Starting phenix.real_space_refine on Wed May 8 17:42:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zzu_11587/05_2024/6zzu_11587.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zzu_11587/05_2024/6zzu_11587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zzu_11587/05_2024/6zzu_11587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zzu_11587/05_2024/6zzu_11587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zzu_11587/05_2024/6zzu_11587.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zzu_11587/05_2024/6zzu_11587.pdb" } resolution = 3.5 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= 0.010 sd= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 36 5.16 5 C 6848 2.51 5 N 1828 2.21 5 O 2044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ASP 190": "OD1" <-> "OD2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 273": "OE1" <-> "OE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B ASP 341": "OD1" <-> "OD2" Residue "B ASP 350": "OD1" <-> "OD2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 442": "OD1" <-> "OD2" Residue "B TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 460": "OD1" <-> "OD2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "A ASP 190": "OD1" <-> "OD2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 217": "OD1" <-> "OD2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A ASP 413": "OD1" <-> "OD2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A ASP 470": "OD1" <-> "OD2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A ASP 484": "OD1" <-> "OD2" Residue "C ASP 190": "OD1" <-> "OD2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 217": "OD1" <-> "OD2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C ASP 267": "OD1" <-> "OD2" Residue "C GLU 273": "OE1" <-> "OE2" Residue "C ASP 274": "OD1" <-> "OD2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 341": "OD1" <-> "OD2" Residue "C ASP 350": "OD1" <-> "OD2" Residue "C GLU 361": "OE1" <-> "OE2" Residue "C GLU 405": "OE1" <-> "OE2" Residue "C PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 460": "OD1" <-> "OD2" Residue "C ASP 470": "OD1" <-> "OD2" Residue "C ASP 484": "OD1" <-> "OD2" Residue "C GLU 485": "OE1" <-> "OE2" Residue "D ASP 190": "OD1" <-> "OD2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 223": "OE1" <-> "OE2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "D PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 341": "OD1" <-> "OD2" Residue "D ASP 360": "OD1" <-> "OD2" Residue "D TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 408": "OE1" <-> "OE2" Residue "D ASP 413": "OD1" <-> "OD2" Residue "D GLU 415": "OE1" <-> "OE2" Residue "D PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D ASP 442": "OD1" <-> "OD2" Residue "D TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 460": "OD1" <-> "OD2" Residue "D ASP 470": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 10760 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "A" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "C" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "D" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2688 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 316} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.80, per 1000 atoms: 0.54 Number of scatterers: 10760 At special positions: 0 Unit cell: (99.75, 66.15, 119.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 36 16.00 O 2044 8.00 N 1828 7.00 C 6848 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=0, symmetry=0 Time building additional restraints: 4.16 Conformation dependent library (CDL) restraints added in 1.9 seconds 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 14 sheets defined 51.3% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 174 through 182 removed outlier: 4.507A pdb=" N VAL B 180 " --> pdb=" O CYS B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 208 Processing helix chain 'B' and resid 225 through 242 removed outlier: 3.751A pdb=" N GLY B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 271 through 283 removed outlier: 3.769A pdb=" N VAL B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 305 removed outlier: 3.744A pdb=" N LEU B 300 " --> pdb=" O ALA B 296 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 335 removed outlier: 4.059A pdb=" N LEU B 333 " --> pdb=" O CYS B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 341 through 355 removed outlier: 3.734A pdb=" N GLY B 352 " --> pdb=" O SER B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 374 removed outlier: 3.514A pdb=" N PHE B 372 " --> pdb=" O THR B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 402 removed outlier: 3.884A pdb=" N LEU B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 451 removed outlier: 3.770A pdb=" N ARG B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 496 removed outlier: 4.091A pdb=" N GLY B 481 " --> pdb=" O ARG B 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 4.459A pdb=" N LYS A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N CYS A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 171 through 176' Processing helix chain 'A' and resid 196 through 209 Processing helix chain 'A' and resid 225 through 240 removed outlier: 3.709A pdb=" N THR A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 244 removed outlier: 3.936A pdb=" N ALA A 244 " --> pdb=" O GLY A 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 241 through 244' Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 271 through 283 removed outlier: 3.547A pdb=" N VAL A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 removed outlier: 3.745A pdb=" N PHE A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 335 removed outlier: 4.399A pdb=" N LEU A 333 " --> pdb=" O CYS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 341 through 354 Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.557A pdb=" N PHE A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 395 removed outlier: 4.158A pdb=" N SER A 395 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 removed outlier: 4.499A pdb=" N LEU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 450 removed outlier: 3.735A pdb=" N ARG A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 496 removed outlier: 3.506A pdb=" N VAL A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY A 481 " --> pdb=" O ARG A 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 176 removed outlier: 4.041A pdb=" N LYS C 175 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N CYS C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 171 through 176' Processing helix chain 'C' and resid 196 through 208 Processing helix chain 'C' and resid 225 through 242 removed outlier: 3.511A pdb=" N GLY C 241 " --> pdb=" O THR C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 