Starting phenix.real_space_refine on Sat Mar 16 13:14:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhs_24468/03_2024/7rhs_24468.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhs_24468/03_2024/7rhs_24468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhs_24468/03_2024/7rhs_24468.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhs_24468/03_2024/7rhs_24468.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhs_24468/03_2024/7rhs_24468.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhs_24468/03_2024/7rhs_24468.pdb" } resolution = 2.93 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= 0.002 sd= 0.070 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 S 66 5.16 5 Na 1 4.78 5 C 9644 2.51 5 N 2398 2.21 5 O 2658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ASP 375": "OD1" <-> "OD2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 432": "OD1" <-> "OD2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A GLU 455": "OE1" <-> "OE2" Residue "A ARG 499": "NH1" <-> "NH2" Residue "A PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 507": "OD1" <-> "OD2" Residue "A TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 563": "NH1" <-> "NH2" Residue "A ARG 569": "NH1" <-> "NH2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A ARG 603": "NH1" <-> "NH2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 221": "NH1" <-> "NH2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B ASP 375": "OD1" <-> "OD2" Residue "B ARG 410": "NH1" <-> "NH2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 432": "OD1" <-> "OD2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B ASP 452": "OD1" <-> "OD2" Residue "B GLU 455": "OE1" <-> "OE2" Residue "B ASP 475": "OD1" <-> "OD2" Residue "B ARG 499": "NH1" <-> "NH2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 507": "OD1" <-> "OD2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 514": "OD1" <-> "OD2" Residue "B ASP 532": "OD1" <-> "OD2" Residue "B ASP 543": "OD1" <-> "OD2" Residue "B TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 563": "NH1" <-> "NH2" Residue "B ARG 569": "NH1" <-> "NH2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 575": "OD1" <-> "OD2" Residue "B ASP 583": "OD1" <-> "OD2" Residue "B ARG 603": "NH1" <-> "NH2" Residue "B ASP 609": "OD1" <-> "OD2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 170": "NH1" <-> "NH2" Residue "C ASP 193": "OD1" <-> "OD2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 289": "OD1" <-> "OD2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 347": "NH1" <-> "NH2" Residue "C ASP 375": "OD1" <-> "OD2" Residue "C ARG 410": "NH1" <-> "NH2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C GLU 453": "OE1" <-> "OE2" Residue "C GLU 455": "OE1" <-> "OE2" Residue "C GLU 487": "OE1" <-> "OE2" Residue "C ARG 499": "NH1" <-> "NH2" Residue "C ASP 507": "OD1" <-> "OD2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 532": "OD1" <-> "OD2" Residue "C ASP 533": "OD1" <-> "OD2" Residue "C PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 563": "NH1" <-> "NH2" Residue "C ARG 569": "NH1" <-> "NH2" Residue "C GLU 590": "OE1" <-> "OE2" Residue "C GLU 599": "OE1" <-> "OE2" Residue "C ARG 603": "NH1" <-> "NH2" Residue "D ASP 211": "OD1" <-> "OD2" Residue "D TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 279": "NH1" <-> "NH2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "D ARG 295": "NH1" <-> "NH2" Residue "D PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 311": "OD1" <-> "OD2" Residue "D PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 352": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D ARG 396": "NH1" <-> "NH2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 456": "NH1" <-> "NH2" Residue "D ASP 460": "OD1" <-> "OD2" Residue "D TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 480": "NH1" <-> "NH2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D ASP 497": "OD1" <-> "OD2" Residue "D ASP 513": "OD1" <-> "OD2" Residue "D ARG 539": "NH1" <-> "NH2" Residue "D TYR 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 603": "NH1" <-> "NH2" Residue "D PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 635": "OE1" <-> "OE2" Residue "D ARG 636": "NH1" <-> "NH2" Residue "D ARG 643": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14767 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3725 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 456, 3717 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 14, 'TRANS': 441} Conformer: "B" Number of residues, atoms: 456, 3717 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 14, 'TRANS': 441} bond proxies already assigned to first conformer: 3791 Chain: "B" Number of atoms: 