight residual 1.700 1.527 0.173 2.00e-02 2.50e+03 7.52e+01 bond pdb=" O3A ANP B 701 " pdb=" PB ANP B 701 " ideal model delta sigma weight residual 1.700 1.527 0.173 2.00e-02 2.50e+03 7.46e+01 bond pdb=" O3A ANP A 701 " pdb=" PB ANP A 701 " ideal model delta sigma weight residual 1.700 1.527 0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" O3A ANP D 701 " pdb=" PB ANP D 701 " ideal model delta sigma weight residual 1.700 1.533 0.167 2.00e-02 2.50e+03 6.96e+01 bond pdb=" O3A ANP E 701 " pdb=" PB ANP E 701 " ideal model delta sigma weight residual 1.700 1.535 0.165 2.00e-02 2.50e+03 6.83e+01 ... (remaining 19567 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.11: 609 106.11 - 113.11: 10904 113.11 - 120.12: 7041 120.12 - 127.13: 7643 127.13 - 134.14: 203 Bond angle restraints: 26400 Sorted by residual: angle pdb=" PB ANP F 701 " pdb=" N3B ANP F 701 " pdb=" PG ANP F 701 " ideal model delta sigma weight residual 126.95 104.69 22.26 3.00e+00 1.11e-01 5.50e+01 angle pdb=" PB ANP C 701 " pdb=" N3B ANP C 701 " pdb=" PG ANP C 701 " ideal model delta sigma weight residual 126.95 105.07 21.88 3.00e+00 1.11e-01 5.32e+01 angle pdb=" PB ANP E 701 " pdb=" N3B ANP E 701 " pdb=" PG ANP E 701 " ideal model delta sigma weight residual 126.95 107.28 19.67 3.00e+00 1.11e-01 4.30e+01 angle pdb=" PA ANP A 701 " pdb=" O3A ANP A 701 " pdb=" PB ANP A 701 " ideal model delta sigma weight residual 125.41 106.21 19.20 3.00e+00 1.11e-01 4.10e+01 angle pdb=" PA ANP B 701 " pdb=" O3A ANP B 701 " pdb=" PB ANP B 701 " ideal model delta sigma weight residual 125.41 107.23 18.18 3.00e+00 1.11e-01 3.67e+01 ... (remaining 26395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.68: 10633 19.68 - 39.36: 1062 39.36 - 59.05: 390 59.05 - 78.73: 64 78.73 - 98.41: 19 Dihedral angle restraints: 12168 sinusoidal: 5160 harmonic: 7008 Sorted by residual: dihedral pdb=" CA ILE A 455 " pdb=" C ILE A 455 " pdb=" N SER A 456 " pdb=" CA SER A 456 " ideal model delta harmonic sigma weight residual -180.00 -124.84 -55.16 0 5.00e+00 4.00e-02 1.22e+02 dihedral pdb=" CA PHE F 213 " pdb=" C PHE F 213 " pdb=" N PHE F 214 " pdb=" CA PHE F 214 " ideal model delta harmonic sigma weight residual 180.00 135.98 44.02 0 5.00e+00 4.00e-02 7.75e+01 dihedral pdb=" CA THR F 215 " pdb=" C THR F 215 " pdb=" N ILE F 216 " pdb=" CA ILE F 216 " ideal model delta harmonic sigma weight residual -180.00 -144.26 -35.74 0 5.00e+00 4.00e-02 5.11e+01 ... (remaining 12165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2268 0.064 - 0.129: 624 0.129 - 0.193: 57 0.193 - 0.257: 2 0.257 - 0.321: 7 Chirality restraints: 2958 Sorted by residual: chirality pdb=" C3' ANP A 701 " pdb=" C2' ANP A 701 " pdb=" C4' ANP A 701 " pdb=" O3' ANP A 701 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA ILE C 184 " pdb=" N ILE C 184 " pdb=" C ILE C 184 " pdb=" CB ILE C 184 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C3' ANP D 701 " pdb=" C2' ANP D 701 " pdb=" C4' ANP D 701 " pdb=" O3' ANP D 701 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 2955 not shown) Planarity restraints: 3432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 425 " 0.050 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO B 426 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 426 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 426 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 184 " -0.048 5.00e-02 4.00e+02 7.15e-02 8.18e+00 pdb=" N PRO F 185 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO F 185 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 185 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 244 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO D 245 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 245 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 245 " -0.038 5.00e-02 4.00e+02 ... (remaining 3429 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 167 2.43 - 3.05: 13315 3.05 - 3.67: 27778 3.67 - 4.28: 39800 4.28 - 4.90: 63926 Nonbonded interactions: 144986 Sorted by model distance: nonbonded pdb=" O2G ANP E 701 " pdb="MG MG E 703 " model vdw 1.813 2.170 nonbonded pdb=" OD2 ASP F 492 " pdb="ZN ZN F 702 " model vdw 1.834 2.230 nonbonded pdb=" O2A ANP C 701 " pdb="MG MG C 703 " model vdw 1.853 2.170 nonbonded pdb=" O3A ANP D 701 " pdb="MG MG D 703 " model vdw 1.883 2.170 nonbonded pdb=" N3B ANP C 701 " pdb="MG MG C 703 " model vdw 1.904 2.250 ... (remaining 144981 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 141 through 147 or resid 149 through 156 or resid 158 thro \ ugh 250 or resid 252 through 362 or resid 364 through 380 or resid 382 through 6 \ 04 or resid 701 through 703)) selection = (chain 'B' and (resid 141 through 147 or resid 149 through 156 or resid 158 thro \ ugh 250 or resid 252 through 362 or resid 364 through 380 or resid 382 through 6 \ 04 or resid 701 through 703)) selection = (chain 'C' and (resid 141 through 147 or resid 149 through 156 or resid 158 thro \ ugh 250 or resid 252 through 362 or resid 364 through 380 or resid 382 through 6 \ 04 or resid 701 through 703)) selection = (chain 'D' and (resid 141 through 147 or resid 149 through 156 or resid 158 thro \ ugh 250 or resid 252 through 362 or resid 364 through 380 or resid 382 through 6 \ 04 or resid 701 through 703)) selection = (chain 'E' and (resid 141 through 147 or resid 149 through 156 or resid 158 thro \ ugh 250 or resid 252 through 362 or resid 364 through 380 or resid 382 through 6 \ 04 or resid 701 through 703)) selection = (chain 'F' and (resid 141 through 147 or resid 149 through 156 or resid 158 thro \ ugh 250 or resid 252 through 362 or resid 364 through 380 or resid 382 through 6 \ 04 or resid 701 through 703)) } 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=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.960 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 63.960 Find NCS groups from input model: 1.340 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 0.012 0.173 19572 Z= 0.817 Angle : 1.086 22.258 26400 Z= 0.578 Chirality : 0.056 0.321 2958 Planarity : 0.006 0.076 3432 Dihedral : 18.321 98.410 7632 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.29 % Favored : 91.54 % Rotamer: Outliers : 18.40 % Allowed : 16.32 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -2.33 (0.16), residues: 2400 helix: -1.06 (0.13), residues: 1264 sheet: -0.63 (0.54), residues: 101 loop : -2.20 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP B 507 HIS 0.010 0.002 HIS A 418 PHE 0.022 0.003 PHE C 214 TYR 0.030 0.004 TYR E 557 ARG 0.008 0.001 ARG E 232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 368 poor density : 593 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLU cc_start: 0.7542 (pp20) cc_final: 0.7149 (pp20) REVERT: A 237 PHE cc_start: 0.7550 (m-10) cc_final: 0.7148 (m-80) REVERT: A 238 GLU cc_start: 0.7831 (tt0) cc_final: 0.7561 (tt0) REVERT: A 293 VAL cc_start: 0.8044 (OUTLIER) cc_final: 0.7768 (p) REVERT: A 323 ASP cc_start: 0.7101 (m-30) cc_final: 0.6888 (m-30) REVERT: A 332 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7954 (mtpp) REVERT: A 367 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7697 (mm-30) REVERT: A 382 MET cc_start: 0.6633 (pp-130) cc_final: 0.6396 (pp-130) REVERT: A 398 ARG cc_start: 0.7549 (ttt180) cc_final: 0.7318 (ttp80) REVERT: A 405 GLU cc_start: 0.7929 (tp30) cc_final: 0.7711 (tm-30) REVERT: A 491 ASN cc_start: 0.7656 (t0) cc_final: 0.7163 (t0) REVERT: A 554 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6844 (mm-30) REVERT: A 559 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8440 (ttt180) REVERT: A 562 GLN cc_start: 0.7858 (tp40) cc_final: 0.7654 (tp40) REVERT: A 566 ASP cc_start: 0.8261 (m-30) cc_final: 0.7945 (m-30) REVERT: A 582 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6904 (mt-10) REVERT: D 237 PHE cc_start: 0.7608 (m-80) cc_final: 0.6983 (m-10) REVERT: D 323 ASP cc_start: 0.7531 (p0) cc_final: 0.7029 (p0) REVERT: D 327 ARG cc_start: 0.7902 (mtt90) cc_final: 0.7630 (mtt180) REVERT: D 367 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: D 377 LYS cc_start: 0.6131 (OUTLIER) cc_final: 0.5714 (mmtm) REVERT: D 403 MET cc_start: 0.7469 (mpp) cc_final: 0.7249 (mpp) REVERT: D 443 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8721 (mm) REVERT: D 451 GLU cc_start: 0.7766 (tt0) cc_final: 0.7375 (tm-30) REVERT: D 456 SER cc_start: 0.8764 (t) cc_final: 0.8521 (p) REVERT: D 491 ASN cc_start: 0.8113 (t0) cc_final: 0.7857 (t0) REVERT: D 495 VAL cc_start: 0.8076 (OUTLIER) cc_final: 0.7733 (t) REVERT: D 539 ASP cc_start: 0.7833 (t0) cc_final: 0.7504 (t0) REVERT: D 543 ARG cc_start: 0.7791 (ttp80) cc_final: 0.7353 (ttp-110) REVERT: D 554 GLU cc_start: 0.7285 (mt-10) cc_final: 0.7047 (mm-30) REVERT: D 566 ASP cc_start: 0.8286 (m-30) cc_final: 0.7980 (m-30) REVERT: D 579 MET cc_start: 0.8554 (mmm) cc_final: 0.8251 (mtp) REVERT: D 582 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6766 (mt-10) REVERT: D 591 ASP cc_start: 0.7227 (m-30) cc_final: 0.6993 (m-30) REVERT: D 604 TRP cc_start: 0.7225 (OUTLIER) cc_final: 0.6050 (t60) REVERT: E 141 MET cc_start: 0.6556 (ttm) cc_final: 0.6350 (ttm) REVERT: E 142 LEU cc_start: 0.5472 (OUTLIER) cc_final: 0.5250 (pp) REVERT: E 163 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7062 (mm-30) REVERT: E 186 LYS cc_start: 0.5389 (OUTLIER) cc_final: 0.3938 (mptp) REVERT: E 233 VAL cc_start: 0.8562 (m) cc_final: 0.8298 (p) REVERT: E 238 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7360 (mm-30) REVERT: E 242 LYS cc_start: 0.2312 (OUTLIER) cc_final: 0.1720 (tptp) REVERT: E 298 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7908 (m-40) REVERT: E 319 VAL cc_start: 0.7568 (t) cc_final: 0.7255 (m) REVERT: E 331 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8300 (mp) REVERT: E 367 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7953 (mm-30) REVERT: E 370 LEU cc_start: 0.8383 (mt) cc_final: 0.8110 (mp) REVERT: E 377 LYS cc_start: 0.6257 (OUTLIER) cc_final: 0.5702 (mmtm) REVERT: E 425 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7954 (t) REVERT: E 491 ASN cc_start: 0.8235 (t0) cc_final: 0.7869 (t0) REVERT: E 498 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.7833 (m110) REVERT: E 540 GLU cc_start: 0.7377 (tp30) cc_final: 0.7172 (tp30) REVERT: E 566 ASP cc_start: 0.7992 (m-30) cc_final: 0.7775 (m-30) REVERT: F 213 PHE cc_start: 0.4505 (OUTLIER) cc_final: 0.3700 (t80) REVERT: F 237 PHE cc_start: 0.7754 (m-10) cc_final: 0.6364 (m-10) REVERT: F 238 GLU cc_start: 0.7996 (tt0) cc_final: 0.7261 (tt0) REVERT: F 281 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.4418 (pt0) REVERT: F 293 VAL cc_start: 0.8053 (m) cc_final: 0.7821 (p) REVERT: F 367 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7718 (mm-30) REVERT: F 398 ARG cc_start: 0.7464 (ttp-170) cc_final: 0.6990 (ttp80) REVERT: F 401 MET cc_start: 0.5624 (mtp) cc_final: 0.4437 (mtp) REVERT: F 407 GLN cc_start: 0.8052 (tt0) cc_final: 0.7692 (tt0) REVERT: F 408 LYS cc_start: 0.8612 (ptpt) cc_final: 0.8302 (ptpp) REVERT: F 413 TYR cc_start: 0.8929 (m-80) cc_final: 0.8585 (m-80) REVERT: F 433 LYS cc_start: 0.8266 (tttt) cc_final: 