261 Processing helix chain 'C' and resid 271 through 283 removed outlier: 3.782A pdb=" N VAL C 275 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE C 278 " --> pdb=" O ASP C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 304 removed outlier: 3.538A pdb=" N LEU C 300 " --> pdb=" O ALA C 296 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 332 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 341 through 354 Processing helix chain 'C' and resid 359 through 374 removed outlier: 3.582A pdb=" N PHE C 372 " --> pdb=" O THR C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 403 removed outlier: 4.024A pdb=" N LEU C 399 " --> pdb=" O SER C 395 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU C 400 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 448 Processing helix chain 'C' and resid 471 through 496 removed outlier: 3.835A pdb=" N GLY C 481 " --> pdb=" O ARG C 477 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 485 " --> pdb=" O GLY C 481 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER C 494 " --> pdb=" O ALA C 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 176 removed outlier: 4.242A pdb=" N LYS D 175 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N CYS D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 171 through 176' Processing helix chain 'D' and resid 196 through 209 removed outlier: 3.587A pdb=" N ALA D 207 " --> pdb=" O ARG D 203 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 242 removed outlier: 3.736A pdb=" N THR D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 261 Processing helix chain 'D' and resid 271 through 283 removed outlier: 3.730A pdb=" N VAL D 275 " --> pdb=" O GLN D 271 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 304 removed outlier: 3.555A pdb=" N PHE D 299 " --> pdb=" O SER D 295 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 332 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 341 through 354 Processing helix chain 'D' and resid 359 through 374 removed outlier: 3.727A pdb=" N PHE D 372 " --> pdb=" O THR D 368 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 374 " --> pdb=" O TYR D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 395 removed outlier: 4.198A pdb=" N SER D 395 " --> pdb=" O LEU D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 403 removed outlier: 4.507A pdb=" N LEU D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 451 removed outlier: 3.528A pdb=" N SER D 449 " --> pdb=" O ARG D 445 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG D 450 " --> pdb=" O SER D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 496 removed outlier: 3.984A pdb=" N GLY D 481 " --> pdb=" O ARG D 477 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU D 485 " --> pdb=" O GLY D 481 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER D 494 " --> pdb=" O ALA D 490 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 286 through 289 removed outlier: 6.372A pdb=" N GLN B 286 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N CYS B 310 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ARG B 288 " --> pdb=" O CYS B 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 384 through 387 removed outlier: 6.464A pdb=" N LEU B 378 " --> pdb=" O SER B 434 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLU B 408 " --> pdb=" O TYR B 431 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL B 433 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG B 410 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 456 through 460 Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 289 removed outlier: 6.427A pdb=" N GLN A 286 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N CYS A 310 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ARG A 288 " --> pdb=" O CYS A 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 378 through 380 Processing sheet with id=AA6, first strand: chain 'A' and resid 408 through 411 removed outlier: 6.828A pdb=" N GLU A 408 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL A 433 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ARG A 410 " --> pdb=" O VAL A 433 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 456 through 460 removed outlier: 3.544A pdb=" N SER A 456 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 286 through 289 Processing sheet with id=AA9, first strand: chain 'C' and resid 384 through 387 removed outlier: 6.589A pdb=" N LEU C 378 " --> pdb=" O SER C 434 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLU C 408 " --> pdb=" O TYR C 431 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL C 433 " --> pdb=" O GLU C 408 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ARG C 410 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 456 through 460 Processing sheet with id=AB2, first strand: chain 'D' and resid 286 through 289 removed outlier: 6.461A pdb=" N GLN D 286 " --> pdb=" O PHE D 308 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N CYS D 310 " --> pdb=" O GLN D 286 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ARG D 288 " --> pdb=" O CYS D 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 378 through 381 Processing sheet with id=AB4, first strand: chain 'D' and resid 408 through 411 Processing sheet with id=AB5, first strand: chain 'D' and resid 456 through 460 removed outlier: 3.567A pdb=" N SER D 456 " --> pdb=" O LEU D 469 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1308 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: 3.00 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3572 1.34 - 1.46: 2610 1.46 - 1.58: 4806 1.58 - 1.70: 0 1.70 - 1.81: 44 Bond restraints: 11032 Sorted by residual: bond pdb=" CA VAL A 336 " pdb=" C VAL A 336 " ideal model delta sigma weight residual 1.520 1.537 -0.017 8.80e-03 1.29e+04 3.89e+00 bond pdb=" C VAL C 336 " pdb=" N PRO C 337 " ideal model delta sigma weight residual 1.337 1.354 -0.018 1.06e-02 8.90e+03 2.86e+00 bond pdb=" C VAL B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 1.337 1.354 -0.018 1.06e-02 8.90e+03 2.81e+00 bond pdb=" C VAL A 336 " pdb=" N PRO A 337 " ideal model delta sigma weight residual 1.337 1.355 -0.019 1.11e-02 8.12e+03 2.78e+00 bond pdb=" C LEU D 287 " pdb=" N ARG D 288 " ideal model delta sigma weight residual 1.331 1.316 0.016 1.05e-02 9.07e+03 2.30e+00 ... (remaining 11027 not shown) Histogram of bond angle deviations from ideal: 98.67 - 106.36: 338 106.36 - 114.04: 6011 114.04 - 121.72: 6256 121.72 - 129.41: 2281 129.41 - 137.09: 82 Bond angle restraints: 14968 Sorted by residual: angle pdb=" C LEU B 293 " pdb=" N LEU B 294 " pdb=" CA LEU B 294 " ideal model delta sigma weight residual 120.38 128.27 -7.89 1.46e+00 4.69e-01 2.92e+01 angle pdb=" C LEU C 293 " pdb=" N LEU C 294 " pdb=" CA LEU C 294 " ideal