3692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3692 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 14, 'TRANS': 438} Chain: "C" Number of atoms: 3697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3697 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} Chain: "D" Number of atoms: 3610 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 441, 3602 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 13, 'TRANS': 427} Conformer: "B" Number of residues, atoms: 441, 3602 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 13, 'TRANS': 427} bond proxies already assigned to first conformer: 3684 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.59, per 1000 atoms: 0.78 Number of scatterers: 14767 At special positions: 0 Unit cell: (129.478, 118.757, 109.685, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 Na 1 11.00 O 2658 8.00 N 2398 7.00 C 9644 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 Links applied NAG-ASN " NAG A 801 " - " ASN A 339 " " NAG B 801 " - " ASN B 339 " " NAG C 801 " - " ASN C 339 " Time building additional restraints: 5.63 Conformation dependent library (CDL) restraints added in 4.1 seconds 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3420 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 12 sheets defined 67.5% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 166 through 193 Proline residue: A 178 - end of helix removed outlier: 3.955A pdb=" N ASP A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 199 through 222 Processing helix chain 'A' and resid 235 through 245 Processing helix chain 'A' and resid 246 through 256 removed outlier: 4.093A pdb=" N LYS A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 261 removed outlier: 3.767A pdb=" N LEU A 261 " --> pdb=" O PRO A 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 258 through 261' Processing helix chain 'A' and resid 262 through 267 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.980A pdb=" N VAL A 273 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASN A 276 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 295 removed outlier: 4.266A pdb=" N LEU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 329 Processing helix chain 'A' and resid 347 through 364 removed outlier: 3.648A pdb=" N THR A 364 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 407 Processing helix chain 'A' and resid 407 through 427 Processing helix chain 'A' and resid 430 through 447 Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 487 through 497 Processing helix chain 'A' and resid 548 through 554 removed outlier: 3.700A pdb=" N ILE A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 591 through 610 Processing helix chain 'B' and resid 165 through 193 removed outlier: 3.718A pdb=" N TYR B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Proline residue: B 178 - end of helix removed outlier: 3.939A pdb=" N ASP B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 199 through 223 Processing helix chain 'B' and resid 235 through 245 Processing helix chain 'B' and resid 246 through 256 removed outlier: 3.913A pdb=" N LYS B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 removed outlier: 3.692A pdb=" N LEU B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 258 through 261' Processing helix chain 'B' and resid 262 through 267 Processing helix chain 'B' and resid 270 through 279 removed outlier: 4.002A pdb=" N VAL B 273 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 275 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN B 276 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 295 removed outlier: 4.371A pdb=" N LEU B 284 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 329 Processing helix chain 'B' and resid 347 through 364 Processing helix chain 'B' and resid 374 through 407 Processing helix chain 'B' and resid 407 through 427 Processing helix chain 'B' and resid 430 through 447 Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 461 through 478 removed outlier: 6.421A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N THR B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 497 Processing helix chain 'B' and resid 581 through 588 Processing helix chain 'B' and resid 591 through 610 Processing helix chain 'C' and resid 165 through 193 removed outlier: 3.758A pdb=" N TYR C 169 " --> pdb=" O SER C 165 " (cutoff:3.500A) Proline residue: C 178 - end of helix removed outlier: 3.852A pdb=" N ASP C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 199 removed outlier: 3.721A pdb=" N SER C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 222 Processing helix chain 'C' and resid 235 through 245 Processing helix chain 'C' and resid 246 through 256 removed