0.7869 (ttmm) REVERT: F 467 SER cc_start: 0.8817 (m) cc_final: 0.8515 (t) REVERT: F 511 GLU cc_start: 0.7351 (mp0) cc_final: 0.7033 (mp0) REVERT: F 562 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.6546 (tm-30) REVERT: F 566 ASP cc_start: 0.8075 (m-30) cc_final: 0.7180 (m-30) REVERT: B 233 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.7695 (p) REVERT: B 236 MET cc_start: 0.6384 (mpt) cc_final: 0.5961 (mpt) REVERT: B 238 GLU cc_start: 0.7890 (pt0) cc_final: 0.7525 (pp20) REVERT: B 247 ILE cc_start: 0.2390 (OUTLIER) cc_final: 0.1931 (mp) REVERT: B 319 VAL cc_start: 0.7861 (OUTLIER) cc_final: 0.7636 (m) REVERT: B 353 THR cc_start: 0.7968 (p) cc_final: 0.7757 (p) REVERT: B 367 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7641 (mm-30) REVERT: B 455 ILE cc_start: 0.8383 (mm) cc_final: 0.8029 (mp) REVERT: B 462 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.7781 (mp) REVERT: B 504 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.8213 (t) REVERT: B 512 LYS cc_start: 0.8489 (tptp) cc_final: 0.8280 (tptp) REVERT: B 539 ASP cc_start: 0.7807 (t70) cc_final: 0.7366 (t0) REVERT: B 543 ARG cc_start: 0.7439 (ttp-170) cc_final: 0.7129 (ttp80) REVERT: B 547 GLN cc_start: 0.7385 (mt0) cc_final: 0.7130 (mt0) REVERT: B 556 ASN cc_start: 0.8555 (m-40) cc_final: 0.8199 (m110) REVERT: B 566 ASP cc_start: 0.7864 (m-30) cc_final: 0.7618 (m-30) REVERT: B 579 MET cc_start: 0.8523 (mmm) cc_final: 0.8243 (mtp) REVERT: B 604 TRP cc_start: 0.7808 (OUTLIER) cc_final: 0.6591 (t60) REVERT: C 161 LYS cc_start: 0.8443 (ttmt) cc_final: 0.7801 (tptp) REVERT: C 248 ILE cc_start: 0.4825 (OUTLIER) cc_final: 0.4540 (mp) REVERT: C 250 ILE cc_start: 0.7986 (mm) cc_final: 0.7683 (mm) REVERT: C 252 GLN cc_start: 0.6685 (OUTLIER) cc_final: 0.5687 (mp10) REVERT: C 319 VAL cc_start: 0.7820 (t) cc_final: 0.7446 (m) REVERT: C 329 GLN cc_start: 0.8159 (tp40) cc_final: 0.7729 (mm-40) REVERT: C 370 LEU cc_start: 0.8585 (mt) cc_final: 0.8289 (mp) REVERT: C 390 ASP cc_start: 0.7338 (m-30) cc_final: 0.6902 (m-30) REVERT: C 397 GLU cc_start: 0.7044 (pm20) cc_final: 0.6442 (pm20) REVERT: C 398 ARG cc_start: 0.7274 (mtp180) cc_final: 0.6794 (ttt180) REVERT: C 415 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7818 (mp10) REVERT: C 433 LYS cc_start: 0.8379 (ttmm) cc_final: 0.8157 (ttpp) REVERT: C 491 ASN cc_start: 0.8425 (t0) cc_final: 0.8085 (t0) REVERT: C 543 ARG cc_start: 0.7432 (ttm110) cc_final: 0.6967 (ttp80) REVERT: C 544 ILE cc_start: 0.8673 (mm) cc_final: 0.8459 (mt) REVERT: C 547 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.6601 (mp10) REVERT: C 554 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6923 (mm-30) REVERT: C 562 GLN cc_start: 0.8089 (tp40) cc_final: 0.7060 (tp-100) REVERT: C 566 ASP cc_start: 0.8089 (m-30) cc_final: 0.7206 (m-30) REVERT: C 575 LYS cc_start: 0.7896 (tmtp) cc_final: 0.7652 (tmmt) outliers start: 368 outliers final: 223 residues processed: 868 average time/residue: 0.3678 time to fit residues: 454.9245 Evaluate side-chains 822 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 567 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 484 HIS Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 559 ARG Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 298 ASN Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 360 ASP Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 377 LYS Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 537 MET Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 561 ARG Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 569 ASP Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 581 TYR Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 604 TRP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 282 MET Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 325 ARG Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 367 GLU Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 410 SER Chi-restraints excluded: chain E residue 418 HIS Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 439 ARG Chi-restraints excluded: chain E residue 468 THR Chi-restraints excluded: chain E residue 486 SER Chi-restraints excluded: chain E residue 498 ASN Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain E residue 559 ARG Chi-restraints excluded: chain E residue 561 ARG Chi-restraints excluded: chain E residue 568 MET Chi-restraints excluded: chain E residue 580 LYS Chi-restraints excluded: chain E residue 597 ASP Chi-restraints excluded: chain E residue 598 VAL Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 377 LYS Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 403 MET Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 411 THR Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 468 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 548 GLU Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 562 GLN Chi-restraints excluded: chain F residue 569 ASP Chi-restraints excluded: chain F residue 581 TYR Chi-restraints excluded: chain F residue 596 ARG Chi-restraints excluded: chain F residue 598 VAL Chi-restraints excluded: chain F residue 604 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 507 TRP Chi-restraints excluded: chain B residue 538 SER Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 581 TYR Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 604 TRP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 415 GLN Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 581 TYR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 604 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 223 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 HIS D 178 GLN ** D 363 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 GLN ** E 363 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 GLN F 329 GLN F 588 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 19572 Z= 0.253 Angle : 0.692 8.993 26400 Z= 0.357 Chirality : 0.046 0.375 2958 Planarity : 0.005 0.067 3432 Dihedral : 15.988 96.554 3386 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.79 % Favored : 94.17 % Rotamer: Outliers : 13.55 % Allowed : 23.69 % Favored : 62.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.45 (0.17), residues: 2400 helix: -0.19 (0.14), residues: 1268 sheet: -0.97 (0.54), residues: 101 loop : -1.92 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 507 HIS 0.007 0.001 HIS C 414 PHE 0.022 0.002 PHE D 213 TYR 0.016 0.002 TYR E 413 ARG 0.008 0.000 ARG C 325 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 574 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 VAL cc_start: 0.8030 (OUTLIER) cc_final: 0.7777 (p) REVERT: A 332 LYS cc_start: 0.8048 (mtpp) cc_final: 0.7789 (mtpp) REVERT: A 367 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7530 (mm-30) REVERT: A 398 ARG cc_start: 0.7547 (ttt180) cc_final: 0.7317 (ttp80) REVERT: A 491 ASN cc_start: 0.6751 (t0) cc_final: 0.6373 (t0) REVERT: A 554 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6221 (mp0) REVERT: A 591 ASP cc_start: 0.7339 (m-30) cc_final: 0.6988 (m-30) REVERT: A 599 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8094 (ptp-170) REVERT: D 234 ARG cc_start: 0.8077 (mpp-170) cc_final: 0.7631 (mpp80) REVERT: D 237 PHE cc_start: 0.7387 (m-80) cc_final: 0.7034 (m-10) REVERT: D 327 ARG cc_start: 0.7681 (mtt90) cc_final: 0.7283 (mtp85) REVERT: D 332 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7987 (mtmm) REVERT: D 335 MET cc_start: 0.6670 (tpp) cc_final: 0.6142 (tpp) REVERT: D 367 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: D 377 LYS cc_start: 0.6293 (OUTLIER) cc_final: 0.6076 (mmtm) REVERT: D 398 ARG cc_start: 0.7522 (ttt180) cc_final: 0.7240 (ttt180) REVERT: D 420 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8317 (mt) REVERT: D 434 VAL cc_start: 0.9140 (OUTLIER) cc_final: 0.8902 (m) REVERT: D 443 LEU cc_start: 0.8871 (mm) cc_final: 0.8657 (mt) REVERT: D 456 SER cc_start: 0.8804 (t) cc_final: 0.8515 (p) REVERT: D 491 ASN cc_start: 0.7320 (t0) cc_final: 0.7094 (t0) REVERT: D 537 MET cc_start: 0.8246 (ptt) cc_final: 0.8039 (ptm) REVERT: D 539 ASP cc_start: 0.7809 (t0) cc_final: 0.7328 (t0) REVERT: D 543 ARG cc_start: 0.7686 (ttp80) cc_final: 0.7135 (ttp-110) REVERT: D 579 MET cc_start: 0.8638 (mmm) cc_final: 0.8210 (mtp) REVERT: D 604 TRP cc_start: 0.7184 (OUTLIER) cc_final: 0.6154 (t60) REVERT: E 141 MET cc_start: 0.6501 (ttm) cc_final: 0.6291 (ttm) REVERT: E 142 LEU cc_start: 0.5203 (OUTLIER) cc_final: 0.4931 (pp) REVERT: E 161 LYS cc_start: 0.8494 (mmmm) cc_final: 0.8210 (mtmm) REVERT: E 163 GLU cc_start: 0.7267 (mm-30) cc_final: 0.7065 (mm-30) REVERT: E 186 LYS cc_start: 0.4937 (OUTLIER) cc_final: 0.3674 (mptp) REVERT: E 233 VAL cc_start: 0.8609 (m) cc_final: 0.8369 (p) REVERT: E 242 LYS cc_start: 0.2306 (OUTLIER) cc_final: 0.1796 (tptp) REVERT: E 298 ASN cc_start: 0.8032 (OUTLIER) cc_final: 0.7780 (m-40) REVERT: E 319 VAL cc_start: 0.7539 (t) cc_final: 0.7329 (m) REVERT: E 330 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8575 (mp) REVERT: E 370 LEU cc_start: 0.8266 (mt) cc_final: 0.7933 (mp) REVERT: E 425 VAL cc_start: 0.8105 (OUTLIER) cc_final: 0.7902 (t) REVERT: E 439 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7668 (ptp-110) REVERT: E 491 ASN cc_start: 0.8234 (t0) cc_final: 0.7829 (t0) REVERT: E 498 ASN cc_start: 0.8199 (OUTLIER) cc_final: 0.7563 (m110) REVERT: E 512 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8320 (ttpp) REVERT: E 562 GLN cc_start: 0.8295 (tp40) cc_final: 0.7613 (tp40) REVERT: E 566 ASP cc_start: 0.8102 (m-30) cc_final: 0.7775 (m-30) REVERT: E 598 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8854 (m) REVERT: F 179 LYS cc_start: 0.7055 (mmtt) cc_final: 0.6834 (mmtt) REVERT: F 213 PHE cc_start: 0.4504 (OUTLIER) cc_final: 0.4001 (t80) REVERT: F 237 PHE cc_start: 0.7476 (m-10) cc_final: 0.6752 (m-10) REVERT: F 242 LYS cc_start: 0.4184 (OUTLIER) cc_final: 0.3458 (pptt) REVERT: F 281 GLU cc_start: 0.6127 (OUTLIER) cc_final: 0.3576 (pt0) REVERT: F 292 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7323 (mp) REVERT: F 293 VAL cc_start: 0.7874 (m) cc_final: 0.7500 (p) REVERT: F 367 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7586 (mm-30) REVERT: F 397 GLU cc_start: 0.7226 (mp0) cc_final: 0.6951 (mp0) REVERT: F 398 ARG cc_start: 0.7287 (ttp-170) cc_final: 0.6923 (ttp80) REVERT: F 407 GLN cc_start: 0.8118 (tt0) cc_final: 0.7703 (tt0) REVERT: F 408 LYS cc_start: 0.8546 (ptpt) cc_final: 0.8240 (ptpp) REVERT: F 433 LYS cc_start: 0.8136 (tttt) cc_final: 0.7833 (ttmt) REVERT: F 451 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7401 (tm-30) REVERT: F 459 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8206 (ttt180) REVERT: F 467 SER cc_start: 0.8845 (m) cc_final: 0.8643 (t) REVERT: F 485 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8576 (m) REVERT: F 511 GLU cc_start: 0.7284 (mp0) cc_final: 0.7035 (mp0) REVERT: F 562 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7687 (tp-100) REVERT: F 566 ASP cc_start: 0.8185 (m-30) cc_final: 0.7824 (m-30) REVERT: F 582 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6724 (mt-10) REVERT: B 163 