model delta sigma weight residual 120.38 127.73 -7.35 1.46e+00 4.69e-01 2.53e+01 angle pdb=" CA LEU A 464 " pdb=" CB LEU A 464 " pdb=" CG LEU A 464 " ideal model delta sigma weight residual 116.30 132.37 -16.07 3.50e+00 8.16e-02 2.11e+01 angle pdb=" CA LEU C 464 " pdb=" CB LEU C 464 " pdb=" CG LEU C 464 " ideal model delta sigma weight residual 116.30 130.94 -14.64 3.50e+00 8.16e-02 1.75e+01 angle pdb=" CA PRO A 337 " pdb=" N PRO A 337 " pdb=" CD PRO A 337 " ideal model delta sigma weight residual 112.00 106.28 5.72 1.40e+00 5.10e-01 1.67e+01 ... (remaining 14963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5786 17.97 - 35.93: 654 35.93 - 53.90: 114 53.90 - 71.86: 18 71.86 - 89.83: 24 Dihedral angle restraints: 6596 sinusoidal: 2656 harmonic: 3940 Sorted by residual: dihedral pdb=" CA LYS A 182 " pdb=" C LYS A 182 " pdb=" N PHE A 183 " pdb=" CA PHE A 183 " ideal model delta harmonic sigma weight residual -180.00 -153.30 -26.70 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA GLU A 406 " pdb=" C GLU A 406 " pdb=" N PRO A 407 " pdb=" CA PRO A 407 " ideal model delta harmonic sigma weight residual 180.00 155.10 24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA LYS B 182 " pdb=" C LYS B 182 " pdb=" N PHE B 183 " pdb=" CA PHE B 183 " ideal model delta harmonic sigma weight residual -180.00 -156.00 -24.00 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 6593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1099 0.050 - 0.100: 390 0.100 - 0.150: 84 0.150 - 0.200: 24 0.200 - 0.250: 3 Chirality restraints: 1600 Sorted by residual: chirality pdb=" CB ILE B 269 " pdb=" CA ILE B 269 " pdb=" CG1 ILE B 269 " pdb=" CG2 ILE B 269 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CG LEU A 339 " pdb=" CB LEU A 339 " pdb=" CD1 LEU A 339 " pdb=" CD2 LEU A 339 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA GLU B 406 " pdb=" N GLU B 406 " pdb=" C GLU B 406 " pdb=" CB GLU B 406 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1597 not shown) Planarity restraints: 1972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 285 " 0.020 2.00e-02 2.50e+03 1.74e-02 5.33e+00 pdb=" CG PHE B 285 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE B 285 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 285 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 285 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 285 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 285 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 406 " -0.037 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO A 407 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 407 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 407 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 468 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C VAL A 468 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL A 468 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 469 " 0.012 2.00e-02 2.50e+03 ... (remaining 1969 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 370 2.68 - 3.23: 10474 3.23 - 3.79: 20139 3.79 - 4.34: 25679 4.34 - 4.90: 39044 Nonbonded interactions: 95706 Sorted by model distance: nonbonded pdb=" OE2 GLU C 375 " pdb="FE FE C 500 " model vdw 2.125 2.260 nonbonded pdb=" NE2 HIS A 330 " pdb="FE FE A 500 " model vdw 2.175 2.340 nonbonded pdb=" NE2 HIS C 330 " pdb="FE FE C 500 " model vdw 2.185 2.340 nonbonded pdb=" NE2 HIS D 330 " pdb="FE FE D 500 " model vdw 2.189 2.340 nonbonded pdb=" NE2 HIS C 335 " pdb="FE FE C 500 " model vdw 2.189 2.340 ... (remaining 95701 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 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: 1.850 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.370 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 11032 Z= 0.348 Angle : 0.959 16.071 14968 Z= 0.518 Chirality : 0.054 0.250 1600 Planarity : 0.006 0.055 1972 Dihedral : 16.185 89.827 4052 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.17 % Allowed : 7.99 % Favored : 91.84 % 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: -4.89 (0.18), residues: 1332 helix: -3.89 (0.10), residues: 688 sheet: -2.07 (0.45), residues: 128 loop : -2.28 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 165 HIS 0.007 0.002 HIS A 251 PHE 0.037 0.003 PHE B 285 TYR 0.013 0.002 TYR D 199 ARG 0.008 0.001 ARG D 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 449 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 174 ASP cc_start: 0.7459 (m-30) cc_final: 0.6935 (m-30) REVERT: B 178 HIS cc_start: 0.7540 (m-70) cc_final: 0.7142 (m-70) REVERT: B 321 MET cc_start: 0.9082 (mmt) cc_final: 0.8880 (mmt) REVERT: B 460 ASP cc_start: 0.8569 (t70) cc_final: 0.8185 (t0) REVERT: B 464 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8676 (tt) REVERT: B 487 ASP cc_start: 0.8355 (t70) cc_final: 0.8077 (t70) REVERT: A 178 HIS cc_start: 0.7679 (m170) cc_final: 0.7371 (m170) REVERT: A 197 GLN cc_start: 0.8796 (tp40) cc_final: 0.8254 (tp-100) REVERT: A 214 ARG cc_start: 0.7771 (mmm160) cc_final: 0.7420 (mmm160) REVERT: A 215 HIS cc_start: 0.8286 (t70) cc_final: 0.7803 (t70) REVERT: A 240 LYS cc_start: 0.8437 (tttp) cc_final: 0.8178 (tttm) REVERT: A 280 LYS cc_start: 0.8471 (mmmm) cc_final: 0.8033 (mmmm) REVERT: A 286 GLN cc_start: 0.7930 (pm20) cc_final: 0.7637 (pm20) REVERT: A 321 MET cc_start: 0.8974 (mmt) cc_final: 0.8690 (mmt) REVERT: A 370 TYR cc_start: 0.9061 (t80) cc_final: 0.8827 (t80) REVERT: A 447 TYR cc_start: 0.8361 (t80) cc_final: 0.7247 (t80) REVERT: A 460 ASP cc_start: 0.8453 (t0) cc_final: 0.7942 (t0) REVERT: A 464 LEU cc_start: 0.9034 (tp) cc_final: 0.8785 (tp) REVERT: A 473 GLN cc_start: 0.8537 (tp40) cc_final: 0.8324 (tp40) REVERT: A 476 ARG cc_start: 0.7896 (ttt90) cc_final: 0.7624 (ttt-90) REVERT: C 172 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7055 (mm-30) REVERT: C 214 ARG cc_start: 0.8185 (tpp-160) cc_final: 0.7959 (tpp-160) REVERT: C 312 GLN cc_start: 0.8393 (mt0) cc_final: 0.8192 (mt0) REVERT: C 343 THR cc_start: 0.8596 (p) cc_final: 0.8353 (t) REVERT: C 443 LYS cc_start: 0.7902 (ttmm) cc_final: 0.7449 (ttmm) REVERT: C 466 ILE cc_start: 0.8394 (mm) cc_final: 0.7873 (mt) REVERT: C 480 GLU cc_start: 0.7680 (mp0) cc_final: 0.7107 (mp0) REVERT: D 172 GLU cc_start: 0.7539 (mm-30) cc_final: 0.6990 (mm-30) REVERT: D 197 GLN cc_start: 0.8763 (tp40) cc_final: 0.8392 (tp40) REVERT: D 224 TYR cc_start: 0.8682 (m-80) cc_final: 0.8434 (m-80) REVERT: D 243 TYR cc_start: 0.7608 (m-10) cc_final: 0.7342 (m-10) REVERT: D 268 ASN cc_start: 0.9218 (t0) cc_final: 0.8910 (t0) REVERT: D 278 PHE cc_start: 0.8013 (t80) cc_final: 0.7406 (t80) REVERT: D 286 GLN cc_start: 0.7853 (pm20) cc_final: 0.7524 (pm20) REVERT: D 321 MET cc_start: 0.9063 (mmt) cc_final: 0.8689 (mmt) REVERT: D 346 GLN cc_start: 