outlier: 3.959A pdb=" N LYS C 250 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 251 " --> pdb=" O THR C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 266 Processing helix chain 'C' and resid 270 through 279 removed outlier: 4.212A pdb=" N VAL C 273 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASN C 276 " --> pdb=" O VAL C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 295 removed outlier: 4.052A pdb=" N LEU C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 329 Processing helix chain 'C' and resid 347 through 364 Processing helix chain 'C' and resid 374 through 407 Processing helix chain 'C' and resid 407 through 427 Processing helix chain 'C' and resid 430 through 447 Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 461 through 478 removed outlier: 6.710A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N THR C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 497 Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 591 through 610 Processing helix chain 'D' and resid 215 through 242 removed outlier: 3.722A pdb=" N LEU D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Proline residue: D 237 - end of helix Processing helix chain 'D' and resid 249 through 271 removed outlier: 3.513A pdb=" N TRP D 253 " --> pdb=" O ASN D 249 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 275 removed outlier: 3.767A pdb=" N LEU D 275 " --> pdb=" O GLN D 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 272 through 275' Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 298 through 307 removed outlier: 3.830A pdb=" N LEU D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 315 removed outlier: 3.824A pdb=" N ILE D 312 " --> pdb=" O PRO D 309 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 315 " --> pdb=" O ILE D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 329 removed outlier: 4.490A pdb=" N ASN D 326 " --> pdb=" O PHE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 345 removed outlier: 4.140A pdb=" N PHE D 334 " --> pdb=" O LYS D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 379 removed outlier: 4.385A pdb=" N TYR D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 406 Processing helix chain 'D' and resid 416 through 449 Processing helix chain 'D' and resid 449 through 469 Processing helix chain 'D' and resid 472 through 490 Processing helix chain 'D' and resid 495 through 500 Processing helix chain 'D' and resid 503 through 521 removed outlier: 3.617A pdb=" N VAL D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER D 517 " --> pdb=" O ASP D 513 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 592 through 596 removed outlier: 3.504A pdb=" N LEU D 595 " --> pdb=" O GLU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 629 Processing helix chain 'D' and resid 631 through 646 Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 228 Processing sheet with id=AA2, first strand: chain 'A' and resid 499 through 503 removed outlier: 3.585A pdb=" N ASN A 523 " --> pdb=" O ASP A 575 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 508 through 510 removed outlier: 6.837A pdb=" N ILE A 568 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN A 567 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A 539 " --> pdb=" O VAL A 529 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 227 through 228 Processing sheet with id=AA5, first strand: chain 'B' and resid 499 through 503 Processing sheet with id=AA6, first strand: chain 'B' and resid 508 through 510 removed outlier: 6.567A pdb=" N TYR B 508 " --> pdb=" O SER B 570 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER B 570 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS B 510 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN B 567 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B 527 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL B 540 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B 529 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 227 through 228 Processing sheet with id=AA8, first strand: chain 'C' and resid 499 through 503 Processing sheet with id=AA9, first strand: chain 'C' and resid 508 through 510 removed outlier: 6.791A pdb=" N ILE C 568 " --> pdb=" O ILE C 509 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN C 567 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL C 539 " --> pdb=" O VAL C 529 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 277 through 279 removed outlier: 4.098A pdb=" N PHE D 277 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP D 282 " --> pdb=" O ARG D 279 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 541 through 545 removed outlier: 3.628A pdb=" N SER D 588 " --> pdb=" O ILE D 564 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 550 through 552 removed outlier: 6.687A pdb=" N PHE D 550 " --> pdb=" O ALA D 610 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA D 610 " --> pdb=" O PHE D 550 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN D 607 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL D 582 " --> pdb=" O VAL D 571 " (cutoff:3.500A) 945 hydrogen bonds defined for protein. 