Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 5 13:12:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zzu_11587/10_2023/6zzu_11587.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zzu_11587/10_2023/6zzu_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_11587/10_2023/6zzu_11587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zzu_11587/10_2023/6zzu_11587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zzu_11587/10_2023/6zzu_11587.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zzu_11587/10_2023/6zzu_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-1.21rc1-5097/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: 5.56, per 1000 atoms: 0.52 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: 4.24 Conformation dependent library (CDL) restraints added in 1.4 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: 0.98 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: 2.98 Time building geometry restraints manager: 4.60 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: 0.290 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: 1.770 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 29.400 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.580 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.196 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 outliers start: 2 outliers final: 0 residues processed: 449 average time/residue: 0.2810 time to fit residues: 167.0822 Evaluate side-chains 324 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 1.143 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 178 HIS 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 C 425 GLN C 483 GLN D 178 HIS D 201 GLN D 246 HIS ** 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11032 Z= 0.230 Angle : 0.678 12.497 14968 Z= 0.347 Chirality : 0.042 0.180 1600 Planarity : 0.005 0.058 1972 Dihedral : 5.618 20.350 1484 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.12 % Allowed : 19.01 % Favored : 77.86 % 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: -3.04 (0.20), residues: 1332 helix: -1.97 (0.16), residues: 688 sheet: -2.22 (0.42), residues: 136 loop : -1.74 (0.27), residues: 508 *********************** 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 401 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 365 time to evaluate : 1.194 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 outliers start: 36 outliers final: 22 residues processed: 377 average time/residue: 0.2769 time to fit residues: 139.6049 Evaluate side-chains 318 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 296 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1088 time to fit residues: 5.9725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 99 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 HIS A 201 GLN ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN C 483 GLN ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11032 Z= 0.237 Angle : 0.660 12.963 14968 Z= 0.336 Chirality : 0.043 0.210 1600 Planarity : 0.004 0.039 1972 Dihedral : 5.352 19.634 1484 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.56 % Allowed : 23.26 % Favored : 75.17 % 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: -2.06 (0.21), residues: 1332 helix: -0.97 (0.18), residues: 664 sheet: -2.09 (0.42), residues: 136 loop : -1.49 (0.26), residues: 532 *********************** 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 348 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 330 time to evaluate : 1.300 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 outliers start: 18 outliers final: 12 residues processed: 337 average time/residue: 0.2827 time to fit residues: 126.7364 Evaluate side-chains 305 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 293 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1039 time to fit residues: 4.0112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 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 215 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 GLN ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11032 Z= 0.223 Angle : 0.652 13.994 14968 Z= 0.331 Chirality : 0.043 0.144 1600 Planarity : 0.004 0.040 1972 Dihedral : 5.152 19.956 1484 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.26 % Allowed : 23.00 % Favored : 74.74 % 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: -1.56 (0.22), residues: 1332 helix: -0.45 (0.19), residues: 664 sheet: -2.19 (0.42), residues: 140 loop : -1.29 (0.27), residues: 528 *********************** 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 356 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 330 time to evaluate : 1.288 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 outliers start: 26 outliers final: 13 residues processed: 339 average time/residue: 0.2764 time to fit residues: 126.0820 Evaluate side-chains 301 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 288 time to evaluate : 1.269 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1018 time to fit residues: 4.1898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 HIS ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN A 312 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 HIS ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 GLN ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11032 Z= 0.228 Angle : 0.694 14.297 14968 Z= 0.343 Chirality : 0.044 0.171 1600 Planarity : 0.004 0.040 1972 Dihedral : 5.124 18.883 1484 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 23.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.00 % Allowed : 25.17 % 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: -1.31 (0.23), residues: 1332 helix: -0.20 (0.20), residues: 664 sheet: -2.22 (0.42), residues: 140 loop : -1.17 (0.28), residues: 528 *********************** 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 349 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 326 time to evaluate : 1.278 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 outliers start: 23 outliers final: 9 residues processed: 335 average time/residue: 0.2696 time to fit residues: 122.4653 Evaluate side-chains 296 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 287 time to evaluate : 1.261 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.1008 time to fit residues: 3.4057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 6.9990 chunk 25 optimal weight: 0.0570 chunk 74 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 chunk 10 optimal weight: 0.0770 chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.4656 ------------------------------------------------------------------------------- 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 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN ** 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: 0.7789 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11032 Z= 0.210 Angle : 0.716 14.675 14968 Z= 0.352 Chirality : 0.044 0.226 1600 Planarity : 0.004 0.041 1972 Dihedral : 4.991 18.412 1484 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 23.