0.8579 (tp-100) cc_final: 0.8125 (tp40) REVERT: D 450 ARG cc_start: 0.8069 (ptp90) cc_final: 0.7542 (ptp90) REVERT: D 460 ASP cc_start: 0.8120 (t0) cc_final: 0.7836 (t0) outliers start: 2 outliers final: 0 residues processed: 449 average time/residue: 0.2851 time to fit residues: 169.3343 Evaluate side-chains 332 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 331 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 464 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN B 349 GLN B 425 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS A 425 GLN A 473 GLN C 425 GLN C 483 GLN D 178 HIS D 201 GLN D 246 HIS D 346 GLN ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 GLN D 425 GLN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11032 Z= 0.219 Angle : 0.654 7.295 14968 Z= 0.337 Chirality : 0.042 0.163 1600 Planarity : 0.005 0.044 1972 Dihedral : 5.724 52.263 1486 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.04 % Allowed : 18.14 % Favored : 78.82 % 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: -3.02 (0.20), residues: 1332 helix: -1.96 (0.16), residues: 688 sheet: -2.23 (0.42), residues: 136 loop : -1.71 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 371 HIS 0.009 0.001 HIS D 215 PHE 0.023 0.002 PHE C 344 TYR 0.017 0.002 TYR B 370 ARG 0.008 0.001 ARG B 476 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 372 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 GLU cc_start: 0.6601 (mt-10) cc_final: 0.6235 (mt-10) REVERT: B 177 HIS cc_start: 0.6695 (m90) cc_final: 0.6374 (m-70) REVERT: B 178 HIS cc_start: 0.7505 (m-70) cc_final: 0.7163 (m-70) REVERT: B 288 ARG cc_start: 0.8077 (ttt-90) cc_final: 0.7824 (ttt180) REVERT: B 331 GLU cc_start: 0.8587 (pt0) cc_final: 0.8277 (pt0) REVERT: B 447 TYR cc_start: 0.8046 (t80) cc_final: 0.7766 (t80) REVERT: B 460 ASP cc_start: 0.8501 (t70) cc_final: 0.8020 (t0) REVERT: B 464 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8675 (tt) REVERT: A 169 LYS cc_start: 0.8054 (mmtm) cc_final: 0.7219 (mmtm) REVERT: A 280 LYS cc_start: 0.8462 (mmmm) cc_final: 0.7995 (mmmm) REVERT: A 447 TYR cc_start: 0.8231 (t80) cc_final: 0.6993 (t80) REVERT: A 460 ASP cc_start: 0.8202 (t0) cc_final: 0.7919 (t0) REVERT: C 172 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7047 (mm-30) REVERT: C 224 TYR cc_start: 0.8296 (m-80) cc_final: 0.8087 (m-80) REVERT: C 312 GLN cc_start: 0.8602 (mt0) cc_final: 0.8401 (mt0) REVERT: C 443 LYS cc_start: 0.8018 (ttmm) cc_final: 0.7496 (ttmm) REVERT: C 476 ARG cc_start: 0.7943 (ttt90) cc_final: 0.7444 (ttt90) REVERT: C 480 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: D 172 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7087 (mm-30) REVERT: D 211 PHE cc_start: 0.8272 (t80) cc_final: 0.7096 (t80) REVERT: D 280 LYS cc_start: 0.8343 (mmtt) cc_final: 0.8125 (mttt) REVERT: D 286 GLN cc_start: 0.7718 (pm20) cc_final: 0.7406 (pm20) REVERT: D 321 MET cc_start: 0.8906 (mmt) cc_final: 0.8705 (mmt) REVERT: D 346 GLN cc_start: 0.8467 (tp40) cc_final: 0.8197 (tp40) REVERT: D 460 ASP cc_start: 0.8275 (t0) cc_final: 0.8024 (t0) REVERT: D 476 ARG cc_start: 0.7778 (ttt90) cc_final: 0.7266 (ttt90) REVERT: D 480 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6364 (mp0) outliers start: 35 outliers final: 21 residues processed: 383 average time/residue: 0.2751 time to fit residues: 140.4234 Evaluate side-chains 327 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 303 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 480 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 ASN ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11032 Z= 0.280 Angle : 0.660 12.486 14968 Z= 0.337 Chirality : 0.043 0.148 1600 Planarity : 0.004 0.039 1972 Dihedral : 5.541 48.969 1486 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 23.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.82 % Allowed : 20.75 % Favored : 75.43 % 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: -1.97 (0.22), residues: 1332 helix: -0.95 (0.18), residues: 668 sheet: -1.84 (0.42), residues: 128 loop : -1.45 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 232 HIS 0.009 0.001 HIS B 177 PHE 0.024 0.002 PHE B 285 TYR 0.019 0.002 TYR B 264 ARG 0.006 0.001 ARG C 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 328 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 GLU cc_start: 0.6775 (mt-10) cc_final: 0.6438 (mt-10) REVERT: B 177 HIS cc_start: 0.6839 (m90) cc_final: 0.6485 (m90) REVERT: B 178 HIS cc_start: 0.7476 (m-70) cc_final: 0.7272 (m-70) REVERT: B 201 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8684 (mm110) REVERT: B 281 GLU cc_start: 0.8024 (tt0) cc_final: 0.7754 (tt0) REVERT: B 447 TYR cc_start: 0.8074 (t80) cc_final: 0.7768 (t80) REVERT: B 460 ASP cc_start: 0.8439 (t0) cc_final: 0.7931 (t0) REVERT: B 464 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8707 (tt) REVERT: A 214 ARG cc_start: 0.7686 (mmm160) cc_final: 0.7247 (mmm160) REVERT: A 280 LYS cc_start: 0.8348 (mmmm) cc_final: 0.7878 (mmmm) REVERT: A 346 GLN cc_start: 0.8516 (tp-100) cc_final: 0.8231 (tp40) REVERT: A 367 SER cc_start: 0.9316 (m) cc_final: 0.8940 (p) REVERT: A 447 TYR cc_start: 0.8248 (t80) cc_final: 0.7101 (t80) REVERT: A 460 ASP cc_start: 0.8332 (t0) cc_final: 0.7983 (t0) REVERT: A 476 ARG cc_start: 0.8197 (ttt-90) cc_final: 0.7878 (ttm-80) REVERT: A 477 ARG cc_start: 0.8097 (ptt-90) cc_final: 0.7749 (ptt-90) REVERT: A 484 ASP cc_start: 0.7910 (m-30) cc_final: 0.7691 (m-30) REVERT: C 168 ARG cc_start: 0.7910 (mmm160) cc_final: 0.7082 (mmm160) REVERT: C 172 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7136 (mm-30) REVERT: C 252 LEU cc_start: 0.7338 (mt) cc_final: 0.7093 (mm) REVERT: C 443 LYS cc_start: 0.8074 (ttmm) cc_final: 0.7842 (ttmt) REVERT: C 476 ARG cc_start: 0.7971 (ttt90) cc_final: 0.7468 (ttt90) REVERT: C 480 GLU cc_start: 0.7482 (mp0) cc_final: 0.6827 (mp0) REVERT: D 178 HIS cc_start: 0.7261 (m170) cc_final: 0.6796 (m170) REVERT: D 280 LYS cc_start: 0.8387 (mmtt) cc_final: 0.8139 (mttt) REVERT: D 286 GLN cc_start: 0.7822 (pm20) cc_final: 0.7495 (pm20) REVERT: D 380 LYS cc_start: 0.9065 (ttmm) cc_final: 0.8823 (mmmm) REVERT: D 410 ARG cc_start: 0.8482 (ptp-110) cc_final: 0.8260 (ptp-170) REVERT: D 460 ASP cc_start: 0.8504 (t0) cc_final: 0.8165 (t0) REVERT: D 476 ARG cc_start: 0.7659 (ttt90) cc_final: 0.7326 (ttt90) REVERT: D 480 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6480 (mp0) REVERT: D 486 LEU cc_start: 0.9180 (tp) cc_final: 0.8856 (tp) outliers start: 44 outliers final: 31 residues processed: 340 average time/residue: 0.2752 time to fit residues: 125.3228 Evaluate side-chains 328 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 295 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain D residue 197 GLN Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 480 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN A 483 GLN C 246 HIS ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11032 Z= 0.245 Angle : 0.637 13.197 14968 Z= 0.325 Chirality : 0.042 0.161 1600 Planarity : 0.004 0.038 1972 Dihedral : 5.373 48.764 1486 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 22.