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6657 (mt-10) REVERT: B 186 LYS cc_start: 0.6560 (OUTLIER) cc_final: 0.5950 (pttt) REVERT: B 233 VAL cc_start: 0.7748 (OUTLIER) cc_final: 0.7370 (p) REVERT: B 236 MET cc_start: 0.6535 (mpt) cc_final: 0.6185 (mpt) REVERT: B 247 ILE cc_start: 0.1600 (OUTLIER) cc_final: 0.1086 (mp) REVERT: B 327 ARG cc_start: 0.7789 (mtt180) cc_final: 0.7549 (mtt-85) REVERT: B 367 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7560 (mm-30) REVERT: B 408 LYS cc_start: 0.8468 (mttp) cc_final: 0.7857 (mtpp) REVERT: B 455 ILE cc_start: 0.8255 (mm) cc_final: 0.7792 (mp) REVERT: B 604 TRP cc_start: 0.7754 (OUTLIER) cc_final: 0.6611 (t60) REVERT: C 161 LYS cc_start: 0.8291 (ttmt) cc_final: 0.7535 (tptp) REVERT: C 179 LYS cc_start: 0.7659 (mmtt) cc_final: 0.7454 (mmtp) REVERT: C 200 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6808 (mm) REVERT: C 236 MET cc_start: 0.7906 (mmt) cc_final: 0.7669 (mmt) REVERT: C 250 ILE cc_start: 0.7790 (mm) cc_final: 0.7586 (mt) REVERT: C 319 VAL cc_start: 0.7628 (t) cc_final: 0.7334 (m) REVERT: C 324 VAL cc_start: 0.8256 (p) cc_final: 0.7991 (t) REVERT: C 329 GLN cc_start: 0.8055 (tp40) cc_final: 0.7625 (mm-40) REVERT: C 357 SER cc_start: 0.7796 (m) cc_final: 0.7462 (p) REVERT: C 370 LEU cc_start: 0.8336 (mt) cc_final: 0.8052 (mp) REVERT: C 390 ASP cc_start: 0.7235 (m-30) cc_final: 0.6812 (m-30) REVERT: C 397 GLU cc_start: 0.6985 (pm20) cc_final: 0.6466 (pm20) REVERT: C 398 ARG cc_start: 0.7239 (mtp180) cc_final: 0.6919 (mtm110) REVERT: C 433 LYS cc_start: 0.8331 (ttmm) cc_final: 0.8105 (ttpp) REVERT: C 491 ASN cc_start: 0.8383 (t0) cc_final: 0.7983 (t0) REVERT: C 562 GLN cc_start: 0.8286 (tp40) cc_final: 0.7511 (tp-100) REVERT: C 566 ASP cc_start: 0.8262 (m-30) cc_final: 0.7657 (m-30) outliers start: 270 outliers final: 181 residues processed: 765 average time/residue: 0.3679 time to fit residues: 401.2406 Evaluate side-chains 753 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 540 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 484 HIS Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 298 ASN Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 360 ASP Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 377 LYS Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 389 LYS Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 569 ASP Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 581 TYR Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 604 TRP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 282 MET Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 439 ARG Chi-restraints excluded: chain E residue 468 THR Chi-restraints excluded: chain E residue 498 ASN Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 512 LYS Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain E residue 559 ARG Chi-restraints excluded: chain E residue 597 ASP Chi-restraints excluded: chain E residue 598 VAL Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain F residue 239 GLN Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 562 GLN Chi-restraints excluded: chain F residue 569 ASP Chi-restraints excluded: chain F residue 596 ARG Chi-restraints excluded: chain F residue 598 VAL Chi-restraints excluded: chain F residue 604 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 507 TRP Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 604 TRP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 581 TYR Chi-restraints excluded: chain C residue 604 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 185 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 241 optimal weight: 0.7980 chunk 199 optimal weight: 0.8980 chunk 221 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 179 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 GLN D 562 GLN E 363 ASN A E 363 ASN B E 414 HIS F 588 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 GLN C 407 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 19572 Z= 0.210 Angle : 0.646 8.694 26400 Z= 0.330 Chirality : 0.044 0.246 2958 Planarity : 0.005 0.064 3432 Dihedral : 13.933 90.835 3239 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.50 % Favored : 94.46 % Rotamer: Outliers : 11.33 % Allowed : 25.37 % Favored : 63.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 (0.17), residues: 2400 helix: 0.17 (0.15), residues: 1288 sheet: -0.91 (0.55), residues: 101 loop : -1.74 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 507 HIS 0.006 0.001 HIS A 418 PHE 0.025 0.002 PHE D 213 TYR 0.016 0.002 TYR D 557 ARG 0.008 0.000 ARG B 543 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 566 time to evaluate : 2.223 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 236 MET cc_start: 0.7277 (mpt) cc_final: 0.6962 (mmt) REVERT: A 237 PHE cc_start: 0.7249 (m-80) cc_final: 0.6859 (m-80) REVERT: A 275 LEU cc_start: 0.3035 (OUTLIER) cc_final: 0.2749 (pp) REVERT: A 293 VAL cc_start: 0.8080 (OUTLIER) cc_final: 0.7818 (p) REVERT: A 332 LYS cc_start: 0.8062 (mtpp) cc_final: 0.7806 (mtpp) REVERT: A 354 PRO cc_start: 0.8673 (Cg_endo) cc_final: 0.8466 (Cg_exo) REVERT: A 367 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7494 (mm-30) REVERT: A 398 ARG cc_start: 0.7520 (ttt180) cc_final: 0.7272 (ttp80) REVERT: A 407 GLN cc_start: 0.8270 (mt0) cc_final: 0.7850 (mt0) REVERT: A 539 ASP cc_start: 0.7416 (t70) cc_final: 0.6944 (t0) REVERT: A 554 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6194 (mp0) REVERT: A 591 ASP cc_start: 0.7350 (m-30) cc_final: 0.7015 (m-30) REVERT: A 599 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8152 (ptp-170) REVERT: D 332 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7913 (mtmm) REVERT: D 420 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8295 (mt) REVERT: D 443 LEU cc_start: 0.8755 (mm) cc_final: 0.8517 (mt) REVERT: D 451 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7315 (tm-30) REVERT: D 491 ASN cc_start: 0.7014 (t0) cc_final: 0.6691 (t0) REVERT: D 537 MET cc_start: 0.8268 (ptt) cc_final: 0.8026 (ptm) REVERT: D 539 ASP cc_start: 0.7674 (t0) cc_final: 0.7339 (t0) REVERT: D 543 ARG cc_start: 0.7611 (ttp80) cc_final: 0.7239 (ttp-110) REVERT: D 579 MET cc_start: 0.8567 (mmm) cc_final: 0.8235 (mtp) REVERT: D 604 TRP cc_start: 0.7148 (OUTLIER) cc_final: 0.6108 (t60) REVERT: E 142 LEU cc_start: 0.5083 (OUTLIER) cc_final: 0.4792 (pp) REVERT: E 186 LYS cc_start: 0.4805 (OUTLIER) cc_final: 0.3649 (mptp) REVERT: E 242 LYS cc_start: 0.2194 (OUTLIER) cc_final: 0.1686 (tptp) REVERT: E 319 VAL cc_start: 0.7526 (t) cc_final: 0.7246 (m) REVERT: E 325 ARG cc_start: 0.8165 (tpm-80) cc_final: 0.7822 (tpm-80) REVERT: E 330 ILE cc_start: 0.8853 (mt) cc_final: 0.8539 (mp) REVERT: E 370 LEU cc_start: 0.8211 (mt) cc_final: 0.7963 (mp) REVERT: E 377 LYS cc_start: 0.6144 (OUTLIER) cc_final: 0.5532 (mmtm) REVERT: E 398 ARG cc_start: 0.7532 (mtp180) cc_final: 0.7306 (mtp180) REVERT: E 491 ASN cc_start: 0.8249 (t0) cc_final: 0.7853 (t0) REVERT: E 498 ASN cc_start: 0.8215 (OUTLIER) cc_final: 0.7604 (m110) REVERT: E 512 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8314 (ttpp) REVERT: E 562 GLN cc_start: 0.8243 (tp40) cc_final: 0.7236 (tp-100) REVERT: E 566 ASP cc_start: 0.8136 (m-30) cc_final: 0.7753 (m-30) REVERT: F 161 LYS cc_start: 0.8267 (mmmm) cc_final: 0.7916 (mttp) REVERT: F 213 PHE cc_start: 0.4775 (OUTLIER) cc_final: 0.4149 (t80) REVERT: F 237 PHE cc_start: 0.7608 (m-10) cc_final: 0.7038 (m-10) REVERT: F 238 GLU cc_start: 0.8017 (tt0) cc_final: 0.7290 (tp30) REVERT: F 242 LYS cc_start: 0.4242 (OUTLIER) cc_final: 0.3534 (pptt) REVERT: F 281 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.5214 (tt0) REVERT: F 293 VAL cc_start: 0.7805 (m) cc_final: 0.7458 (p) REVERT: F 397 GLU cc_start: 0.7252 (mp0) cc_final: 0.6992 (mp0) REVERT: F 398 ARG cc_start: 0.7294 (ttp-170) cc_final: 0.6929 (ttp80) REVERT: F 407 GLN cc_start: 0.8028 (tt0) cc_final: 0.7715 (tt0) REVERT: F 408 LYS cc_start: 0.8478 (ptpt) cc_final: 0.8228 (ptpp) REVERT: F 433 LYS cc_start: 0.8114 (tttt) cc_final: 0.7796 (ttmt) REVERT: F 443 LEU cc_start: 0.8400 (mm) cc_final: 0.8155 (mp) REVERT: F 451 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: F 459 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7909 (ttt180) REVERT: F 467 SER cc_start: 0.8878 (m) cc_final: 0.8569 (t) REVERT: F 485 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8544 (m) REVERT: F 504 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8642 (t) REVERT: F 511 GLU cc_start: 0.7279 (mp0) cc_final: 0.7049 (mp0) REVERT: F 562 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7778 (tp-100) REVERT: F 566 ASP cc_start: 0.8202 (m-30) cc_final: 0.7874 (m-30) REVERT: B 163 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6796 (mt-10) REVERT: B 179 LYS cc_start: 0.7614 (mmtp) cc_final: 0.7230 (mmtt) REVERT: B 186 LYS cc_start: 0.6484 (OUTLIER) cc_final: 0.6059 (pttt) REVERT: B 233 VAL cc_start: 0.7669 (OUTLIER) cc_final: 0.7178 (p) REVERT: B 236 MET cc_start: 0.6455 (mpt) cc_final: 0.6036 (mpt) REVERT: B 238 GLU cc_start: 0.7860 (tp30) cc_final: 0.7577 (pp20) REVERT: B 247 ILE cc_start: 0.1557 (OUTLIER) cc_final: 0.0944 (mp) REVERT: B 367 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7476 (mm-30) REVERT: B 408 LYS cc_start: 0.8472 (mttp) cc_final: 0.7873 (mtpp) REVERT: B 439 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8132 (mtp85) REVERT: B 455 ILE cc_start: 0.8208 (mm) cc_final: 0.7893 (mp) REVERT: B 539 ASP cc_start: 0.7579 (t70) cc_final: 0.7037 (t0) REVERT: B 604 TRP cc_start: 0.7728 (OUTLIER) cc_final: 0.6516 (t60) REVERT: C 161 LYS cc_start: 0.8250 (ttmt) cc_final: 0.8047 (ttpp) REVERT: C 179 LYS cc_start: 0.7487 (mmtt) cc_final: 0.7280 (mmtp) REVERT: C 200 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6543 (mm) REVERT: C 236 MET cc_start: 0.7855 (mmt) cc_final: 0.7582 (tpp) REVERT: C 319 VAL cc_start: 0.7621 (t) cc_final: 0.7383 (m) REVERT: C 324 VAL cc_start: 0.8227 (p) cc_final: 0.7947 (t) REVERT: C 329 GLN cc_start: 0.8017 (tp40) cc_final: 0.7580 (mm-40) REVERT: C 367 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7762 (mm-30) REVERT: C 370 LEU cc_start: 0.8297 (mt) cc_final: 0.8005 (mp) REVERT: C 390 ASP cc_start: 0.7249 (m-30) cc_final: 0.6901 (m-30) REVERT: C 397 GLU cc_start: 0.6999 (pm20) cc_final: 0.6431 (pm20) REVERT: C 398 ARG cc_start: 0.7211 (mtp180) cc_final: 0.6912 (mtm110) REVERT: C 433 LYS cc_start: 0.8364 (ttmm) cc_final: 0.8053 (ttpp) REVERT: C 491 ASN cc_start: 0.8373 (t0) cc_final: 0.8000 (t0) REVERT: C 547 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6433 (mt0) REVERT: C 562 GLN cc_start: 0.8322 (tp40) cc_final: 0.7568 (tp-100) REVERT: C 566 ASP cc_start: 0.8298 (m-30) cc_final: 0.7596 (m-30) outliers start: 227 outliers final: 170 residues processed: 716 average time/residue: 0.3630 time to fit residues: 370.0118 Evaluate side-chains 744 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 545 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 360 ASP Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 389 LYS Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 569 ASP Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 604 TRP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 282 MET Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 468 THR Chi-restraints excluded: chain E residue 498 ASN Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 512 LYS Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain E residue 559 ARG Chi-restraints excluded: chain E residue 569 ASP Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 562 GLN Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain F residue 569 ASP Chi-restraints excluded: chain F residue 574 MET Chi-restraints excluded: chain F residue 598 VAL Chi-restraints excluded: chain F residue 604 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 507 TRP Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 604 TRP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 569 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 0.0070 chunk 168 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 237 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 HIS ** D 363 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 GLN D 547 GLN D 562 GLN E 329 GLN F 572 HIS F 588 GLN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19572 Z= 0.208 Angle : 0.624 10.646 26400 Z= 0.317 Chirality : 0.044 0.230 2958 Planarity : 0.004 0.066 3432 Dihedral : 12.877 82.604 3160 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.75 % Favored : 94.21 % Rotamer: Outliers : 10.44 % Allowed : 26.90 % Favored : 62.