2722 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.62 Time building geometry restraints manager: 6.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3105 1.33 - 1.45: 3524 1.45 - 1.57: 8377 1.57 - 1.69: 1 1.69 - 1.81: 105 Bond restraints: 15112 Sorted by residual: bond pdb=" N PRO B 163 " pdb=" CD PRO B 163 " ideal model delta sigma weight residual 1.473 1.354 0.119 1.40e-02 5.10e+03 7.24e+01 bond pdb=" C ARG D 442 " pdb=" O ARG D 442 " ideal model delta sigma weight residual 1.237 1.315 -0.079 1.17e-02 7.31e+03 4.52e+01 bond pdb=" C PHE A 392 " pdb=" O PHE A 392 " ideal model delta sigma weight residual 1.236 1.310 -0.074 1.25e-02 6.40e+03 3.53e+01 bond pdb=" N PRO D 309 " pdb=" CD PRO D 309 " ideal model delta sigma weight residual 1.473 1.413 0.060 1.40e-02 5.10e+03 1.82e+01 bond pdb=" C PHE A 392 " pdb=" CA APHE A 392 " ideal model delta sigma weight residual 1.522 1.577 -0.055 1.39e-02 5.18e+03 1.58e+01 ... (remaining 15107 not shown) Histogram of bond angle deviations from ideal: 97.89 - 105.24: 214 105.24 - 112.60: 7547 112.60 - 119.95: 6112 119.95 - 127.31: 6470 127.31 - 134.66: 156 Bond angle restraints: 20499 Sorted by residual: angle pdb=" O PHE A 392 " pdb=" C PHE A 392 " pdb=" CA BPHE A 392 " ideal model delta sigma weight residual 120.10 129.67 -9.57 1.13e+00 7.83e-01 7.17e+01 angle pdb=" O ARG D 442 " pdb=" C ARG D 442 " pdb=" CA BARG D 442 " ideal model delta sigma weight residual 120.55 129.48 -8.93 1.06e+00 8.90e-01 7.10e+01 angle pdb=" O ARG D 442 " pdb=" C ARG D 442 " pdb=" CA AARG D 442 " ideal model delta sigma weight residual 120.55 129.46 -8.91 1.06e+00 8.90e-01 7.07e+01 angle pdb=" N SER B 560 " pdb=" CA SER B 560 " pdb=" C SER B 560 " ideal model delta sigma weight residual 111.14 120.19 -9.05 1.08e+00 8.57e-01 7.02e+01 angle pdb=" N PHE A 392 " pdb=" CA BPHE A 392 " pdb=" C PHE A 392 " ideal model delta sigma weight residual 111.71 118.98 -7.27 1.15e+00 7.56e-01 3.99e+01 ... (remaining 20494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.38: 7987 16.38 - 32.75: 825 32.75 - 49.13: 140 49.13 - 65.51: 29 65.51 - 81.89: 13 Dihedral angle restraints: 8994 sinusoidal: 3666 harmonic: 5328 Sorted by residual: dihedral pdb=" CA ILE B 366 " pdb=" C ILE B 366 " pdb=" N GLY B 367 " pdb=" CA GLY B 367 " ideal model delta harmonic sigma weight residual 180.00 156.95 23.05 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA MET A 607 " pdb=" C MET A 607 " pdb=" N LYS A 608 " pdb=" CA LYS A 608 " ideal model delta harmonic sigma weight residual 180.00 157.16 22.84 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA LEU B 227 " pdb=" C LEU B 227 " pdb=" N GLU B 228 " pdb=" CA GLU B 228 " ideal model delta harmonic sigma weight residual 180.00 157.23 22.77 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 8991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1971 0.073 - 0.147: 299 0.147 - 0.220: 52 0.220 - 0.293: 9 0.293 - 0.367: 1 Chirality restraints: 2332 Sorted by residual: chirality pdb=" CB ILE D 564 " pdb=" CA ILE D 564 " pdb=" CG1 ILE D 564 " pdb=" CG2 ILE D 564 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CB ILE B 303 " pdb=" CA ILE B 303 " pdb=" CG1 ILE B 303 " pdb=" CG2 ILE B 303 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE C 159 " pdb=" CA ILE C 159 " pdb=" CG1 ILE C 159 " pdb=" CG2 ILE C 159 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 2329 not shown) Planarity restraints: 2541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 272 " 0.052 5.00e-02 4.00e+02 7.83e-02 9.80e+00 pdb=" N PRO D 273 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 504 " -0.045 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO C 505 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 505 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 505 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 546 " -0.044 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO D 547 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 547 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 547 " -0.036 5.00e-02 4.00e+02 ... (remaining 2538 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 4773 2.83 - 3.35: 13251 3.35 - 3.87: 25562 3.87 - 4.38: 29160 4.38 - 4.90: 50341 Nonbonded interactions: 123087 Sorted by model distance: nonbonded