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.43 % Allowed : 21.88 % Favored : 73.70 % 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: -1.36 (0.22), residues: 1332 helix: -0.30 (0.20), residues: 640 sheet: -1.99 (0.43), residues: 132 loop : -1.20 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP A 232 HIS 0.006 0.001 HIS B 177 PHE 0.026 0.002 PHE B 308 TYR 0.020 0.002 TYR B 264 ARG 0.006 0.000 ARG D 260 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 328 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 GLU cc_start: 0.6645 (mt-10) cc_final: 0.6054 (mt-10) REVERT: B 280 LYS cc_start: 0.8335 (mmmm) cc_final: 0.7925 (mmmm) REVERT: B 447 TYR cc_start: 0.7999 (t80) cc_final: 0.7733 (t80) REVERT: B 455 PHE cc_start: 0.8436 (p90) cc_final: 0.8197 (p90) REVERT: B 460 ASP cc_start: 0.8472 (t0) cc_final: 0.7935 (t0) REVERT: B 464 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8670 (tt) REVERT: A 178 HIS cc_start: 0.7869 (m170) cc_final: 0.7268 (m170) REVERT: A 277 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.7759 (ttm-80) REVERT: A 280 LYS cc_start: 0.8220 (mmmm) cc_final: 0.7761 (mmmm) REVERT: A 346 GLN cc_start: 0.8466 (tp-100) cc_final: 0.8192 (tp40) REVERT: A 367 SER cc_start: 0.9316 (m) cc_final: 0.8976 (p) REVERT: A 443 LYS cc_start: 0.7955 (ttmt) cc_final: 0.7736 (ttmt) REVERT: A 447 TYR cc_start: 0.8233 (t80) cc_final: 0.7072 (t80) REVERT: A 460 ASP cc_start: 0.8327 (t0) cc_final: 0.8010 (t0) REVERT: A 476 ARG cc_start: 0.8191 (ttt-90) cc_final: 0.7835 (ttm-80) REVERT: A 477 ARG cc_start: 0.8100 (ptt-90) cc_final: 0.7803 (ptt-90) REVERT: C 168 ARG cc_start: 0.7787 (mmm160) cc_final: 0.7413 (mmm-85) REVERT: C 169 LYS cc_start: 0.8125 (mmtt) cc_final: 0.7852 (mmtt) REVERT: C 172 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7166 (mm-30) REVERT: C 252 LEU cc_start: 0.7281 (mt) cc_final: 0.7019 (mm) REVERT: C 443 LYS cc_start: 0.8106 (ttmm) cc_final: 0.7810 (ttmt) REVERT: C 473 GLN cc_start: 0.8441 (tp40) cc_final: 0.8160 (tp40) REVERT: C 476 ARG cc_start: 0.7967 (ttt90) cc_final: 0.7424 (ttt90) REVERT: C 480 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: D 178 HIS cc_start: 0.7220 (m170) cc_final: 0.6944 (m170) REVERT: D 274 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.7941 (t0) REVERT: D 280 LYS cc_start: 0.8351 (mmtt) cc_final: 0.8083 (mttt) REVERT: D 286 GLN cc_start: 0.7822 (pm20) cc_final: 0.7486 (pm20) REVERT: D 386 LYS cc_start: 0.7910 (mmtm) cc_final: 0.7662 (mmmm) REVERT: D 410 ARG cc_start: 0.8597 (ptp-110) cc_final: 0.8346 (ptp-170) REVERT: D 460 ASP cc_start: 0.8454 (t0) cc_final: 0.8115 (t0) REVERT: D 476 ARG cc_start: 0.7642 (ttt90) cc_final: 0.7425 (ttt90) REVERT: D 477 ARG cc_start: 0.7723 (ptt-90) cc_final: 0.7299 (ptt-90) REVERT: D 480 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6425 (mp0) REVERT: D 486 LEU cc_start: 0.9206 (tp) cc_final: 0.8819 (tp) outliers start: 51 outliers final: 38 residues processed: 349 average time/residue: 0.2828 time to fit residues: 131.5497 Evaluate side-chains 333 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 291 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 480 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 52 optimal weight: 0.3980 chunk 108 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 114 optimal weight: 0.0070 chunk 32 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 HIS B 178 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN A 312 GLN C 215 HIS C 473 GLN ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11032 Z= 0.205 Angle : 0.653 13.442 14968 Z= 0.326 Chirality : 0.042 0.143 1600 Planarity : 0.004 0.040 1972 Dihedral : 5.227 48.290 1486 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.69 % Allowed : 22.14 % Favored : 73.18 % 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: -1.28 (0.23), residues: 1332 helix: -0.14 (0.20), residues: 664 sheet: -2.28 (0.42), residues: 140 loop : -1.20 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP D 232 HIS 0.010 0.001 HIS C 215 PHE 0.024 0.002 PHE C 308 TYR 0.021 0.002 TYR A 264 ARG 0.005 0.000 ARG D 260 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 352 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 GLU cc_start: 0.6630 (mt-10) cc_final: 0.5863 (mt-10) REVERT: B 174 ASP cc_start: 0.7557 (m-30) cc_final: 0.7051 (m-30) REVERT: B 252 LEU cc_start: 0.7196 (mt) cc_final: 0.6885 (mm) REVERT: B 280 LYS cc_start: 0.8307 (mmmm) cc_final: 0.7848 (mmmm) REVERT: B 447 TYR cc_start: 0.7992 (t80) cc_final: 0.7729 (t80) REVERT: B 460 ASP cc_start: 0.8471 (t0) cc_final: 0.7911 (t0) REVERT: A 214 ARG cc_start: 0.7703 (mmm160) cc_final: 0.7371 (mmm160) REVERT: A 280 LYS cc_start: 0.8247 (mmmm) cc_final: 0.7812 (mmmm) REVERT: A 286 GLN cc_start: 0.7855 (pm20) cc_final: 0.7378 (pm20) REVERT: A 290 VAL cc_start: 0.8828 (p) cc_final: 0.8533 (m) REVERT: A 346 GLN cc_start: 0.8407 (tp-100) cc_final: 0.8119 (tp40) REVERT: A 367 SER cc_start: 0.9313 (m) cc_final: 0.8951 (p) REVERT: A 447 TYR cc_start: 0.8208 (t80) cc_final: 0.7185 (t80) REVERT: A 460 ASP cc_start: 0.8299 (t0) cc_final: 0.8003 (t0) REVERT: A 476 ARG cc_start: 0.8138 (ttt-90) cc_final: 0.7661 (ttt-90) REVERT: A 477 ARG cc_start: 0.8088 (ptt-90) cc_final: 0.7757 (ptt-90) REVERT: C 172 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7028 (mm-30) REVERT: C 473 GLN cc_start: 0.8430 (tp-100) cc_final: 0.8116 (tp40) REVERT: C 476 ARG cc_start: 0.7860 (ttt90) cc_final: 0.7302 (ttt90) REVERT: C 480 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6756 (mp0) REVERT: D 178 HIS cc_start: 0.7343 (m170) cc_final: 0.7001 (m170) REVERT: D 264 TYR cc_start: 0.5914 (m-10) cc_final: 0.5534 (m-10) REVERT: D 274 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8023 (t0) REVERT: D 280 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7974 (mttt) REVERT: D 286 GLN cc_start: 0.7736 (pm20) cc_final: 0.7419 (pm20) REVERT: D 342 ARG cc_start: 0.8416 (mmm-85) cc_final: 0.8177 (mmm160) REVERT: D 380 LYS cc_start: 0.8796 (mmmm) cc_final: 0.8506 (mmmt) REVERT: D 386 LYS cc_start: 0.7794 (mmtm) cc_final: 0.7591 (mmmm) REVERT: D 443 LYS cc_start: 0.7905 (ttmt) cc_final: 0.7652 (ttmt) REVERT: D 458 LYS cc_start: 0.7917 (ttpt) cc_final: 0.7564 (ttpt) REVERT: D 460 ASP cc_start: 0.8330 (t0) cc_final: 0.7947 (t0) REVERT: D 467 ASP cc_start: 0.8162 (m-30) cc_final: 0.7907 (m-30) REVERT: D 473 GLN cc_start: 0.8110 (tp40) cc_final: 0.7054 (tp40) REVERT: D 476 ARG cc_start: 0.7651 (ttt90) cc_final: 0.7320 (ttt90) REVERT: D 477 ARG cc_start: 0.7774 (ptt-90) cc_final: 0.7265 (ptt-90) REVERT: D 480 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6401 (mp0) outliers start: 54 outliers final: 36 residues processed: 373 average time/residue: 0.2868 time to fit residues: 142.8836 Evaluate side-chains 354 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 315 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 480 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.0470 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 0.0060 chunk 123 optimal weight: 2.9990 overall best weight: 0.6096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 HIS A 191 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11032 Z= 0.213 Angle : 0.687 14.436 14968 Z= 0.339 Chirality : 0.043 0.177 1600 Planarity : 0.004 0.041 1972 Dihedral : 4.953 18.503 1484 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 23.