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.83 (0.17), residues: 2400 helix: 0.31 (0.15), residues: 1295 sheet: -0.75 (0.50), residues: 113 loop : -1.67 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 507 HIS 0.010 0.001 HIS E 414 PHE 0.024 0.001 PHE B 237 TYR 0.017 0.002 TYR D 557 ARG 0.006 0.000 ARG E 234 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 547 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.6245 (tpp) cc_final: 0.5959 (tpp) REVERT: A 153 ASP cc_start: 0.7394 (m-30) cc_final: 0.6995 (m-30) REVERT: A 236 MET cc_start: 0.7360 (mpt) cc_final: 0.6912 (mmt) REVERT: A 237 PHE cc_start: 0.7208 (m-80) cc_final: 0.6945 (m-80) REVERT: A 293 VAL cc_start: 0.8081 (OUTLIER) cc_final: 0.7828 (p) REVERT: A 332 LYS cc_start: 0.8041 (mtpp) cc_final: 0.7805 (mtpp) REVERT: A 367 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7498 (mm-30) REVERT: A 398 ARG cc_start: 0.7488 (ttt180) cc_final: 0.7276 (ttp80) REVERT: A 539 ASP cc_start: 0.7442 (t70) cc_final: 0.6979 (t0) REVERT: A 554 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6168 (mp0) REVERT: A 591 ASP cc_start: 0.7347 (m-30) cc_final: 0.7032 (m-30) REVERT: A 599 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8286 (ptp-170) REVERT: D 158 ASP cc_start: 0.7877 (t0) cc_final: 0.7601 (t70) REVERT: D 443 LEU cc_start: 0.8710 (mm) cc_final: 0.8503 (mt) REVERT: D 451 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7383 (tm-30) REVERT: D 462 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7828 (mp) REVERT: D 491 ASN cc_start: 0.6959 (t0) cc_final: 0.6578 (t0) REVERT: D 537 MET cc_start: 0.8256 (ptt) cc_final: 0.8029 (ptm) REVERT: D 539 ASP cc_start: 0.7660 (t0) cc_final: 0.7354 (t0) REVERT: D 543 ARG cc_start: 0.7628 (ttp80) cc_final: 0.7356 (ttp-170) REVERT: D 579 MET cc_start: 0.8545 (mmm) cc_final: 0.8305 (mtp) REVERT: D 604 TRP cc_start: 0.7193 (OUTLIER) cc_final: 0.6107 (t60) REVERT: E 161 LYS cc_start: 0.8493 (mmmm) cc_final: 0.8203 (mtmm) REVERT: E 186 LYS cc_start: 0.4805 (OUTLIER) cc_final: 0.3766 (mptp) REVERT: E 242 LYS cc_start: 0.2558 (OUTLIER) cc_final: 0.2061 (tptp) REVERT: E 319 VAL cc_start: 0.7529 (t) cc_final: 0.7195 (m) REVERT: E 330 ILE cc_start: 0.8814 (mt) cc_final: 0.8405 (mm) REVERT: E 377 LYS cc_start: 0.6258 (OUTLIER) cc_final: 0.5741 (mmtm) REVERT: E 491 ASN cc_start: 0.8260 (t0) cc_final: 0.7878 (t0) REVERT: E 498 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7643 (m110) REVERT: E 512 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8322 (ttpp) REVERT: E 562 GLN cc_start: 0.8224 (tp40) cc_final: 0.7311 (tp-100) REVERT: E 566 ASP cc_start: 0.8159 (m-30) cc_final: 0.7788 (m-30) REVERT: F 237 PHE cc_start: 0.7532 (m-10) cc_final: 0.6920 (m-10) REVERT: F 238 GLU cc_start: 0.7925 (tt0) cc_final: 0.7223 (tm-30) REVERT: F 281 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.5258 (tt0) REVERT: F 293 VAL cc_start: 0.7909 (m) cc_final: 0.7656 (p) REVERT: F 366 ASN cc_start: 0.8380 (t0) cc_final: 0.8077 (t0) REVERT: F 367 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7637 (mm-30) REVERT: F 398 ARG cc_start: 0.7285 (ttp-170) cc_final: 0.6852 (ttp80) REVERT: F 401 MET cc_start: 0.5542 (mtp) cc_final: 0.4404 (mtp) REVERT: F 407 GLN cc_start: 0.8027 (tt0) cc_final: 0.7743 (tt0) REVERT: F 408 LYS cc_start: 0.8512 (ptpt) cc_final: 0.8254 (ptpp) REVERT: F 433 LYS cc_start: 0.8076 (tttt) cc_final: 0.7755 (ttmt) REVERT: F 443 LEU cc_start: 0.8542 (mm) cc_final: 0.8314 (mp) REVERT: F 459 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7885 (ttt180) REVERT: F 467 SER cc_start: 0.8851 (m) cc_final: 0.8549 (t) REVERT: F 485 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8553 (m) REVERT: F 504 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8629 (t) REVERT: F 511 GLU cc_start: 0.7275 (mp0) cc_final: 0.7063 (mp0) REVERT: F 562 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7860 (tp-100) REVERT: F 566 ASP cc_start: 0.8148 (m-30) cc_final: 0.7802 (m-30) REVERT: F 568 MET cc_start: 0.8486 (tpp) cc_final: 0.8050 (tpt) REVERT: F 604 TRP cc_start: 0.6962 (OUTLIER) cc_final: 0.6647 (t60) REVERT: B 179 LYS cc_start: 0.7557 (mmtp) cc_final: 0.7179 (mmtt) REVERT: B 186 LYS cc_start: 0.6458 (OUTLIER) cc_final: 0.5976 (pttt) REVERT: B 233 VAL cc_start: 0.7526 (OUTLIER) cc_final: 0.7180 (p) REVERT: B 236 MET cc_start: 0.6458 (mpt) cc_final: 0.6174 (mpt) REVERT: B 238 GLU cc_start: 0.7846 (tp30) cc_final: 0.7595 (pp20) REVERT: B 247 ILE cc_start: 0.1384 (OUTLIER) cc_final: 0.0845 (mp) REVERT: B 367 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7456 (mm-30) REVERT: B 394 MET cc_start: 0.6790 (ptm) cc_final: 0.6477 (ptm) REVERT: B 408 LYS cc_start: 0.8548 (mttp) cc_final: 0.7940 (mtpp) REVERT: B 439 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7212 (mtp-110) REVERT: B 455 ILE cc_start: 0.8220 (mm) cc_final: 0.7853 (mp) REVERT: B 539 ASP cc_start: 0.7567 (t70) cc_final: 0.7017 (t0) REVERT: B 604 TRP cc_start: 0.7711 (OUTLIER) cc_final: 0.6437 (t60) REVERT: C 200 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6556 (mm) REVERT: C 236 MET cc_start: 0.7790 (mmt) cc_final: 0.7453 (tpp) REVERT: C 237 PHE cc_start: 0.6151 (OUTLIER) cc_final: 0.5741 (t80) REVERT: C 319 VAL cc_start: 0.7550 (t) cc_final: 0.7304 (m) REVERT: C 324 VAL cc_start: 0.8178 (p) cc_final: 0.7896 (t) REVERT: C 329 GLN cc_start: 0.8000 (tp40) cc_final: 0.7574 (mm-40) REVERT: C 367 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7753 (mm-30) REVERT: C 370 LEU cc_start: 0.8269 (mt) cc_final: 0.7996 (mp) REVERT: C 397 GLU cc_start: 0.7036 (pm20) cc_final: 0.6466 (pm20) REVERT: C 398 ARG cc_start: 0.7216 (mtp180) cc_final: 0.6911 (mtm110) REVERT: C 433 LYS cc_start: 0.8373 (ttmm) cc_final: 0.8054 (ttpp) REVERT: C 491 ASN cc_start: 0.8359 (t0) cc_final: 0.7919 (t0) REVERT: C 512 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8220 (ttpp) REVERT: C 547 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6741 (mt0) REVERT: C 562 GLN cc_start: 0.8341 (tp40) cc_final: 0.7624 (tp-100) REVERT: C 566 ASP cc_start: 0.8299 (m-30) cc_final: 0.7631 (m-30) REVERT: C 591 ASP cc_start: 0.7031 (m-30) cc_final: 0.6702 (m-30) outliers start: 209 outliers final: 151 residues processed: 688 average time/residue: 0.3552 time to fit residues: 348.8362 Evaluate side-chains 718 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 541 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 569 ASP Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 604 TRP Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 282 MET Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 389 LYS Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 468 THR Chi-restraints excluded: chain E residue 498 ASN Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 512 LYS Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain E residue 559 ARG Chi-restraints excluded: chain E residue 569 ASP Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 562 GLN Chi-restraints excluded: chain F residue 569 ASP Chi-restraints excluded: chain F residue 598 VAL Chi-restraints excluded: chain F residue 604 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 507 TRP Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 604 TRP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 367 GLU Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 512 LYS Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 569 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 0.0010 chunk 134 optimal weight: 9.9990 chunk 3 optimal weight: 0.0570 chunk 177 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 202 optimal weight: 0.6980 chunk 164 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 121 optimal weight: 5.9990 chunk 213 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 overall best weight: 0.9506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN B ** D 363 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 GLN D 562 GLN E 329 GLN F 178 GLN F 588 GLN B 178 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19572 Z= 0.180 Angle : 0.595 8.675 26400 Z= 0.303 Chirality : 0.042 0.171 2958 Planarity : 0.004 0.064 3432 Dihedral : 12.072 80.504 3122 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 9.69 % Allowed : 27.89 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.62 (0.17), residues: 2400 helix: 0.53 (0.15), residues: 1294 sheet: -0.81 (0.50), residues: 113 loop : -1.62 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 507 HIS 0.005 0.001 HIS C 414 PHE 0.026 0.001 PHE B 237 TYR 0.015 0.001 TYR D 557 ARG 0.008 0.000 ARG F 399 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 554 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.6266 (tpp) cc_final: 0.5991 (tpp) REVERT: A 153 ASP cc_start: 0.7397 (m-30) cc_final: 0.6990 (m-30) REVERT: A 236 MET cc_start: 0.7277 (mpt) cc_final: 0.7059 (mmt) REVERT: A 237 PHE cc_start: 0.7226 (m-80) cc_final: 0.6879 (m-80) REVERT: A 293 VAL cc_start: 0.8068 (OUTLIER) cc_final: 0.7817 (p) REVERT: A 332 LYS cc_start: 0.8030 (mtpp) cc_final: 0.7805 (mtpp) REVERT: A 367 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7510 (mm-30) REVERT: A 539 ASP cc_start: 0.7380 (t70) cc_final: 0.6909 (t0) REVERT: A 554 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6167 (mp0) REVERT: A 591 ASP cc_start: 0.7355 (m-30) cc_final: 0.7002 (m-30) REVERT: A 599 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8288 (ptp-170) REVERT: D 158 ASP cc_start: 0.7841 (t0) cc_final: 0.7578 (t70) REVERT: D 190 MET cc_start: 0.6394 (OUTLIER) cc_final: 0.5635 (mmt) REVERT: D 451 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7293 (tm-30) REVERT: D 491 ASN cc_start: 0.6886 (t0) cc_final: 0.6623 (t0) REVERT: D 537 MET cc_start: 0.8245 (ptt) cc_final: 0.8023 (ptm) REVERT: D 539 ASP cc_start: 0.7613 (t0) cc_final: 0.7248 (t0) REVERT: D 543 ARG cc_start: 0.7470 (ttp80) cc_final: 0.7163 (ttp-110) REVERT: D 579 MET cc_start: 0.8573 (mmm) cc_final: 0.8310 (mtp) REVERT: D 604 TRP cc_start: 0.7166 (OUTLIER) cc_final: 0.6025 (t60) REVERT: E 161 LYS cc_start: 0.8495 (mmmm) cc_final: 0.8166 (mtmm) REVERT: E 186 LYS cc_start: 0.4596 (OUTLIER) cc_final: 0.3711 (mptp) REVERT: E 242 LYS cc_start: 0.3086 (OUTLIER) cc_final: 0.2438 (tptp) REVERT: E 319 VAL cc_start: 0.7447 (t) cc_final: 0.7144 (m) REVERT: E 325 ARG cc_start: 0.8195 (tpm-80) cc_final: 0.7906 (tpm-80) REVERT: E 329 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7426 (mm-40) REVERT: E 330 ILE cc_start: 0.8804 (mt) cc_final: 0.8404 (mm) REVERT: E 360 ASP cc_start: 0.6613 (OUTLIER) cc_final: 0.6360 (m-30) REVERT: E 370 LEU cc_start: 0.8162 (mt) cc_final: 0.7786 (mp) REVERT: E 377 LYS cc_start: 0.6183 (OUTLIER) cc_final: 0.5733 (mmtm) REVERT: E 398 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7105 (ptm-80) REVERT: E 401 MET cc_start: 0.6119 (mtt) cc_final: 0.5649 (mtt) REVERT: E 409 GLU cc_start: 0.7706 (tt0) cc_final: 0.7499 (mt-10) REVERT: E 443 LEU cc_start: 0.8523 (mt) cc_final: 0.8306 (mp) REVERT: E 491 ASN cc_start: 0.8263 (t0) cc_final: 0.7927 (t0) REVERT: E 498 ASN cc_start: 0.8218 (OUTLIER) cc_final: 0.7659 (m110) REVERT: E 512 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8326 (ttpp) REVERT: E 537 MET cc_start: 0.8367 (ptt) cc_final: 0.8079 (ptm) REVERT: E 562 GLN cc_start: 0.8198 (tp40) cc_final: 0.7351 (tp-100) REVERT: E 566 ASP cc_start: 0.8148 (m-30) cc_final: 0.7799 (m-30) REVERT: F 143 THR cc_start: 0.7269 (p) cc_final: 0.6983 (p) REVERT: F 161 LYS cc_start: 0.8299 (mmmm) cc_final: 0.7945 (mttp) REVERT: F 190 MET cc_start: 0.6641 (ptp) cc_final: 0.6427 (ptp) REVERT: F 237 PHE cc_start: 0.7516 (m-10) cc_final: 0.6867 (m-10) REVERT: F 238 GLU cc_start: 0.7939 (tt0) cc_final: 0.7231 (tm-30) REVERT: F 281 GLU cc_start: 0.6313 (OUTLIER) cc_final: 0.5159 (tt0) REVERT: F 293 VAL cc_start: 0.7920 (m) cc_final: 0.7652 (p) REVERT: F 329 GLN cc_start: 0.7729 (mp10) cc_final: 0.7476 (mp10) REVERT: F 332 LYS cc_start: 0.8414 (mmmt) cc_final: 0.8210 (mtmm) REVERT: F 398 ARG cc_start: 0.7257 (ttp-170) cc_final: 0.6834 (ttp80) REVERT: F 401 MET cc_start: 0.5550 (mtp) cc_final: 0.4481 (mtp) REVERT: F 407 GLN cc_start: 0.8011 (tt0) cc_final: 0.7753 (tt0) REVERT: F 408 LYS cc_start: 0.8446 (ptpt) cc_final: 0.8241 (ptpp) REVERT: F 433 LYS cc_start: 0.8032 (tttt) cc_final: 0.7760 (ttmt) REVERT: F 451 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7374 (tm-30) REVERT: F 459 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7794 (ttt180) REVERT: F 467 SER cc_start: 0.8830 (m) cc_final: 0.8552 (t) REVERT: F 562 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7879 (tp-100) REVERT: F 566 ASP cc_start: 0.8147 (m-30) cc_final: 0.7913 (m-30) REVERT: F 568 MET cc_start: 0.8403 (tpp) cc_final: 0.8088 (tpp) REVERT: F 604 TRP cc_start: 0.6978 (OUTLIER) cc_final: 0.6777 (t60) REVERT: B 172 ARG cc_start: 0.5744 (OUTLIER) cc_final: 0.4320 (mmm160) REVERT: B 179 LYS cc_start: 0.7533 (mmtp) cc_final: 0.7211 (mmtt) REVERT: B 233 VAL cc_start: 0.7407 (m) cc_final: 0.7050 (p) REVERT: B 236 MET cc_start: 0.6338 (mpt) cc_final: 0.6031 (mpt) REVERT: B 238 GLU cc_start: 0.7824 (tp30) cc_final: 0.7577 (pp20) REVERT: B 247 ILE cc_start: 0.1103 (OUTLIER) cc_final: 0.0504 (mp) REVERT: B 367 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7209 (mm-30) REVERT: B 370 LEU cc_start: 0.7731 (mm) cc_final: 0.7250 (mp) REVERT: B 394 MET cc_start: 0.6737 (ptm) cc_final: 0.6416 (ptm) REVERT: B 408 LYS cc_start: 0.8501 (mttp) cc_final: 0.7980 (mtpp) REVERT: B 413 TYR cc_start: 0.8513 (m-80) cc_final: 0.7924 (m-80) REVERT: B 455 ILE cc_start: 0.8179 (mm) cc_final: 0.7850 (mp) REVERT: B 539 ASP cc_start: 0.7563 (t70) cc_final: 0.7012 (t0) REVERT: B 604 TRP cc_start: 0.7666 (OUTLIER) cc_final: 0.6259 (t60) REVERT: C 161 LYS cc_start: 0.8292 (ttpt) cc_final: 0.7540 (tptp) REVERT: C 200 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6541 (mm) REVERT: C 319 VAL cc_start: 0.7462 (t) cc_final: 0.7242 (m) REVERT: C 324 VAL cc_start: 0.8090 (p) cc_final: 0.7788 (t) REVERT: C 329 GLN cc_start: 0.7976 (tp40) cc_final: 0.7564 (mm-40) REVERT: C 367 GLU cc_start: 0.7983 (tp30) cc_final: 0.7720 (mm-30) REVERT: C 370 LEU cc_start: 0.8259 (mt) cc_final: 0.7975 (mp) REVERT: C 397 GLU cc_start: 0.7030 (pm20) cc_final: 0.6461 (pm20) REVERT: C 398 ARG cc_start: 0.7318 (mtp180) cc_final: 0.7004 (mtm110) REVERT: C 433 LYS cc_start: 0.8360 (ttmm) cc_final: 0.8042 (ttpp) REVERT: C 491 ASN cc_start: 0.8346 (t0) cc_final: 0.7977 (t0) REVERT: C 547 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6738 (mt0) REVERT: C 562 GLN cc_start: 0.8329 (tp40) cc_final: 0.7648 (tp-100) REVERT: C 566 ASP cc_start: 0.8285 (m-30) cc_final: 0.7635 (m-30) REVERT: C 591 ASP cc_start: 0.7020 (m-30) cc_final: 0.6679 (m-30) outliers start: 192 outliers final: 133 residues processed: 682 average time/residue: 0.3741 time to fit residues: 364.4100 Evaluate side-chains 705 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 549 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 569 ASP Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 604 TRP Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 282 MET Chi-restraints excluded: chain E residue 329 GLN Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 398 ARG Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 498 ASN Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 512 LYS Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 569 ASP Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 562 GLN Chi-restraints excluded: chain F residue 569 ASP Chi-restraints excluded: chain F residue 574 MET Chi-restraints excluded: chain F residue 598 VAL Chi-restraints excluded: chain F residue 604 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 507 TRP Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 604 TRP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 604 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 0.7980 chunk 214 optimal weight: 0.4980 chunk 47 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 238 optimal weight: 0.9980 chunk 197 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 124 optimal weight: 9.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 363 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 GLN D 418 HIS D 562 GLN E 556 ASN F 588 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19572 Z= 0.221 Angle : 0.607 8.496 26400 Z= 0.309 Chirality : 0.043 0.195 2958 Planarity : 0.004 0.065 3432 Dihedral : 11.585 80.751 3077 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.83 % Favored : 94.12 % Rotamer: Outliers : 9.40 % Allowed : 27.89 % Favored : 62.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.62 (0.17), residues: 2400 helix: 0.52 (0.15), residues: 1292 sheet: -0.83 (0.50), residues: 113 loop : -1.59 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 507 HIS 0.005 0.001 HIS F 418 PHE 0.028 0.001 PHE B 237 TYR 0.017 0.002 TYR D 557 ARG 0.005 0.000 ARG F 399 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 557 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.6299 (tpp) cc_final: 0.5996 (tpp) REVERT: A 153 ASP cc_start: 0.7401 (m-30) cc_final: 0.7016 (m-30) REVERT: A 236 MET cc_start: 0.7307 (mpt) cc_final: 0.7077 (mmt) REVERT: A 237 PHE cc_start: 0.7320 (m-80) cc_final: 0.6868 (m-80) REVERT: A 293 VAL cc_start: 0.8070 (OUTLIER) cc_final: 0.7825 (p) REVERT: A 332 LYS cc_start: 0.8024 (mtpp) cc_final: 0.7801 (mtpp) REVERT: A 367 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7503 (mm-30) REVERT: A 539 ASP cc_start: 0.7440 (t70) cc_final: 0.6988 (t0) REVERT: A 554 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6191 (mp0) REVERT: A 579 MET cc_start: 0.8695 (mmm) cc_final: 0.8456 (mmm) REVERT: A 591 ASP cc_start: 0.7374 (m-30) cc_final: 0.7021 (m-30) REVERT: A 599 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8288 (ptp-170) REVERT: D 158 ASP cc_start: 0.7801 (t0) cc_final: 0.7492 (t70) REVERT: D 190 MET cc_start: 0.6477 (OUTLIER) cc_final: 0.5868 (mmt) REVERT: D 327 ARG cc_start: 0.7356 (mtt180) cc_final: 0.6976 (ptp-170) REVERT: D 451 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7459 (tm-30) REVERT: D 491 ASN cc_start: 0.6966 (t0) cc_final: 0.6706 (t0) REVERT: D 537 MET cc_start: 0.8251 (ptt) cc_final: 0.8025 (ptm) REVERT: D 539 ASP cc_start: 0.7651 (t0) cc_final: 0.7295 (t0) REVERT: D 543 ARG cc_start: 0.7529 (ttp80) cc_final: 0.7211 (ttp-110) REVERT: D 579 MET cc_start: 0.8536 (mmm) cc_final: 0.8287 (mtp) REVERT: D 604 TRP cc_start: 0.7162 (OUTLIER) cc_final: 0.6031 (t60) REVERT: E 161 LYS cc_start: 0.8498 (mmmm) cc_final: 0.8152 (mtmm) REVERT: E 186 LYS cc_start: 0.4633 (OUTLIER) cc_final: 0.3699 (mptp) REVERT: E 242 LYS cc_start: 0.3260 (OUTLIER) cc_final: 0.2581 (tptp) REVERT: E 325 ARG cc_start: 0.8250 (tpm-80) cc_final: 0.7996 (tpm-80) REVERT: E 330 ILE cc_start: 0.8856 (mt) cc_final: 0.8475 (mm) REVERT: E 360 ASP cc_start: 0.6655 (OUTLIER) cc_final: 0.6417 (m-30) REVERT: E 377 LYS cc_start: 0.6147 (OUTLIER) cc_final: 0.5615 (mmtm) REVERT: E 398 ARG cc_start: 0.7444 (mtp180) cc_final: 0.7209 (ptm-80) REVERT: E 409 GLU cc_start: 0.7747 (tt0) cc_final: 0.7534 (mt-10) REVERT: E 491 ASN cc_start: 0.8262 (t0) cc_final: 0.7916 (t0) REVERT: E 498 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7667 (m110) REVERT: E 512 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8330 (ttpp) REVERT: E 537 MET cc_start: 0.8359 (ptt) cc_final: 0.8068 (ptm) REVERT: E 562 GLN cc_start: 0.8204 (tp40) cc_final: 0.7579 (tp-100) REVERT: E 566 ASP cc_start: 0.8140 (m-30) cc_final: 0.7727 (m-30) REVERT: F 143 THR cc_start: 0.7271 (p) cc_final: 0.6995 (p) REVERT: F 161 LYS cc_start: 0.8284 (mmmm) cc_final: 0.7984 (mttp) REVERT: F 190 MET cc_start: 0.6498 (ptp) cc_final: 0.6224 (ptp) REVERT: F 237 PHE cc_start: 0.7549 (m-10) cc_final: 0.7208 (m-10) REVERT: F 238 GLU cc_start: 0.7988 (tt0) cc_final: 0.7715 (tt0) REVERT: F 281 GLU cc_start: 0.6415 (OUTLIER) cc_final: 0.5834 (tm-30) REVERT: F 293 VAL cc_start: 0.7930 (m) cc_final: 0.7714 (p) REVERT: F 329 GLN cc_start: 0.7748 (mp10) cc_final: 0.7489 (mp10) REVERT: F 332 LYS cc_start: 0.8424 (mmmt) cc_final: 0.8206 (mtmm) REVERT: F 398 ARG cc_start: 0.7292 (ttp-170) cc_final: 0.6842 (ttp80) REVERT: F 401 MET cc_start: 0.5593 (mtp) cc_final: 0.4399 (mtp) REVERT: F 408 LYS cc_start: 0.8493 (ptpt) cc_final: 0.8248 (ptpp) REVERT: F 433 LYS cc_start: 0.8052 (tttt) cc_final: 0.7763 (ttmt) REVERT: F 451 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7528 (tm-30) REVERT: F 459 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7849 (ttt180) REVERT: F 467 SER cc_start: 0.8844 (m) cc_final: 0.8529 (t) REVERT: F 562 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.6982 (tm-30) REVERT: F 566 ASP cc_start: 0.8143 (m-30) cc_final: 0.7460 (m-30) REVERT: F 568 MET cc_start: 0.8391 (tpp) cc_final: 0.7992 (tpt) REVERT: B 172 ARG cc_start: 0.5744 (OUTLIER) cc_final: 0.4233 (mmm160) REVERT: B 179 LYS cc_start: 0.7533 (mmtp) cc_final: 0.7187 (mmtt) REVERT: B 186 LYS cc_start: 0.6461 (OUTLIER) cc_final: 0.6046 (pttt) REVERT: B 233 VAL cc_start: 0.7497 (m) cc_final: 0.7190 (p) REVERT: B 236 MET cc_start: 0.6399 (mpt) cc_final: 0.6091 (mpt) REVERT: B 238 GLU cc_start: 0.7871 (tp30) cc_final: 0.7601 (pp20) REVERT: B 247 ILE cc_start: 0.1266 (OUTLIER) cc_final: 0.0767 (mp) REVERT: B 367 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7241 (mm-30) REVERT: B 394 MET cc_start: 0.6729 (ptm) cc_final: 0.6389 (ptp) REVERT: B 408 LYS cc_start: 0.8513 (mttp) cc_final: 0.7985 (mtpp) REVERT: B 539 ASP cc_start: 0.7599 (t70) cc_final: 0.7042 (t0) REVERT: B 547 GLN cc_start: 0.7069 (mt0) cc_final: 0.6803 (mt0) REVERT: B 604 TRP cc_start: 0.7663 (OUTLIER) cc_final: 0.6240 (t60) REVERT: C 161 LYS cc_start: 0.8309 (ttpt) cc_final: 0.7573 (tptp) REVERT: C 200 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6538 (mm) REVERT: C 216 ILE cc_start: 0.8019 (mm) cc_final: 0.7625 (mm) REVERT: C 236 MET cc_start: 0.7568 (tpp) cc_final: 0.7122 (tpp) REVERT: C 319 VAL cc_start: 0.7470 (t) cc_final: 0.7199 (m) REVERT: C 324 VAL cc_start: 0.8060 (p) cc_final: 0.7782 (t) REVERT: C 329 GLN cc_start: 0.8001 (tp40) cc_final: 0.7579 (mm-40) REVERT: C 367 GLU cc_start: 0.8041 (tp30) cc_final: 0.7763 (mm-30) REVERT: C 370 LEU cc_start: 0.8314 (mt) cc_final: 0.8011 (mp) REVERT: C 397 GLU cc_start: 0.7046 (pm20) cc_final: 0.6468 (pm20) REVERT: C 398 ARG cc_start: 0.7316 (mtp180) cc_final: 0.6952 (mtm110) REVERT: C 433 LYS cc_start: 0.8374 (ttmm) cc_final: 0.8059 (ttpp) REVERT: C 491 ASN cc_start: 0.8358 (t0) cc_final: 0.7994 (t0) REVERT: C 547 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6927 (mt0) REVERT: C 562 GLN cc_start: 0.8343 (tp40) cc_final: 0.7658 (tp-100) REVERT: C 566 ASP cc_start: 0.8284 (m-30) cc_final: 0.7649 (m-30) REVERT: C 591 ASP cc_start: 0.7023 (m-30) cc_final: 0.6688 (m-30) outliers start: 186 outliers final: 140 residues processed: 676 average time/residue: 0.3827 time to fit residues: 367.9229 Evaluate side-chains 710 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 549 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 429 ASP Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 604 TRP Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 282 MET Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 498 ASN Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 512 LYS Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain E residue 569 ASP Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 278 MET Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 562 GLN Chi-restraints excluded: chain F residue 574 MET Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 507 TRP Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 604 TRP Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 604 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 173 optimal weight: 0.0870 chunk 134 optimal weight: 5.9990 chunk 200 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 237 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 144 optimal weight: 0.0870 chunk 109 optimal weight: 10.0000 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 363 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 GLN D 418 HIS D 556 ASN D 562 GLN F 407 GLN F 414 HIS B 273 GLN B 407 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 19572 Z= 0.162 Angle : 0.583 8.669 26400 Z= 0.296 Chirality : 0.042 0.154 2958 Planarity : 0.004 0.063 3432 Dihedral : 11.021 80.108 3065 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 8.06 % Allowed : 29.43 % Favored : 62.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.38 (0.17), residues: 2400 helix: 0.71 (0.15), residues: 1288 sheet: -0.79 (0.51), residues: 113 loop : -1.45 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 507 HIS 0.005 0.001 HIS F 418 PHE 0.027 0.001 PHE B 237 TYR 0.015 0.001 TYR C 557 ARG 0.005 0.000 ARG F 399 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 546 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.6260 (tpp) cc_final: 0.5986 (tpp) REVERT: A 153 ASP cc_start: 0.7377 (m-30) cc_final: 0.6978 (m-30) REVERT: A 293 VAL cc_start: 0.8045 (OUTLIER) cc_final: 0.7799 (p) REVERT: A 332 LYS cc_start: 0.8003 (mtpp) cc_final: 0.7782 (mtpp) REVERT: A 367 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7496 (mm-30) REVERT: A 384 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7260 (tt0) REVERT: A 407 GLN cc_start: 0.7956 (mt0) cc_final: 0.7572 (mt0) REVERT: A 498 ASN cc_start: 0.7969 (m-40) cc_final: 0.7659 (t0) REVERT: A 539 ASP cc_start: 0.7284 (t70) cc_final: 0.6838 (t0) REVERT: A 554 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6161 (mp0) REVERT: A 588 GLN cc_start: 0.8075 (mt0) cc_final: 0.7774 (mt0) REVERT: A 591 ASP cc_start: 0.7356 (m-30) cc_final: 0.7059 (m-30) REVERT: D 158 ASP cc_start: 0.7614 (t0) cc_final: 0.7351 (t0) REVERT: D 237 PHE cc_start: 0.7274 (m-80) cc_final: 0.6924 (m-10) REVERT: D 327 ARG cc_start: 0.7341 (mtt180) cc_final: 0.7052 (ptp-170) REVERT: D 408 LYS cc_start: 0.8687 (ttmm) cc_final: 0.8265 (mtpp) REVERT: D 451 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7425 (tm-30) REVERT: D 485 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8448 (t) REVERT: D 537 MET cc_start: 0.8250 (ptt) cc_final: 0.8028 (ptm) REVERT: D 539 ASP cc_start: 0.7554 (t0) cc_final: 0.7095 (t0) REVERT: D 543 ARG cc_start: 0.7316 (ttp80) cc_final: 0.7026 (ttp-110) REVERT: D 579 MET cc_start: 0.8525 (mmm) cc_final: 0.8221 (mtp) REVERT: D 604 TRP cc_start: 0.7174 (OUTLIER) cc_final: 0.5863 (t60) REVERT: E 161 LYS cc_start: 0.8489 (mmmm) cc_final: 0.8140 (mtmm) REVERT: E 186 LYS cc_start: 0.4727 (OUTLIER) cc_final: 0.3764 (mptp) REVERT: E 190 MET cc_start: 0.6663 (mtm) cc_final: 0.6423 (mtm) REVERT: E 242 LYS cc_start: 0.3237 (OUTLIER) cc_final: 0.2576 (tptp) REVERT: E 325 ARG cc_start: 0.8339 (tpm-80) cc_final: 0.8031 (tpm-80) REVERT: E 330 ILE cc_start: 0.8811 (mt) cc_final: 0.8409 (mm) REVERT: E 366 ASN cc_start: 0.8472 (t0) cc_final: 0.8216 (t0) REVERT: E 491 ASN cc_start: 0.8257 (t0) cc_final: 0.7833 (t0) REVERT: E 498 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7645 (m110) REVERT: E 537 MET cc_start: 0.8358 (ptt) cc_final: 0.8093 (ptm) REVERT: E 562 GLN cc_start: 0.8189 (tp40) cc_final: 0.7698 (tp-100) REVERT: E 566 ASP cc_start: 0.8124 (m-30) cc_final: 0.7783 (m-30) REVERT: F 143 THR cc_start: 0.7487 (p) cc_final: 0.7146 (p) REVERT: F 179 LYS cc_start: 0.5822 (mmtt) cc_final: 0.5618 (mmtt) REVERT: F 237 PHE cc_start: 0.7402 (m-10) cc_final: 0.7078 (m-10) REVERT: F 238 GLU cc_start: 0.7927 (tt0) cc_final: 0.7680 (tt0) REVERT: F 281 GLU cc_start: 0.6290 (OUTLIER) cc_final: 0.5700 (tm-30) REVERT: F 293 VAL cc_start: 0.7934 (m) cc_final: 0.7729 (p) REVERT: F 329 GLN cc_start: 0.7740 (mp10) cc_final: 0.7471 (mp10) REVERT: F 332 LYS cc_start: 0.8429 (mmmt) cc_final: 0.8213 (mtmm) REVERT: F 398 ARG cc_start: 0.7299 (ttp-170) cc_final: 0.6738 (ttp80) REVERT: F 401 MET cc_start: 0.5664 (mtp) cc_final: 0.4366 (mtp) REVERT: F 407 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7766 (tt0) REVERT: F 433 LYS cc_start: 0.8019 (tttt) cc_final: 0.7748 (ttmt) REVERT: F 451 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7515 (tm-30) REVERT: F 467 SER cc_start: 0.8825 (m) cc_final: 0.8480 (t) REVERT: F 483 GLU cc_start: 0.7499 (pt0) cc_final: 0.7179 (pm20) REVERT: F 562 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7783 (tp-100) REVERT: F 566 ASP cc_start: 0.8055 (m-30) cc_final: 0.7827 (m-30) REVERT: F 568 MET cc_start: 0.8350 (tpp) cc_final: 0.7968 (tpt) REVERT: B 172 ARG cc_start: 0.5672 (OUTLIER) cc_final: 0.4411 (mmm160) REVERT: B 179 LYS cc_start: 0.7492 (mmtp) cc_final: 0.7223 (mmtt) REVERT: B 233 VAL cc_start: 0.7399 (m) cc_final: 0.7184 (p) REVERT: B 236 MET cc_start: 0.6318 (mpt) cc_final: 0.6025 (mpt) REVERT: B 238 GLU cc_start: 0.7836 (tp30) cc_final: 0.7393 (pp20) REVERT: B 247 ILE cc_start: 0.1158 (OUTLIER) cc_final: 0.0691 (mp) REVERT: B 351 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7559 (ttm-80) REVERT: B 367 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7291 (mm-30) REVERT: B 370 LEU cc_start: 0.7700 (mm) cc_final: 0.7254 (mp) REVERT: B 394 MET cc_start: 0.6705 (ptm) cc_final: 0.6324 (ptp) REVERT: B 408 LYS cc_start: 0.8456 (mttp) cc_final: 0.7900 (mtpp) REVERT: B 413 TYR cc_start: 0.8448 (m-80) cc_final: 0.7900 (m-80) REVERT: B 565 THR cc_start: 0.8550 (m) cc_final: 0.8242 (m) REVERT: B 604 TRP cc_start: 0.7653 (OUTLIER) cc_final: 0.6130 (t60) REVERT: C 161 LYS cc_start: 0.8181 (ttpt) cc_final: 0.7453 (tptp) REVERT: C 200 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6539 (mm) REVERT: C 216 ILE cc_start: 0.7922 (mm) cc_final: 0.7520 (mm) REVERT: C 236 MET cc_start: 0.7471 (tpp) cc_final: 0.7056 (tpp) REVERT: C 237 PHE cc_start: 0.6147 (OUTLIER) cc_final: 0.5642 (t80) REVERT: C 319 VAL cc_start: 0.7366 (t) cc_final: 0.7141 (m) REVERT: C 324 VAL cc_start: 0.7979 (p) cc_final: 0.7694 (t) REVERT: C 329 GLN cc_start: 0.7946 (tp40) cc_final: 0.7539 (mm-40) REVERT: C 367 GLU cc_start: 0.7968 (tp30) cc_final: 0.7673 (mm-30) REVERT: C 397 GLU cc_start: 0.7024 (pm20) cc_final: 0.6445 (pm20) REVERT: C 398 ARG cc_start: 0.7280 (mtp180) cc_final: 0.6893 (mtm110) REVERT: C 433 LYS cc_start: 0.8332 (ttmm) cc_final: 0.8020 (ttpp) REVERT: C 491 ASN cc_start: 0.8339 (t0) cc_final: 0.7932 (t0) REVERT: C 562 GLN cc_start: 0.8027 (tp40) cc_final: 0.7452 (tp-100) REVERT: C 566 ASP cc_start: 0.8254 (m-30) cc_final: 0.7648 (m-30) REVERT: C 591 ASP cc_start: 0.7011 (m-30) cc_final: 0.6667 (m-30) outliers start: 159 outliers final: 114 residues processed: 650 average time/residue: 0.3633 time to fit residues: 336.2183 Evaluate side-chains 677 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 547 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 604 TRP Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 498 ASN Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 407 GLN Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 562 GLN Chi-restraints excluded: chain F residue 574 MET Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 507 TRP Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 604 TRP Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 455 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 141 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 150 optimal weight: 0.0010 chunk 161 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 186 optimal weight: 4.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 407 GLN D 418 HIS D 556 ASN ** F 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 556 ASN F 588 GLN B 407 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19572 Z= 0.164 Angle : 0.588 9.888 26400 Z= 0.298 Chirality : 0.042 0.180 2958 Planarity : 0.004 0.063 3432 Dihedral : 10.449 79.992 3025 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 7.07 % Allowed : 30.42 % Favored : 62.