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.08 % Allowed : 24.65 % Favored : 73.26 % 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: -1.08 (0.23), residues: 1332 helix: -0.04 (0.20), residues: 656 sheet: -2.13 (0.43), residues: 140 loop : -1.01 (0.27), residues: 536 *********************** 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 359 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 335 time to evaluate : 1.321 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 outliers start: 24 outliers final: 15 residues processed: 344 average time/residue: 0.2771 time to fit residues: 128.1446 Evaluate side-chains 315 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 300 time to evaluate : 1.425 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1058 time to fit residues: 4.6390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 71 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 HIS B 268 ASN ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 ASN ** D 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 HIS ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11032 Z= 0.237 Angle : 0.730 14.827 14968 Z= 0.358 Chirality : 0.044 0.178 1600 Planarity : 0.004 0.043 1972 Dihedral : 5.018 18.101 1484 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 24.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.39 % Allowed : 26.56 % Favored : 72.05 % 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: -1.03 (0.23), residues: 1332 helix: -0.03 (0.20), residues: 664 sheet: -2.12 (0.43), residues: 140 loop : -0.94 (0.28), residues: 528 *********************** 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 337 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 321 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 329 average time/residue: 0.2751 time to fit residues: 122.0569 Evaluate side-chains 303 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 296 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1051 time to fit residues: 2.9812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 0.0030 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 62 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 HIS A 178 HIS ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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: 0.7793 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11032 Z= 0.229 Angle : 0.759 14.742 14968 Z= 0.370 Chirality : 0.045 0.257 1600 Planarity : 0.004 0.050 1972 Dihedral : 5.057 18.098 1484 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 24.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.30 % Allowed : 27.52 % Favored : 71.18 % 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: -0.99 (0.23), residues: 1332 helix: 0.01 (0.20), residues: 660 sheet: -2.04 (0.44), residues: 140 loop : -0.95 (0.28), residues: 532 *********************** 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 340 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 325 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 332 average time/residue: 0.2628 time to fit residues: 118.6179 Evaluate side-chains 310 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 303 time to evaluate : 1.249 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1022 time to fit residues: 2.9447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 HIS ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 HIS ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 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: 0.7786 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11032 Z= 0.241 Angle : 0.808 17.580 14968 Z= 0.389 Chirality : 0.045 0.254 1600 Planarity : 0.005 0.041 1972 Dihedral : 5.053 18.147 1484 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 26.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.69 % Allowed : 28.12 % Favored : 71.18 % 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: -0.97 (0.23), residues: 1332 helix: -0.02 (0.20), residues: 664 sheet: -2.26 (0.42), residues: 148 loop : -0.75 (0.28), residues: 520 *********************** 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 322 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 314 time to evaluate : 1.188 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 outliers start: 8 outliers final: 6 residues processed: 317 average time/residue: 0.2773 time to fit residues: 119.2810 Evaluate side-chains 305 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 299 time to evaluate : 1.154 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1006 time to fit residues: 2.6891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.4980 chunk 87 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 121 optimal weight: 0.8980 chunk 104 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 111 optimal weight: 0.0270 chunk 32 optimal weight: 0.7980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 HIS ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 HIS ** 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: 0.7740 moved from start: 0.4680 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= 0.221 Angle : 0.811 17.315 14968 Z= 0.390 Chirality : 0.045 0.218 1600 Planarity : 0.005 0.053 1972 Dihedral : 5.023 18.077 1484 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 25.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.69 % Allowed : 28.39 % Favored : 70.92 % 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: -0.01 (0.20), residues: 660 sheet: -2.30 (0.41), residues: 148 loop : -0.80 (0.27), residues: 524 ********************** 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 329 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 321 time to evaluate : 1.156 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 outliers start: 8 outliers final: 4 residues processed: 323 average time/residue: 0.2701 time to fit residues: 118.1154 Evaluate side-chains 296 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 292 time to evaluate : 1.265 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1137 time to fit residues: 2.5497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 6.9990 chunk 15 optimal weight: 30.0000 chunk 29 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 43 optimal weight: 0.0470 chunk 107 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 177 HIS ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 HIS ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.118002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.105707 restraints weight = 25626.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.108817 restraints weight = 14706.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.110746 restraints weight = 9528.642| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4835 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= 0.242 Angle : 0.833 17.230 14968 Z= 0.401 Chirality : 0.045 0.214 1600 Planarity : 0.005 0.042 1972 Dihedral : 5.104 19.396 1484 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 25.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.26 % Allowed : 30.12 % Favored : 69.62 % 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: -1.05 (0.23), residues: 1332 helix: -0.08 (0.20), residues: 664 sheet: -2.30 (0.41), residues: 148 loop : -0.80 (0.28), residues: 520 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2749.86 seconds wall clock time: 50 minutes 44.72 seconds (3044.72 seconds total)