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.86 % Allowed : 22.14 % Favored : 73.00 % 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: -1.06 (0.23), residues: 1332 helix: 0.04 (0.20), residues: 660 sheet: -2.18 (0.43), residues: 140 loop : -1.08 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.005 TRP B 232 HIS 0.005 0.001 HIS D 251 PHE 0.027 0.002 PHE A 308 TYR 0.026 0.002 TYR A 264 ARG 0.004 0.000 ARG C 260 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 335 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 GLU cc_start: 0.6593 (mt-10) cc_final: 0.5861 (mt-10) REVERT: B 174 ASP cc_start: 0.7443 (m-30) cc_final: 0.6857 (m-30) REVERT: B 252 LEU cc_start: 0.7132 (mt) cc_final: 0.6874 (mm) REVERT: B 260 ARG cc_start: 0.8945 (ptp-110) cc_final: 0.8544 (ptp-110) REVERT: B 280 LYS cc_start: 0.8315 (mmmm) cc_final: 0.7802 (mmmm) REVERT: B 281 GLU cc_start: 0.8041 (tt0) cc_final: 0.7679 (tt0) REVERT: B 460 ASP cc_start: 0.8466 (t0) cc_final: 0.8137 (t0) REVERT: A 178 HIS cc_start: 0.7710 (m170) cc_final: 0.7123 (m170) REVERT: A 280 LYS cc_start: 0.8186 (mmmm) cc_final: 0.7787 (mmmm) REVERT: A 346 GLN cc_start: 0.8382 (tp-100) cc_final: 0.8101 (tp40) REVERT: A 447 TYR cc_start: 0.8186 (t80) cc_final: 0.7236 (t80) REVERT: A 460 ASP cc_start: 0.8360 (t0) cc_final: 0.8067 (t0) REVERT: A 476 ARG cc_start: 0.8174 (ttt-90) cc_final: 0.7934 (ttm-80) REVERT: A 491 HIS cc_start: 0.7357 (m-70) cc_final: 0.7140 (m-70) REVERT: C 168 ARG cc_start: 0.7651 (mmm160) cc_final: 0.6844 (mmm160) REVERT: C 172 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7012 (mm-30) REVERT: C 214 ARG cc_start: 0.7892 (tpp-160) cc_final: 0.7636 (mmp-170) REVERT: C 286 GLN cc_start: 0.7817 (pm20) cc_final: 0.7577 (pm20) REVERT: C 398 GLU cc_start: 0.7921 (tp30) cc_final: 0.6939 (tp30) REVERT: C 413 ASP cc_start: 0.8991 (m-30) cc_final: 0.8688 (m-30) REVERT: C 473 GLN cc_start: 0.8448 (tp-100) cc_final: 0.8127 (tp40) REVERT: C 476 ARG cc_start: 0.7866 (ttt90) cc_final: 0.7321 (ttt90) REVERT: C 480 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6765 (mp0) REVERT: D 178 HIS cc_start: 0.7374 (m170) cc_final: 0.6889 (m170) REVERT: D 274 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8147 (t0) REVERT: D 280 LYS cc_start: 0.8302 (mmtt) cc_final: 0.8006 (mttt) REVERT: D 286 GLN cc_start: 0.7732 (pm20) cc_final: 0.7383 (pm20) REVERT: D 342 ARG cc_start: 0.8467 (mmm-85) cc_final: 0.8205 (mmm160) REVERT: D 364 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8649 (tm-30) REVERT: D 380 LYS cc_start: 0.8906 (mmmm) cc_final: 0.8575 (mmmt) REVERT: D 443 LYS cc_start: 0.7947 (ttmt) cc_final: 0.7607 (ttmt) REVERT: D 460 ASP cc_start: 0.8337 (t0) cc_final: 0.7981 (t0) REVERT: D 476 ARG cc_start: 0.7670 (ttt90) cc_final: 0.7357 (ttt90) REVERT: D 477 ARG cc_start: 0.7654 (ptt-90) cc_final: 0.6967 (ptt-90) REVERT: D 480 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6343 (mp0) REVERT: D 486 LEU cc_start: 0.9221 (tp) cc_final: 0.8904 (tp) outliers start: 56 outliers final: 37 residues processed: 357 average time/residue: 0.2662 time to fit residues: 127.3246 Evaluate side-chains 355 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 315 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 480 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11032 Z= 0.283 Angle : 0.733 14.599 14968 Z= 0.358 Chirality : 0.045 0.275 1600 Planarity : 0.004 0.038 1972 Dihedral : 5.078 19.576 1484 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 26.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.21 % Allowed : 21.96 % Favored : 72.83 % 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: -1.06 (0.23), residues: 1332 helix: 0.07 (0.20), residues: 664 sheet: -2.23 (0.43), residues: 140 loop : -1.11 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.004 TRP B 232 HIS 0.006 0.001 HIS B 177 PHE 0.027 0.003 PHE B 261 TYR 0.027 0.002 TYR A 264 ARG 0.004 0.000 ARG C 260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 320 time to evaluate : 1.116 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: B 227 GLU cc_start: 0.7564 (pm20) cc_final: 0.7287 (pm20) REVERT: B 228 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.5955 (pm20) REVERT: B 252 LEU cc_start: 0.7070 (mt) cc_final: 0.6796 (mm) REVERT: B 280 LYS cc_start: 0.8294 (mmmm) cc_final: 0.7819 (mmmm) REVERT: B 447 TYR cc_start: 0.7868 (t80) cc_final: 0.7475 (t80) REVERT: B 460 ASP cc_start: 0.8440 (t0) cc_final: 0.7921 (t0) REVERT: A 178 HIS cc_start: 0.7736 (m170) cc_final: 0.7076 (m170) REVERT: A 214 ARG cc_start: 0.7729 (mmm160) cc_final: 0.7447 (mmm160) REVERT: A 346 GLN cc_start: 0.8387 (tp-100) cc_final: 0.8109 (tp40) REVERT: A 447 TYR cc_start: 0.8203 (t80) cc_final: 0.7382 (t80) REVERT: A 460 ASP cc_start: 0.8344 (t0) cc_final: 0.8010 (t0) REVERT: A 476 ARG cc_start: 0.8190 (ttt-90) cc_final: 0.7706 (ttt-90) REVERT: C 168 ARG cc_start: 0.7608 (mmm160) cc_final: 0.6891 (mmm160) REVERT: C 172 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6953 (mm-30) REVERT: C 312 GLN cc_start: 0.8378 (mt0) cc_final: 0.8170 (tt0) REVERT: C 398 GLU cc_start: 0.8051 (tp30) cc_final: 0.7794 (mm-30) REVERT: C 413 ASP cc_start: 0.9098 (m-30) cc_final: 0.8762 (m-30) REVERT: C 443 LYS cc_start: 0.8031 (tttt) cc_final: 0.7749 (pttt) REVERT: C 473 GLN cc_start: 0.8426 (tp-100) cc_final: 0.8116 (tp40) REVERT: C 476 ARG cc_start: 0.7934 (ttt90) cc_final: 0.7422 (ttt90) REVERT: C 480 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6771 (mp0) REVERT: D 214 ARG cc_start: 0.7281 (mmp-170) cc_final: 0.7050 (mmp-170) REVERT: D 264 TYR cc_start: 0.5827 (m-10) cc_final: 0.5408 (m-10) REVERT: D 274 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.7946 (t0) REVERT: D 280 LYS cc_start: 0.8316 (mmtt) cc_final: 0.8028 (mttt) REVERT: D 286 