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.18), residues: 2400 helix: 0.79 (0.15), residues: 1287 sheet: -0.79 (0.52), residues: 108 loop : -1.39 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 507 HIS 0.005 0.001 HIS F 418 PHE 0.035 0.001 PHE A 237 TYR 0.014 0.001 TYR B 557 ARG 0.004 0.000 ARG F 399 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 543 time to evaluate : 2.322 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: A 153 ASP cc_start: 0.7402 (m-30) cc_final: 0.7007 (m-30) REVERT: A 190 MET cc_start: 0.6296 (mpp) cc_final: 0.5680 (mpp) REVERT: A 293 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7815 (p) REVERT: A 332 LYS cc_start: 0.8007 (mtpp) cc_final: 0.7787 (mtpp) REVERT: A 367 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7507 (mm-30) REVERT: A 384 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7288 (tt0) REVERT: A 539 ASP cc_start: 0.7280 (t70) cc_final: 0.6822 (t0) REVERT: A 554 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6157 (mp0) REVERT: D 158 ASP cc_start: 0.7535 (t0) cc_final: 0.7297 (t0) REVERT: D 237 PHE cc_start: 0.7260 (m-80) cc_final: 0.6884 (m-10) REVERT: D 327 ARG cc_start: 0.7332 (mtt180) cc_final: 0.6964 (ptp-170) REVERT: D 451 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7401 (tm-30) REVERT: D 485 VAL cc_start: 0.8734 (OUTLIER) cc_final: 0.8443 (t) REVERT: D 537 MET cc_start: 0.8245 (ptt) cc_final: 0.8022 (ptm) REVERT: D 539 ASP cc_start: 0.7532 (t0) cc_final: 0.7093 (t0) REVERT: D 543 ARG cc_start: 0.7269 (ttp80) cc_final: 0.7001 (ttp-110) REVERT: D 579 MET cc_start: 0.8456 (mmm) cc_final: 0.8115 (mtp) REVERT: D 595 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8554 (mpt90) REVERT: D 604 TRP cc_start: 0.7111 (OUTLIER) cc_final: 0.5714 (t60) REVERT: E 186 LYS cc_start: 0.4663 (OUTLIER) cc_final: 0.3724 (mptp) REVERT: E 190 MET cc_start: 0.6669 (mtm) cc_final: 0.6414 (mtm) REVERT: E 242 LYS cc_start: 0.3175 (OUTLIER) cc_final: 0.2477 (tptp) REVERT: E 325 ARG cc_start: 0.8328 (tpm-80) cc_final: 0.8008 (tpm-80) REVERT: E 330 ILE cc_start: 0.8817 (mt) cc_final: 0.8433 (mm) REVERT: E 366 ASN cc_start: 0.8446 (t0) cc_final: 0.8165 (t0) REVERT: E 398 ARG cc_start: 0.7426 (ptm-80) cc_final: 0.7131 (ptm160) REVERT: E 491 ASN cc_start: 0.8246 (t0) cc_final: 0.7824 (t0) REVERT: E 498 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7649 (m110) REVERT: E 537 MET cc_start: 0.8378 (ptt) cc_final: 0.8109 (ptm) REVERT: E 562 GLN cc_start: 0.8189 (tp40) cc_final: 0.7703 (tp-100) REVERT: E 566 ASP cc_start: 0.8112 (m-30) cc_final: 0.7635 (m-30) REVERT: F 143 THR cc_start: 0.7482 (p) cc_final: 0.7141 (p) REVERT: F 237 PHE cc_start: 0.7455 (m-10) cc_final: 0.6890 (m-10) REVERT: F 238 GLU cc_start: 0.7984 (tt0) cc_final: 0.7347 (tm-30) REVERT: F 281 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.5270 (tt0) REVERT: F 282 MET cc_start: 0.6361 (ptp) cc_final: 0.6035 (ptp) REVERT: F 293 VAL cc_start: 0.7916 (m) cc_final: 0.7678 (p) REVERT: F 329 GLN cc_start: 0.7730 (mp10) cc_final: 0.7482 (mp10) REVERT: F 332 LYS cc_start: 0.8417 (mmmt) cc_final: 0.8210 (mtmm) REVERT: F 398 ARG cc_start: 0.7300 (ttp-170) cc_final: 0.6797 (ttp80) REVERT: F 401 MET cc_start: 0.5701 (mtp) cc_final: 0.4401 (mtp) REVERT: F 433 LYS cc_start: 0.8039 (tttt) cc_final: 0.7757 (ttmt) REVERT: F 451 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7213 (tm-30) REVERT: F 467 SER cc_start: 0.8738 (m) cc_final: 0.8492 (t) REVERT: F 483 GLU cc_start: 0.7523 (pt0) cc_final: 0.7153 (pm20) REVERT: F 562 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7836 (tp-100) REVERT: F 566 ASP cc_start: 0.8080 (m-30) cc_final: 0.7859 (m-30) REVERT: F 568 MET cc_start: 0.8327 (tpp) cc_final: 0.7964 (tpt) REVERT: B 172 ARG cc_start: 0.5723 (OUTLIER) cc_final: 0.4545 (mmm160) REVERT: B 179 LYS cc_start: 0.7433 (mmtp) cc_final: 0.7127 (mmtt) REVERT: B 236 MET cc_start: 0.6457 (mpt) cc_final: 0.6178 (mpt) REVERT: B 238 GLU cc_start: 0.7809 (tp30) cc_final: 0.7367 (pp20) REVERT: B 247 ILE cc_start: 0.1016 (OUTLIER) cc_final: 0.0541 (mp) REVERT: B 298 ASN cc_start: 0.7701 (p0) cc_final: 0.7470 (p0) REVERT: B 367 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7247 (mm-30) REVERT: B 370 LEU cc_start: 0.7683 (mm) cc_final: 0.7199 (mp) REVERT: B 393 MET cc_start: 0.7737 (ttm) cc_final: 0.7382 (ttp) REVERT: B 394 MET cc_start: 0.6678 (ptm) cc_final: 0.6282 (ptp) REVERT: B 408 LYS cc_start: 0.8448 (mttp) cc_final: 0.8076 (mtmm) REVERT: B 413 TYR cc_start: 0.8452 (m-80) cc_final: 0.7920 (m-80) REVERT: B 492 ASP cc_start: 0.7324 (m-30) cc_final: 0.6310 (m-30) REVERT: B 565 THR cc_start: 0.8550 (m) cc_final: 0.8230 (m) REVERT: B 604 TRP cc_start: 0.7656 (OUTLIER) cc_final: 0.6031 (t60) REVERT: C 161 LYS cc_start: 0.8121 (ttpt) cc_final: 0.7454 (tptp) REVERT: C 200 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6508 (mm) REVERT: C 216 ILE cc_start: 0.7950 (mm) cc_final: 0.7547 (mm) REVERT: C 236 MET cc_start: 0.7451 (tpp) cc_final: 0.7077 (tpp) REVERT: C 319 VAL cc_start: 0.7311 (t) cc_final: 0.7108 (m) REVERT: C 329 GLN cc_start: 0.7970 (tp40) cc_final: 0.7567 (mm-40) REVERT: C 367 GLU cc_start: 0.8018 (tp30) cc_final: 0.7698 (mm-30) REVERT: C 397 GLU cc_start: 0.7034 (pm20) cc_final: 0.6428 (pm20) REVERT: C 398 ARG cc_start: 0.7279 (mtp180) cc_final: 0.6899 (mtm110) REVERT: C 433 LYS cc_start: 0.8325 (ttmm) cc_final: 0.8012 (ttpp) REVERT: C 491 ASN cc_start: 0.8322 (t0) cc_final: 0.7921 (t0) REVERT: C 562 GLN cc_start: 0.8026 (tp40) cc_final: 0.7515 (tp-100) REVERT: C 566 ASP cc_start: 0.8246 (m-30) cc_final: 0.7682 (m-30) REVERT: C 591 ASP cc_start: 0.7005 (m-30) cc_final: 0.6670 (m-30) outliers start: 139 outliers final: 112 residues processed: 634 average time/residue: 0.3700 time to fit residues: 334.8725 Evaluate side-chains 662 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 535 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 595 ARG Chi-restraints excluded: chain D residue 604 TRP Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 498 ASN Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 538 SER Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 562 GLN Chi-restraints excluded: chain F residue 574 MET Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 507 TRP Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 604 TRP Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 455 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 220 optimal weight: 2.9990 chunk 132 optimal weight: 0.3980 chunk 96 optimal weight: 0.3980 chunk 173 optimal weight: 3.9990 chunk 67 optimal weight: 0.0060 chunk 199 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 145 optimal weight: 8.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 407 GLN D 418 HIS ** F 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 588 GLN B 407 GLN B 547 GLN B 556 ASN C 556 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19572 Z= 0.172 Angle : 0.598 18.268 26400 Z= 0.302 Chirality : 0.042 0.181 2958 Planarity : 0.004 0.062 3432 Dihedral : 10.147 80.555 3014 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 6.63 % Allowed : 30.81 % Favored : 62.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.18), residues: 2400 helix: 0.89 (0.15), residues: 1278 sheet: -0.77 (0.52), residues: 108 loop : -1.37 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 507 HIS 0.007 0.001 HIS D 418 PHE 0.036 0.001 PHE A 237 TYR 0.014 0.001 TYR B 557 ARG 0.004 0.000 ARG A 543 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 542 time to evaluate : 2.187 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: A 141 MET cc_start: 0.6619 (ttt) cc_final: 0.6419 (ttm) REVERT: A 153 ASP cc_start: 0.7416 (m-30) cc_final: 0.7024 (m-30) REVERT: A 190 MET cc_start: 0.6339 (mpp) cc_final: 0.5617 (mpp) REVERT: A 293 VAL cc_start: 0.8053 (OUTLIER) cc_final: 0.7818 (p) REVERT: A 332 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7781 (mtpp) REVERT: A 367 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7496 (mm-30) REVERT: A 407 GLN cc_start: 0.7876 (mt0) cc_final: 0.7505 (mt0) REVERT: A 539 ASP cc_start: 0.7267 (t70) cc_final: 0.6849 (t0) REVERT: A 554 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6156 (mp0) REVERT: D 158 ASP cc_start: 0.7485 (t0) cc_final: 0.7252 (t0) REVERT: D 236 MET cc_start: 0.7678 (tpp) cc_final: 0.7447 (tpp) REVERT: D 237 PHE cc_start: 0.7274 (m-80) cc_final: 0.6962 (m-10) REVERT: D 327 ARG cc_start: 0.7341 (mtt180) cc_final: 0.6970 (ptp-170) REVERT: D 408 LYS cc_start: 0.8589 (ttmm) cc_final: 0.8208 (mtpp) REVERT: D 451 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7394 (tm-30) REVERT: D 485 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8442 (t) REVERT: D 537 MET cc_start: 0.8237 (ptt) cc_final: 0.8012 (ptm) REVERT: D 539 ASP cc_start: 0.7534 (t0) cc_final: 0.7111 (t0) REVERT: D 543 ARG cc_start: 0.7264 (ttp80) cc_final: 0.6596 (ttp-110) REVERT: D 547 GLN cc_start: 0.6842 (mt0) cc_final: 0.6586 (mt0) REVERT: D 579 MET cc_start: 0.8494 (mmm) cc_final: 0.8090 (mtp) REVERT: D 595 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8573 (mpt90) REVERT: D 604 TRP cc_start: 0.7117 (OUTLIER) cc_final: 0.5689 (t60) REVERT: E 186 LYS cc_start: 0.4504 (OUTLIER) cc_final: 0.3584 (mptp) REVERT: E 242 LYS cc_start: 0.3234 (OUTLIER) cc_final: 0.2483 (tptp) REVERT: E 298 ASN cc_start: 0.7834 (OUTLIER) cc_final: 0.7582 (m-40) REVERT: E 325 ARG cc_start: 0.8308 (tpm-80) cc_final: 0.8022 (tpm-80) REVERT: E 330 ILE cc_start: 0.8820 (mt) cc_final: 0.8444 (mm) REVERT: E 366 ASN cc_start: 0.8433 (t0) cc_final: 0.8161 (t0) REVERT: E 491 ASN cc_start: 0.8243 (t0) cc_final: 0.7818 (t0) REVERT: E 498 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7617 (m110) REVERT: E 537 MET cc_start: 0.8378 (ptt) cc_final: 0.8109 (ptm) REVERT: E 562 GLN cc_start: 0.8144 (tp40) cc_final: 0.7675 (tp-100) REVERT: E 566 ASP cc_start: 0.8110 (m-30) cc_final: 0.7645 (m-30) REVERT: F 143 THR cc_start: 0.7469 (p) cc_final: 0.7145 (p) REVERT: F 163 GLU cc_start: 0.7162 (tp30) cc_final: 0.6517 (tp30) REVERT: F 237 PHE cc_start: 0.7472 (m-10) cc_final: 0.6942 (m-10) REVERT: F 238 GLU cc_start: 0.7971 (tt0) cc_final: 0.7409 (tp30) REVERT: F 281 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.5342 (tt0) REVERT: F 282 MET cc_start: 0.6355 (ptp) cc_final: 0.6062 (ptp) REVERT: F 293 VAL cc_start: 0.7882 (m) cc_final: 0.7678 (p) REVERT: F 329 GLN cc_start: 0.7743 (mp10) cc_final: 0.7470 (mp10) REVERT: F 332 LYS cc_start: 0.8458 (mmmt) cc_final: 0.8245 (mtmm) REVERT: F 366 ASN cc_start: 0.8266 (t0) cc_final: 0.8044 (t0) REVERT: F 398 ARG cc_start: 0.7289 (ttp-170) cc_final: 0.6871 (ttp80) REVERT: F 433 LYS cc_start: 0.8050 (tttt) cc_final: 0.7765 (ttmt) REVERT: F 451 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7220 (tm-30) REVERT: F 467 SER cc_start: 0.8742 (m) cc_final: 0.8480 (t) REVERT: F 483 GLU cc_start: 0.7574 (pt0) cc_final: 0.7171 (pm20) REVERT: F 562 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7851 (tp-100) REVERT: F 566 ASP cc_start: 0.8063 (m-30) cc_final: 0.7805 (m-30) REVERT: F 568 MET cc_start: 0.8330 (tpp) cc_final: 0.7969 (tpt) REVERT: B 172 ARG cc_start: 0.5717 (OUTLIER) cc_final: 0.4568 (mmm160) REVERT: B 236 MET cc_start: 0.6345 (mpt) cc_final: 0.5989 (mpt) REVERT: B 238 GLU cc_start: 0.7772 (tp30) cc_final: 