pdb=" O TRP A 358 " pdb=" OG1 THR A 362 " model vdw 2.318 2.440 nonbonded pdb=" O LYS A 431 " pdb=" OG1 THR A 435 " model vdw 2.332 2.440 nonbonded pdb=" O TRP D 482 " pdb=" OG1 THR D 486 " model vdw 2.334 2.440 nonbonded pdb=" O LEU D 222 " pdb=" OG1 THR D 226 " model vdw 2.342 2.440 nonbonded pdb=" O THR B 360 " pdb=" OG1 THR B 364 " model vdw 2.343 2.440 ... (remaining 123082 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 159 through 391 or resid 393 through 611 or resid 801)) selection = (chain 'B' and (resid 159 through 391 or resid 393 through 611 or resid 801)) selection = (chain 'C' and (resid 159 through 391 or resid 393 through 611 or resid 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 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: 10.700 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 44.920 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.090 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:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 15112 Z= 0.388 Angle : 0.955 13.282 20499 Z= 0.563 Chirality : 0.057 0.367 2332 Planarity : 0.008 0.078 2538 Dihedral : 13.639 81.887 5574 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.06 % Allowed : 4.94 % Favored : 95.00 % 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: -3.90 (0.15), residues: 1798 helix: -3.08 (0.09), residues: 1122 sheet: -1.39 (0.64), residues: 53 loop : -1.22 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 171 HIS 0.007 0.002 HIS D 365 PHE 0.025 0.002 PHE C 301 TYR 0.025 0.002 TYR D 351 ARG 0.006 0.000 ARG C 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 284 time to evaluate : 1.764 Fit side-chains REVERT: A 265 LYS cc_start: 0.7604 (tmtt) cc_final: 0.7390 (tptt) REVERT: A 302 ARG cc_start: 0.7693 (mtm-85) cc_final: 0.7114 (mtp-110) REVERT: A 418 ASP cc_start: 0.8259 (m-30) cc_final: 0.7813 (m-30) REVERT: A 455 GLU cc_start: 0.7869 (mp0) cc_final: 0.7563 (mp0) REVERT: A 458 LYS cc_start: 0.8601 (ttpp) cc_final: 0.8090 (pttm) REVERT: A 535 VAL cc_start: 0.8420 (m) cc_final: 0.8162 (t) REVERT: A 556 LYS cc_start: 0.8154 (mtmm) cc_final: 0.7876 (mtmp) REVERT: A 603 ARG cc_start: 0.7206 (ttt-90) cc_final: 0.6864 (ttm-80) REVERT: B 228 GLU cc_start: 0.7687 (pp20) cc_final: 0.7424 (pp20) REVERT: B 499 ARG cc_start: 0.7704 (ttp80) cc_final: 0.7417 (ttp-110) REVERT: B 575 ASP cc_start: 0.7963 (t0) cc_final: 0.7653 (t0) REVERT: C 193 ASP cc_start: 0.8105 (t0) cc_final: 0.7850 (t0) REVERT: C 217 ASP cc_start: 0.8689 (t70) cc_final: 0.8457 (t0) REVERT: C 467 GLU cc_start: 0.7398 (tp30) cc_final: 0.7073 (tp30) REVERT: C 499 ARG cc_start: 0.7814 (ptt90) cc_final: 0.7423 (ptt90) REVERT: C 514 ASP cc_start: 0.7675 (m-30) cc_final: 0.7162 (m-30) REVERT: C 542 SER cc_start: 0.8342 (p) cc_final: 0.8010 (m) REVERT: D 268 MET cc_start: 0.8890 (mtp) cc_final: 0.8674 (mtp) REVERT: D 316 PHE cc_start: 0.8672 (m-80) cc_final: 0.8344 (m-10) REVERT: D 443 ASP cc_start: 0.8163 (t70) cc_final: 0.7908 (t70) REVERT: D 452 GLN cc_start: 0.7638 (tp-100) cc_final: 0.7283 (tm-30) REVERT: D 468 ASN cc_start: 0.8957 (t0) cc_final: 0.8733 (t0) REVERT: D 477 LYS cc_start: 0.7785 (tttm) cc_final: 0.7325 (tppt) REVERT: D 513 ASP cc_start: 0.8006 (t0) cc_final: 0.7707 (t0) REVERT: D 593 ILE cc_start: 0.9134 (tp) cc_final: 0.8837 (mt) outliers start: 1 outliers final: 2 residues processed: 284 average time/residue: 1.2502 time to fit residues: 390.2746 Evaluate side-chains 180 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 178 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain D residue 259 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 85 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 229 GLN A 241 GLN A 248 GLN ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 ASN A 473 HIS A 554 ASN B 196 GLN B 229 GLN B 248 GLN C 241 GLN C 248 GLN C 398 ASN C 422 GLN C 425 GLN C 473 HIS ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 340 HIS D 365 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15112 Z= 0.181 Angle : 0.528 8.557 20499 Z= 0.285 Chirality : 0.041 0.218 2332 Planarity : 0.005 0.050 2538 Dihedral : 5.389 59.613 2069 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.16 % Allowed : 12.59 % Favored : 85.25 % 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: -0.87 (0.18), residues: 1798 helix: -0.46 (0.13), residues: 1125 sheet: -1.10 (0.64), residues: 60 loop : -0.41 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 171 HIS 0.003 0.001 HIS D 365 PHE 0.016 0.001 PHE B 192 TYR 0.012 0.001 TYR C 263 ARG 0.006 0.000 ARG D 279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 208 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 ARG cc_start: 0.7656 (mtm-85) cc_final: 