GLN cc_start: 0.7840 (pm20) cc_final: 0.7457 (pm20) REVERT: D 364 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8695 (tm-30) REVERT: D 380 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8595 (mmmt) REVERT: D 398 GLU cc_start: 0.7921 (tp30) cc_final: 0.7688 (mm-30) REVERT: D 443 LYS cc_start: 0.7906 (ttmt) cc_final: 0.7496 (ttmm) REVERT: D 460 ASP cc_start: 0.8348 (t0) cc_final: 0.7967 (t0) REVERT: D 476 ARG cc_start: 0.7672 (ttt90) cc_final: 0.7310 (ttt90) REVERT: D 480 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6364 (mp0) REVERT: D 486 LEU cc_start: 0.9232 (tp) cc_final: 0.8909 (tp) outliers start: 60 outliers final: 45 residues processed: 341 average time/residue: 0.2660 time to fit residues: 122.3078 Evaluate side-chains 349 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 300 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 480 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11032 Z= 0.231 Angle : 0.727 14.038 14968 Z= 0.356 Chirality : 0.045 0.354 1600 Planarity : 0.004 0.041 1972 Dihedral : 5.053 18.422 1484 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 25.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.25 % Allowed : 24.13 % Favored : 71.61 % 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: -0.98 (0.23), residues: 1332 helix: 0.08 (0.20), residues: 660 sheet: -2.15 (0.43), residues: 140 loop : -0.99 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 232 HIS 0.005 0.001 HIS B 178 PHE 0.026 0.003 PHE A 278 TYR 0.029 0.002 TYR A 264 ARG 0.005 0.000 ARG C 260 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 332 time to evaluate : 1.220 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: B 227 GLU cc_start: 0.7480 (pm20) cc_final: 0.7257 (pm20) REVERT: B 228 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.5974 (pm20) REVERT: B 260 ARG cc_start: 0.8957 (ptp-110) cc_final: 0.8621 (ptp-110) REVERT: B 280 LYS cc_start: 0.8292 (mmmm) cc_final: 0.7771 (mmmm) REVERT: B 281 GLU cc_start: 0.8234 (tt0) cc_final: 0.7845 (tt0) REVERT: B 447 TYR cc_start: 0.7836 (t80) cc_final: 0.7470 (t80) REVERT: B 460 ASP cc_start: 0.8373 (t0) cc_final: 0.8130 (t0) REVERT: B 476 ARG cc_start: 0.7851 (ttt-90) cc_final: 0.7335 (ttt-90) REVERT: A 214 ARG cc_start: 0.7721 (mmm160) cc_final: 0.7435 (mmm160) REVERT: A 308 PHE cc_start: 0.8222 (t80) cc_final: 0.7996 (t80) REVERT: A 346 GLN cc_start: 0.8331 (tp-100) cc_final: 0.8055 (tp40) REVERT: A 447 TYR cc_start: 0.8212 (t80) cc_final: 0.7342 (t80) REVERT: A 476 ARG cc_start: 0.8140 (ttt-90) cc_final: 0.7902 (ttm-80) REVERT: C 168 ARG cc_start: 0.7543 (mmm160) cc_final: 0.7063 (mmm160) REVERT: C 169 LYS cc_start: 0.8416 (mmtt) cc_final: 0.8077 (mmtt) REVERT: C 172 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6945 (mm-30) REVERT: C 214 ARG cc_start: 0.7919 (tpp-160) cc_final: 0.7575 (mmp-170) REVERT: C 278 PHE cc_start: 0.7846 (t80) cc_final: 0.7464 (t80) REVERT: C 413 ASP cc_start: 0.9097 (m-30) cc_final: 0.8779 (m-30) REVERT: C 443 LYS cc_start: 0.7973 (tttt) cc_final: 0.7682 (pttt) REVERT: C 473 GLN cc_start: 0.8429 (tp-100) cc_final: 0.8083 (tp40) REVERT: C 476 ARG cc_start: 0.7856 (ttt90) cc_final: 0.7336 (ttt90) REVERT: C 480 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6673 (mp0) REVERT: D 172 GLU cc_start: 0.6693 (mm-30) cc_final: 0.6013 (mm-30) REVERT: D 178 HIS cc_start: 0.7504 (m170) cc_final: 0.7049 (m170) REVERT: D 214 ARG cc_start: 0.7319 (mmp-170) cc_final: 0.7018 (mmp-170) REVERT: D 264 TYR cc_start: 0.5814 (m-10) cc_final: 0.5458 (m-10) REVERT: D 274 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.7846 (t0) REVERT: D 280 LYS cc_start: 0.8312 (mmtt) cc_final: 0.8015 (mtmt) REVERT: D 286 GLN cc_start: 0.7873 (pm20) cc_final: 0.7492 (pm20) REVERT: D 364 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8678 (tm-30) REVERT: D 380 LYS cc_start: 0.8935 (mmmm) cc_final: 0.8591 (mmmt) REVERT: D 398 GLU cc_start: 0.7841 (tp30) cc_final: 0.7033 (tp30) REVERT: D 443 LYS cc_start: 0.7948 (ttmt) cc_final: 0.7592 (ttmm) REVERT: D 460 ASP cc_start: 0.8298 (t0) cc_final: 0.7947 (t0) REVERT: D 476 ARG cc_start: 0.7565 (ttt90) cc_final: 0.7188 (ttt90) REVERT: D 480 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6301 (mp0) REVERT: D 486 LEU cc_start: 0.9228 (tp) cc_final: 0.8900 (tp) outliers start: 49 outliers final: 41 residues processed: 351 average time/residue: 0.2642 time to fit residues: 125.3413 Evaluate side-chains 349 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 304 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 480 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 HIS B 215 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11032 Z= 0.245 Angle : 0.781 15.455 14968 Z= 0.378 Chirality : 0.045 0.240 1600 Planarity : 0.004 0.049 1972 Dihedral : 5.053 18.456 1484 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 26.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.34 % Allowed : 25.26 % Favored : 70.40 % 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: -0.97 (0.23), residues: 1332 helix: 0.02 (0.20), residues: 664 sheet: -2.13 (0.43), residues: 140 loop : -0.89 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 371 HIS 0.007 0.001 HIS A 215 PHE 0.026 0.003 PHE A 278 TYR 0.030 0.002 TYR A 264 ARG 0.010 0.001 ARG C 260 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 319 time to evaluate : 1.210 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: B 174 ASP cc_start: 0.7437 (m-30) cc_final: 0.7176 (m-30) REVERT: B 177 HIS cc_start: 0.5955 (m170) cc_final: 0.5728 (m170) REVERT: B 227 GLU cc_start: 0.7425 (pm20) cc_final: 0.7172 (pm20) REVERT: B 228 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.5859 (pm20) REVERT: B 260 ARG cc_start: 0.8898 (ptp-110) cc_final: 0.8557 (ptp-110) REVERT: B 280 LYS cc_start: 0.8239 (mmmm) cc_final: 0.7655 (mmmm) REVERT: B 447 TYR cc_start: 0.7802 (t80) cc_final: 0.7507 (t80) REVERT: B 460 ASP cc_start: 0.8356 (t0) cc_final: 0.8031 (t0) REVERT: B 476 ARG cc_start: 0.7802 (ttt-90) cc_final: 0.7375 (ttt-90) REVERT: A 178 HIS cc_start: 0.7412 (m170) cc_final: 0.6913 (m170) REVERT: A 214 ARG cc_start: 0.7717 (mmm160) cc_final: 0.7447 (mmm160) REVERT: A 286 GLN cc_start: 0.8005 (pm20) cc_final: 0.7608 (pm20) REVERT: A 308 PHE cc_start: 0.8272 (t80) cc_final: 0.8015 (t80) REVERT: A 346 GLN cc_start: 0.8304 (tp-100) cc_final: 0.8037 (tp40) REVERT: A 447 TYR cc_start: 0.8190 (t80) cc_final: 0.7422 (t80) REVERT: A 460 ASP cc_start: 0.8375 (t0) cc_final: 0.8146 (t0) REVERT: A 476 ARG cc_start: 0.8179 (ttt-90) cc_final: 0.7855 (ttm-80) REVERT: C 168 ARG cc_start: 0.7498 (mmm160) cc_final: 0.7207 (mmm160) REVERT: C 169 LYS cc_start: 0.8459 (mmtt) cc_final: 0.8200 (mmtt) REVERT: C 172 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6953 (mm-30) REVERT: C 214 ARG cc_start: 0.7969 (tpp-160) cc_final: 0.7553 (mmp-170) REVERT: C 413 ASP cc_start: 0.9091 (m-30) cc_final: 0.8777 (m-30) REVERT: C 443 LYS cc_start: 0.7984 (tttt) cc_final: 0.7681 (pttt) REVERT: C 473 GLN cc_start: 0.8433 (tp-100) cc_final: 0.8091 (tp40) REVERT: C 476 ARG cc_start: 0.7855 (ttt90) cc_final: 0.7315 (ttt90) REVERT: C 480 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6577 (mp0) REVERT: D 172 GLU cc_start: 0.6628 (mm-30) cc_final: 0.6246 (mm-30) REVERT: D 178 HIS cc_start: 0.7493 (m170) cc_final: 0.7047 (m170) REVERT: D 214 ARG cc_start: 0.7322 (mmp-170) cc_final: 0.7075 (mmp-170) REVERT: D 264 TYR cc_start: 0.5879 (m-10) cc_final: 0.5471 (m-10) REVERT: D 274 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.7991 (t0) REVERT: D 280 LYS cc_start: 0.8285 (mmtt) cc_final: 0.7996 (mtmt) REVERT: D 286 GLN cc_start: 0.7890 (pm20) cc_final: 0.7502 (pm20) REVERT: D 364 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8681 (tm-30) REVERT: D 380 LYS cc_start: 0.8926 (mmmm) cc_final: 0.8579 (mmmt) REVERT: D 460 ASP cc_start: 0.8239 (t0) cc_final: 0.7906 (t0) REVERT: D 476 ARG cc_start: 0.7549 (ttt90) cc_final: 0.7130 (ttt90) REVERT: D 480 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6301 (mp0) REVERT: D 486 LEU cc_start: 0.9230 (tp) cc_final: 0.8902 (tp) outliers start: 50 outliers final: 39 residues processed: 339 average time/residue: 0.2842 time to fit residues: 129.5786 Evaluate side-chains 342 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 299 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 480 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 104 optimal weight: 0.0870 chunk 10 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 HIS ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11032 Z= 0.226 Angle : 0.792 16.384 14968 Z= 0.381 Chirality : 0.045 0.259 1600 Planarity : 0.004 0.054 1972 Dihedral : 5.041 18.363 1484 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 25.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.65 % Allowed : 26.22 % Favored : 70.14 % 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: -0.98 (0.23), residues: 1332 helix: 0.00 (0.20), residues: 664 sheet: -2.13 (0.43), residues: 140 loop : -0.90 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 371 HIS 0.007 0.001 HIS A 178 PHE 0.038 0.003 PHE D 412 TYR 0.029 0.002 TYR A 264 ARG 0.010 0.001 ARG C 260 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 322 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 174 ASP cc_start: 0.7345 (m-30) cc_final: 0.7070 (m-30) REVERT: B 227 GLU cc_start: 0.7485 (pm20) cc_final: 0.7156 (pm20) REVERT: B 228 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6116 (pm20) REVERT: B 260 ARG cc_start: 0.8848 (ptp-110) cc_final: 0.8439 (ptp-110) REVERT: B 280 LYS cc_start: 0.8305 (mmmm) cc_final: 0.7858 (mmmm) REVERT: B 398 GLU cc_start: 0.7513 (mm-30) cc_final: 0.6742 (mm-30) REVERT: B 447 TYR cc_start: 0.7798 (t80) cc_final: 0.7512 (t80) REVERT: B 460 ASP cc_start: 0.8406 (t0) cc_final: 0.8141 (t0) REVERT: B 476 ARG cc_start: 0.7831 (ttt-90) cc_final: 0.7336 (ttt-90) REVERT: A 286 GLN cc_start: 0.7983 (pm20) cc_final: 0.7567 (pm20) REVERT: A 308 PHE cc_start: 0.8245 (t80) cc_final: 0.8045 (t80) REVERT: A 447 TYR cc_start: 0.8150 (t80) cc_final: 0.7334 (t80) REVERT: A 460 ASP cc_start: 0.8417 (t0) cc_final: 0.8163 (t0) REVERT: A 464 LEU cc_start: 0.8696 (tp) cc_final: 0.8386 (tp) REVERT: A 473 GLN cc_start: 0.8430 (tp40) cc_final: 0.8070 (tp40) REVERT: A 476 ARG cc_start: 0.8138 (ttt-90) cc_final: 0.7912 (ttm-80) REVERT: C 168 ARG cc_start: 0.7470 (mmm160) cc_final: 0.7150 (mmm160) REVERT: C 169 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8172 (mmtt) REVERT: C 172 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6953 (mm-30) REVERT: C 214 ARG cc_start: 0.7967 (tpp-160) cc_final: 0.7598 (mmp-170) REVERT: C 413 ASP cc_start: 0.9041 (m-30) cc_final: 0.8731 (m-30) REVERT: C 443 LYS cc_start: 0.7871 (tttt) cc_final: 0.7565 (pttt) REVERT: C 473 GLN cc_start: 0.8435 (tp-100) cc_final: 0.8094 (tp40) REVERT: C 476 ARG cc_start: 0.7823 (ttt90) cc_final: 0.7265 (ttt90) REVERT: C 480 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6551 (mp0) REVERT: D 172 GLU cc_start: 0.6681 (mm-30) cc_final: 0.6308 (mm-30) REVERT: D 178 HIS cc_start: 0.7451 (m170) cc_final: 0.7025 (m170) REVERT: D 214 ARG cc_start: 0.7321 (mmp-170) cc_final: 0.7033 (mmp-170) REVERT: D 264 TYR cc_start: 0.5857 (m-10) cc_final: 0.5389 (m-10) REVERT: D 274 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.7995 (t0) REVERT: D 280 LYS cc_start: 0.8267 (mmtt) cc_final: 0.7979 (mtmt) REVERT: D 286 GLN cc_start: 0.7889 (pm20) cc_final: 0.7482 (pm20) REVERT: D 364 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8663 (tm-30) REVERT: D 380 LYS cc_start: 0.8923 (mmmm) cc_final: 0.8560 (mmmt) REVERT: D 443 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.7168 (tmtt) REVERT: D 460 ASP cc_start: 0.8183 (t0) cc_final: 0.7891 (t0) REVERT: D 476 ARG cc_start: 0.7647 (ttt90) cc_final: 0.7193 (ttt90) REVERT: D 480 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6250 (mp0) REVERT: D 486 LEU cc_start: 0.9223 (tp) cc_final: 0.8887 (tp) outliers start: 42 outliers final: 31 residues processed: 334 average time/residue: 0.2751 time to fit residues: 122.5364 Evaluate side-chains 333 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 297 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 443 LYS Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 480 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 92 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 HIS ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.115964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.104170 restraints weight = 25575.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.107196 restraints weight = 14202.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.109117 restraints weight = 9030.798| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11032 Z= 0.231 Angle : 0.808 15.559 14968 Z= 0.389 Chirality : 0.045 0.224 1600 Planarity : 0.005 0.059 1972 Dihedral : 5.093 18.271 1484 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 27.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.56 % Allowed : 26.65 % Favored : 69.79 % 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: -0.99 (0.23), residues: 1332 helix: -0.02 (0.20), residues: 664 sheet: -2.12 (0.43), residues: 140 loop : -0.88 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP B 371 HIS 0.006 0.001 HIS A 215 PHE 0.031 0.003 PHE D 412 TYR 0.025 0.002 TYR B 264 ARG 0.010 0.001 ARG C 260 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2770.00 seconds wall clock time: 51 minutes 21.97 seconds (3081.97 seconds total)