0.7350 (pp20) REVERT: B 247 ILE cc_start: 0.1037 (OUTLIER) cc_final: 0.0573 (mp) REVERT: B 298 ASN cc_start: 0.7690 (p0) cc_final: 0.7475 (p0) REVERT: B 367 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7270 (mm-30) REVERT: B 394 MET cc_start: 0.6699 (ptm) cc_final: 0.6311 (ptp) REVERT: B 408 LYS cc_start: 0.8444 (mttp) cc_final: 0.8114 (mtmm) REVERT: B 413 TYR cc_start: 0.8452 (m-80) cc_final: 0.7870 (m-80) REVERT: B 492 ASP cc_start: 0.7335 (m-30) cc_final: 0.6351 (m-30) REVERT: B 604 TRP cc_start: 0.7642 (OUTLIER) cc_final: 0.5961 (t60) REVERT: C 161 LYS cc_start: 0.8081 (ttpt) cc_final: 0.7417 (tptp) REVERT: C 200 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6507 (mm) REVERT: C 216 ILE cc_start: 0.7972 (mm) cc_final: 0.7565 (mm) REVERT: C 236 MET cc_start: 0.7245 (tpp) cc_final: 0.6885 (tpp) REVERT: C 237 PHE cc_start: 0.5306 (t80) cc_final: 0.4588 (t80) REVERT: C 329 GLN cc_start: 0.7973 (tp40) cc_final: 0.7573 (mm-40) REVERT: C 367 GLU cc_start: 0.8017 (tp30) cc_final: 0.7701 (mm-30) REVERT: C 397 GLU cc_start: 0.7038 (pm20) cc_final: 0.6440 (pm20) REVERT: C 398 ARG cc_start: 0.7271 (mtp180) cc_final: 0.6906 (mtm110) REVERT: C 433 LYS cc_start: 0.8320 (ttmm) cc_final: 0.8008 (ttpp) REVERT: C 491 ASN cc_start: 0.8319 (t0) cc_final: 0.7932 (t0) REVERT: C 547 GLN cc_start: 0.7334 (mm-40) cc_final: 0.6955 (mt0) REVERT: C 562 GLN cc_start: 0.8026 (tp40) cc_final: 0.7563 (tp-100) REVERT: C 566 ASP cc_start: 0.8244 (m-30) cc_final: 0.7731 (m-30) REVERT: C 591 ASP cc_start: 0.7007 (m-30) cc_final: 0.6594 (m-30) outliers start: 130 outliers final: 107 residues processed: 625 average time/residue: 0.3612 time to fit residues: 320.6774 Evaluate side-chains 664 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 541 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 595 ARG Chi-restraints excluded: chain D residue 604 TRP Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 298 ASN Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 498 ASN Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 538 SER Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 562 GLN Chi-restraints excluded: chain F residue 574 MET Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 507 TRP Chi-restraints excluded: chain B residue 591 ASP Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 604 TRP Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 455 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 245 optimal weight: 0.0970 chunk 225 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 150 optimal weight: 0.0670 chunk 119 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 GLN ** F 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 588 GLN B 547 GLN B 556 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19572 Z= 0.174 Angle : 0.598 15.309 26400 Z= 0.303 Chirality : 0.042 0.177 2958 Planarity : 0.004 0.063 3432 Dihedral : 9.908 81.133 3002 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 6.68 % Allowed : 31.01 % Favored : 62.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2400 helix: 0.89 (0.15), residues: 1278 sheet: -1.93 (0.59), residues: 73 loop : -1.25 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 507 HIS 0.008 0.001 HIS D 414 PHE 0.035 0.001 PHE A 237 TYR 0.015 0.001 TYR B 557 ARG 0.005 0.000 ARG E 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 540 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.7427 (m-30) cc_final: 0.7035 (m-30) REVERT: A 190 MET cc_start: 0.6230 (mpp) cc_final: 0.5461 (mpp) REVERT: A 293 VAL cc_start: 0.8068 (OUTLIER) cc_final: 0.7833 (p) REVERT: A 332 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7786 (mtpp) REVERT: A 367 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7489 (mm-30) REVERT: A 407 GLN cc_start: 0.7803 (mt0) cc_final: 0.7534 (mt0) REVERT: A 539 ASP cc_start: 0.7272 (t70) cc_final: 0.6875 (t0) REVERT: A 554 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6166 (mp0) REVERT: D 158 ASP cc_start: 0.7390 (t0) cc_final: 0.7182 (t0) REVERT: D 179 LYS cc_start: 0.7659 (mmtp) cc_final: 0.7296 (tptt) REVERT: D 236 MET cc_start: 0.7722 (tpp) cc_final: 0.7411 (tpp) REVERT: D 327 ARG cc_start: 0.7385 (mtt180) cc_final: 0.7005 (ptp-170) REVERT: D 451 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7385 (tm-30) REVERT: D 537 MET cc_start: 0.8225 (ptt) cc_final: 0.8008 (ptm) REVERT: D 539 ASP cc_start: 0.7539 (t0) cc_final: 0.7169 (t0) REVERT: D 543 ARG cc_start: 0.7276 (ttp80) cc_final: 0.6776 (ttp-170) REVERT: D 547 GLN cc_start: 0.6838 (mt0) cc_final: 0.6629 (mt0) REVERT: D 579 MET cc_start: 0.8497 (mmm) cc_final: 0.8073 (mtp) REVERT: D 604 TRP cc_start: 0.7056 (OUTLIER) cc_final: 0.5647 (t60) REVERT: E 186 LYS cc_start: 0.4540 (OUTLIER) cc_final: 0.3636 (mptp) REVERT: E 242 LYS cc_start: 0.3260 (OUTLIER) cc_final: 0.2502 (tptp) REVERT: E 278 MET cc_start: 0.1248 (ttm) cc_final: 0.0677 (mtp) REVERT: E 325 ARG cc_start: 0.8280 (tpm-80) cc_final: 0.8009 (tpm-80) REVERT: E 330 ILE cc_start: 0.8819 (mt) cc_final: 0.8445 (mm) REVERT: E 366 ASN cc_start: 0.8406 (t0) cc_final: 0.8123 (t0) REVERT: E 491 ASN cc_start: 0.8232 (t0) cc_final: 0.7804 (t0) REVERT: E 498 ASN cc_start: 0.8166 (OUTLIER) cc_final: 0.7612 (m110) REVERT: E 537 MET cc_start: 0.8388 (ptt) cc_final: 0.8130 (ptm) REVERT: E 562 GLN cc_start: 0.8143 (tp40) cc_final: 0.7687 (tp-100) REVERT: E 566 ASP cc_start: 0.8093 (m-30) cc_final: 0.7638 (m-30) REVERT: F 143 THR cc_start: 0.7482 (p) cc_final: 0.7159 (p) REVERT: F 163 GLU cc_start: 0.7203 (tp30) cc_final: 0.6514 (tp30) REVERT: F 237 PHE cc_start: 0.7448 (m-10) cc_final: 0.6930 (m-10) REVERT: F 238 GLU cc_start: 0.7977 (tt0) cc_final: 0.7403 (tp30) REVERT: F 281 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5322 (tt0) REVERT: F 282 MET cc_start: 0.6307 (ptp) cc_final: 0.6065 (ptp) REVERT: F 329 GLN cc_start: 0.7723 (mp10) cc_final: 0.7446 (mp10) REVERT: F 391 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8570 (tttm) REVERT: F 398 ARG cc_start: 0.7293 (ttp-170) cc_final: 0.6803 (ttp80) REVERT: F 401 MET cc_start: 0.5697 (mtp) cc_final: 0.4392 (mtp) REVERT: F 433 LYS cc_start: 0.8061 (tttt) cc_final: 0.7725 (ttmt) REVERT: F 451 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7233 (tm-30) REVERT: F 467 SER cc_start: 0.8736 (m) cc_final: 0.8477 (t) REVERT: F 483 GLU cc_start: 0.7593 (pt0) cc_final: 0.7180 (pm20) REVERT: F 562 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7832 (tp-100) REVERT: F 566 ASP cc_start: 0.8044 (m-30) cc_final: 0.7804 (m-30) REVERT: F 568 MET cc_start: 0.8306 (tpp) cc_final: 0.7947 (tpt) REVERT: B 172 ARG cc_start: 0.5757 (OUTLIER) cc_final: 0.4640 (mmm160) REVERT: B 236 MET cc_start: 0.6341 (mpt) cc_final: 0.6112 (mpt) REVERT: B 238 GLU cc_start: 0.7760 (tp30) cc_final: 0.7325 (pp20) REVERT: B 247 ILE cc_start: 0.1046 (OUTLIER) cc_final: 0.0579 (mp) REVERT: B 367 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7240 (mm-30) REVERT: B 394 MET cc_start: 0.6678 (ptm) cc_final: 0.6271 (ptp) REVERT: B 408 LYS cc_start: 0.8447 (mttp) cc_final: 0.8062 (mtmm) REVERT: B 413 TYR cc_start: 0.8381 (m-80) cc_final: 0.7798 (m-80) REVERT: B 492 ASP cc_start: 0.7332 (m-30) cc_final: 0.6315 (m-30) REVERT: C 161 LYS cc_start: 0.8069 (ttpt) cc_final: 0.7375 (tptp) REVERT: C 200 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6514 (mm) REVERT: C 216 ILE cc_start: 0.8042 (mm) cc_final: 0.7649 (mm) REVERT: C 236 MET cc_start: 0.7315 (tpp) cc_final: 0.6986 (tpp) REVERT: C 237 PHE cc_start: 0.5338 (t80) cc_final: 0.4570 (t80) REVERT: C 329 GLN cc_start: 0.7979 (tp40) cc_final: 0.7579 (mm-40) REVERT: C 367 GLU cc_start: 0.8013 (tp30) cc_final: 0.7698 (mm-30) REVERT: C 397 GLU cc_start: 0.7035 (pm20) cc_final: 0.6441 (pm20) REVERT: C 398 ARG cc_start: 0.7268 (mtp180) cc_final: 0.6908 (mtm110) REVERT: C 433 LYS cc_start: 0.8309 (ttmm) cc_final: 0.8000 (ttpp) REVERT: C 491 ASN cc_start: 0.8315 (t0) cc_final: 0.7926 (t0) REVERT: C 547 GLN cc_start: 0.7302 (mm-40) cc_final: 0.6956 (mt0) REVERT: C 562 GLN cc_start: 0.8022 (tp40) cc_final: 0.7122 (tp-100) REVERT: C 566 ASP cc_start: 0.8258 (m-30) cc_final: 0.7460 (m-30) REVERT: C 591 ASP cc_start: 0.6891 (m-30) cc_final: 0.6687 (m-30) outliers start: 131 outliers final: 106 residues processed: 624 average time/residue: 0.3623 time to fit residues: 322.3189 Evaluate side-chains 654 residues out of total 1962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 535 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain D residue 371 PHE Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 604 TRP Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain E residue 498 ASN Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain E residue 604 TRP Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 281 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 360 ASP Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 391 LYS Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 404 THR Chi-restraints excluded: chain F residue 439 ARG Chi-restraints excluded: chain F residue 443 LEU Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 538 SER Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 562 GLN Chi-restraints excluded: chain F residue 574 MET Chi-restraints excluded: chain F residue 598 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 172 ARG Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 507 TRP Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 455 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 179 optimal weight: 8.9990 chunk 28 optimal weight: 0.4980 chunk 54 optimal weight: 7.9990 chunk 195 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 171 optimal weight: 0.0570 overall best weight: 1.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 HIS A 484 HIS ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 GLN ** F 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 588 GLN B 407 GLN B 547 GLN B 556 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.162364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.128416 restraints weight = 88573.516| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 5.31 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3560 r_free = 0.3560 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 186 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 253 | |-----------------------------------------------------------------------------| r_final: 0.3537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19572 Z= 0.198 Angle : 0.608 8.499 26400 Z= 0.310 Chirality : 0.043 0.278 2958 Planarity : 0.004 0.063 3432 Dihedral : 9.837 80.935 2995 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 6.33 % Allowed : 31.45 % Favored : 62.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.17), residues: 2400 helix: 0.87 (0.15), residues: 1278 sheet: -1.81 (0.60), residues: 73 loop : -1.28 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 507 HIS 0.005 0.001 HIS F 418 PHE 0.031 0.001 PHE A 237 TYR 0.020 0.001 TYR B 170 ARG 0.005 0.000 ARG E 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5936.58 seconds wall clock time: 106 minutes 39.57 seconds (6399.57 seconds total)