0.7270 (mtp-110) REVERT: A 425 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.6430 (mp-120) REVERT: A 458 LYS cc_start: 0.8657 (ttpp) cc_final: 0.8189 (pttm) REVERT: A 556 LYS cc_start: 0.8025 (mtmm) cc_final: 0.7746 (mtmp) REVERT: A 603 ARG cc_start: 0.7027 (ttt-90) cc_final: 0.6736 (ttm-80) REVERT: B 418 ASP cc_start: 0.7926 (m-30) cc_final: 0.7553 (m-30) REVERT: B 425 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.6801 (mp-120) REVERT: B 499 ARG cc_start: 0.7897 (ttp80) cc_final: 0.7691 (ttp-110) REVERT: B 575 ASP cc_start: 0.8012 (t0) cc_final: 0.7717 (t0) REVERT: C 193 ASP cc_start: 0.8118 (t0) cc_final: 0.7841 (t0) REVERT: C 402 MET cc_start: 0.7721 (ttp) cc_final: 0.7450 (ttp) REVERT: C 514 ASP cc_start: 0.7608 (m-30) cc_final: 0.7052 (m-30) REVERT: C 542 SER cc_start: 0.8264 (p) cc_final: 0.7967 (m) REVERT: D 316 PHE cc_start: 0.8630 (m-80) cc_final: 0.8305 (m-10) REVERT: D 443 ASP cc_start: 0.8136 (t70) cc_final: 0.7916 (t70) REVERT: D 452 GLN cc_start: 0.7775 (tp-100) cc_final: 0.7437 (tm-30) REVERT: D 477 LYS cc_start: 0.7864 (tttm) cc_final: 0.7430 (tppt) REVERT: D 513 ASP cc_start: 0.8150 (t0) cc_final: 0.7868 (t0) REVERT: D 593 ILE cc_start: 0.8994 (tp) cc_final: 0.8575 (mt) REVERT: D 636 ARG cc_start: 0.7631 (mtm110) cc_final: 0.7403 (mtm110) outliers start: 35 outliers final: 11 residues processed: 226 average time/residue: 1.1366 time to fit residues: 285.5874 Evaluate side-chains 179 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 166 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 539 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 135 optimal weight: 0.0770 chunk 110 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 161 optimal weight: 0.3980 chunk 55 optimal weight: 0.0060 chunk 130 optimal weight: 5.9990 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 405 ASN ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN C 182 ASN C 241 GLN C 248 GLN C 407 ASN ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15112 Z= 0.140 Angle : 0.481 8.061 20499 Z= 0.258 Chirality : 0.040 0.195 2332 Planarity : 0.004 0.043 2538 Dihedral : 4.856 57.605 2064 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.10 % Allowed : 14.14 % Favored : 83.77 % 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: 0.56 (0.20), residues: 1798 helix: 0.80 (0.15), residues: 1127 sheet: -0.90 (0.65), residues: 60 loop : -0.11 (0.27), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 171 HIS 0.003 0.001 HIS D 365 PHE 0.015 0.001 PHE A 249 TYR 0.014 0.001 TYR B 297 ARG 0.005 0.000 ARG D 279 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 192 time to evaluate : 1.495 Fit side-chains REVERT: A 302 ARG cc_start: 0.7666 (mtm-85) cc_final: 0.7312 (mtp-110) REVERT: A 425 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.6413 (mp-120) REVERT: A 458 LYS cc_start: 0.8658 (ttpp) cc_final: 0.8179 (pttm) REVERT: A 537 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8316 (mt0) REVERT: A 556 LYS cc_start: 0.7878 (mtmm) cc_final: 0.7550 (mtmp) REVERT: A 599 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.5446 (mp0) REVERT: A 603 ARG cc_start: 0.6983 (ttt-90) cc_final: 0.6684 (ttm-80) REVERT: B 418 ASP cc_start: 0.7862 (m-30) cc_final: 0.7478 (m-30) REVERT: B 425 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.6748 (mp-120) REVERT: B 559 LYS cc_start: 0.8242 (mtpp) cc_final: 0.7674 (mmtt) REVERT: C 193 ASP cc_start: 0.8070 (t0) cc_final: 0.7681 (t0) REVERT: C 272 GLU cc_start: 0.5671 (tt0) cc_final: 0.4950 (mp0) REVERT: C 344 GLU cc_start: 0.8085 (tp30) cc_final: 0.7870 (tp30) REVERT: C 514 ASP cc_start: 0.7580 (m-30) cc_final: 0.7039 (m-30) REVERT: C 542 SER cc_start: 0.8235 (p) cc_final: 0.7968 (m) REVERT: D 316 PHE cc_start: 0.8611 (m-80) cc_final: 0.8339 (m-10) REVERT: D 452 GLN cc_start: 0.7761 (tp-100) cc_final: 0.7420 (tm-30) REVERT: D 513 ASP cc_start: 0.8105 (t0) cc_final: 0.7834 (t0) REVERT: D 593 ILE cc_start: 0.8973 (tp) cc_final: 0.8584 (mt) REVERT: D 636 ARG cc_start: 0.7669 (mtm110) cc_final: 0.7429 (mtm110) outliers start: 34 outliers final: 9 residues processed: 210 average time/residue: 1.1183 time to fit residues: 261.2646 Evaluate side-chains 184 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 171 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain D residue 208 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 0.6980 chunk 122 optimal weight: 0.0970 chunk 84 optimal weight: 0.0020 chunk 18 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 163 optimal weight: 3.9990 chunk 173 optimal weight: 0.5980 chunk 85 optimal weight: 9.9990 chunk 154 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 HIS C 248 GLN ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15112 Z= 0.138 Angle : 0.468 8.863 20499 Z= 0.250 Chirality : 0.039 0.183 2332 Planarity : 0.003 0.054 2538 Dihedral : 4.373 49.796 2064 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.60 % Allowed : 15.43 % Favored : 82.96 % 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: 1.35 (0.20), residues: 1798 helix: 1.49 (0.15), residues: 1122 sheet: -0.06 (0.68), residues: 50 loop : 0.01 (0.27), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 171 HIS 0.003 0.001 HIS D 365 PHE 0.012 0.001 PHE C 301 TYR 0.013 0.001 TYR B 297 ARG 0.004 0.000 ARG D 643 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 191 time to evaluate : 1.694 Fit side-chains revert: symmetry clash REVERT: A 302 ARG cc_start: 0.7675 (mtm-85) cc_final: 0.7281 (mtp-110) REVERT: A 425 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.6332 (mp-120) REVERT: A 458 LYS cc_start: 0.8655 (ttpp) cc_final: 0.8152 (pttm) REVERT: A 556 LYS cc_start: 0.7855 (mtmm) cc_final: 0.7583 (mtmp) REVERT: A 599 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.5490 (mp0) REVERT: A 603 ARG cc_start: 0.7010 (ttt-90) cc_final: 0.6704 (ttm-80) REVERT: B 418 ASP cc_start: 0.7901 (m-30) cc_final: 0.7534 (m-30) REVERT: B 425 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.6701 (mp-120) REVERT: B 607 MET cc_start: 0.7522 (ttp) cc_final: 0.7190 (mtm) REVERT: C 193 ASP cc_start: 0.7927 (t0) cc_final: 0.7552 (t0) REVERT: C 272 GLU cc_start: 0.5676 (tt0) cc_final: 0.4942 (mp0) REVERT: C 514 ASP cc_start: 0.7591 (m-30) cc_final: 0.7061 (m-30) REVERT: C 542 SER cc_start: 0.8219 (p) cc_final: 0.7975 (m) REVERT: D 316 PHE cc_start: 0.8600 (m-80) cc_final: 0.8356 (m-10) REVERT: D 452 GLN cc_start: 0.7764 (tp-100) cc_final: 0.7398 (tm-30) REVERT: D 477 LYS cc_start: 0.7925 (tttm) cc_final: 0.7489 (tppt) REVERT: D 513 ASP cc_start: 0.8155 (t0) cc_final: 0.7914 (t0) REVERT: D 593 ILE cc_start: 0.8971 (tp) cc_final: 0.8569 (mt) outliers start: 26 outliers final: 10 residues processed: 205 average time/residue: 1.0808 time to fit residues: 247.7665 Evaluate side-chains 188 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 175 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 582 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 144 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 147 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN C 407 ASN ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15112 Z= 0.182 Angle : 0.489 10.338 20499 Z= 0.258 Chirality : 0.040 0.182 2332 Planarity : 0.004 0.052 2538 Dihedral : 4.187 42.086 2064 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.22 % Allowed : 15.80 % Favored : 81.98 % 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: 1.55 (0.20), residues: 1798 helix: 1.68 (0.15), residues: 1131 sheet: -0.10 (0.66), residues: 50 loop : 0.01 (0.27), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 373 HIS 0.004 0.001 HIS D 365 PHE 0.014 0.001 PHE B 192 TYR 0.013 0.001 TYR B 297 ARG 0.010 0.000 ARG D 636 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 179 time to evaluate : 1.639 Fit side-chains REVERT: A 219 LEU cc_start: 0.7999 (tt) cc_final: 0.7250 (mt) REVERT: A 302 ARG cc_start: 0.7669 (mtm-85) cc_final: 0.7275 (mtp-110) REVERT: A 405 ASN cc_start: 0.7849 (m110) cc_final: 0.7647 (m-40) REVERT: A 425 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.6360 (mp-120) REVERT: A 431 LYS cc_start: 0.8265 (mppt) cc_final: 0.7945 (tppp) REVERT: A 458 LYS cc_start: 0.8681 (ttpp) cc_final: 0.8174 (pttm) REVERT: A 537 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8234 (mt0) REVERT: A 556 LYS cc_start: 0.7861 (mtmm) cc_final: 0.7614 (mtmp) REVERT: A 599 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.5444 (mp0) REVERT: A 603 ARG cc_start: 0.6980 (ttt-90) cc_final: 0.6698 (ttm-80) REVERT: B 418 ASP cc_start: 0.7938 (m-30) cc_final: 0.7569 (m-30) REVERT: B 425 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.6718 (mp-120) REVERT: B 559 LYS cc_start: 0.8272 (mtpp) cc_final: 0.7719 (mmtt) REVERT: B 607 MET cc_start: 0.7513 (ttp) cc_final: 0.7209 (mtm) REVERT: C 193 ASP cc_start: 0.7923 (t0) cc_final: 0.7534 (t0) REVERT: C 272 GLU cc_start: 0.5698 (tt0) cc_final: 0.4967 (mp0) REVERT: C 514 ASP cc_start: 0.7561 (m-30) cc_final: 0.7016 (m-30) REVERT: C 542 SER cc_start: 0.8250 (p) cc_final: 0.7997 (m) REVERT: D 316 PHE cc_start: 0.8600 (m-80) cc_final: 0.8358 (m-10) REVERT: D 452 GLN cc_start: 0.7777 (tp-100) cc_final: 0.7414 (tm-30) REVERT: D 477 LYS cc_start: 0.7905 (tttm) cc_final: 0.7455 (tppt) REVERT: D 513 ASP cc_start: 0.8156 (t0) cc_final: 0.7897 (t0) REVERT: D 593 ILE cc_start: 0.8978 (tp) cc_final: 0.8572 (mt) outliers start: 36 outliers final: 14 residues processed: 201 average time/residue: 1.1065 time to fit residues: 247.6715 Evaluate side-chains 188 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 582 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 0.9980 chunk 155 optimal weight: 0.5980 chunk 34 optimal weight: 0.2980 chunk 101 optimal weight: 0.0980 chunk 42 optimal weight: 0.6980 chunk 173 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 90 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN C 248 GLN ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 ASN D 423 GLN D 426 ASN D 453 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15112 Z= 0.138 Angle : 0.469 8.863 20499 Z= 0.248 Chirality : 0.039 0.167 2332 Planarity : 0.003 0.046 2538 Dihedral : 3.851 26.877 2064 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.85 % Allowed : 16.48 % Favored : 81.67 % 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: 1.81 (0.20), residues: 1798 helix: 1.91 (0.16), residues: 1127 sheet: -0.07 (0.66), residues: 50 loop : 0.07 (0.27), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 171 HIS 0.003 0.001 HIS D 566 PHE 0.010 0.001 PHE C 301 TYR 0.012 0.001 TYR B 297 ARG 0.008 0.000 ARG D 636 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 187 time to evaluate : 1.704 Fit side-chains revert: symmetry clash REVERT: A 219 LEU cc_start: 0.8010 (tt) cc_final: 0.7291 (mt) REVERT: A 302 ARG cc_start: 0.7636 (mtm-85) cc_final: 0.7343 (mtp-110) REVERT: A 425 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.6392 (mp-120) REVERT: A 431 LYS cc_start: 0.8286 (mppt) cc_final: 0.7956 (tppp) REVERT: A 458 LYS cc_start: 0.8668 (ttpp) cc_final: 0.8175 (pttm) REVERT: A 537 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8230 (mt0) REVERT: A 556 LYS cc_start: 0.7910 (mtmm) cc_final: 0.7635 (mtmp) REVERT: A 599 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.5366 (mp0) REVERT: A 603 ARG cc_start: 0.6964 (ttt-90) cc_final: 0.6704 (ttm-80) REVERT: B 418 ASP cc_start: 0.7935 (m-30) cc_final: 0.7566 (m-30) REVERT: B 425 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.6739 (mp-120) REVERT: C 193 ASP cc_start: 0.7800 (t0) cc_final: 0.7304 (t0) REVERT: C 272 GLU cc_start: 0.5633 (tt0) cc_final: 0.4900 (mp0) REVERT: C 514 ASP cc_start: 0.7567 (m-30) cc_final: 0.7019 (m-30) REVERT: C 542 SER cc_start: 0.8209 (p) cc_final: 0.7948 (m) REVERT: D 316 PHE cc_start: 0.8584 (m-80) cc_final: 0.8363 (m-10) REVERT: D 452 GLN cc_start: 0.7772 (tp-100) cc_final: 0.7423 (tm-30) REVERT: D 477 LYS cc_start: 0.7926 (tttm) cc_final: 0.7490 (tppt) REVERT: D 513 ASP cc_start: 0.8131 (t0) cc_final: 0.7863 (t0) REVERT: D 593 ILE cc_start: 0.8987 (tp) cc_final: 0.8582 (mt) outliers start: 30 outliers final: 14 residues processed: 203 average time/residue: 1.0882 time to fit residues: 246.4960 Evaluate side-chains 184 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 166 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 582 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 172 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN C 407 ASN ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15112 Z= 0.232 Angle : 0.506 11.258 20499 Z= 0.266 Chirality : 0.041 0.186 2332 Planarity : 0.004 0.043 2538 Dihedral : 3.886 21.161 2064 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.16 % Allowed : 16.54 % Favored : 81.30 % 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: 1.81 (0.20), residues: 1798 helix: 1.92 (0.15), residues: 1120 sheet: -0.15 (0.66), residues: 50 loop : 0.08 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 373 HIS 0.005 0.001 HIS D 365 PHE 0.016 0.001 PHE B 192 TYR 0.017 0.001 TYR A 297 ARG 0.007 0.000 ARG D 636 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 168 time to evaluate : 1.899 Fit side-chains revert: symmetry clash REVERT: A 219 LEU cc_start: 0.7985 (tt) cc_final: 0.7292 (mt) REVERT: A 302 ARG cc_start: 0.7643 (mtm-85) cc_final: 0.7343 (mtp-110) REVERT: A 425 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.6393 (mp-120) REVERT: A 431 LYS cc_start: 0.8298 (mppt) cc_final: 0.7977 (tppp) REVERT: A 458 LYS cc_start: 0.8684 (ttpp) cc_final: 0.8160 (pttm) REVERT: A 537 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8257 (mt0) REVERT: B 418 ASP cc_start: 0.7950 (m-30) cc_final: 0.7598 (m-30) REVERT: B 425 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.6753 (mp-120) REVERT: B 559 LYS cc_start: 0.8288 (mtpp) cc_final: 0.7710 (mmtt) REVERT: C 193 ASP cc_start: 0.7826 (t0) cc_final: 0.7364 (t0) REVERT: C 272 GLU cc_start: 0.5694 (tt0) cc_final: 0.4908 (mp0) REVERT: C 514 ASP cc_start: 0.7585 (m-30) cc_final: 0.7031 (m-30) REVERT: C 542 SER cc_start: 0.8274 (p) cc_final: 0.8006 (m) REVERT: C 559 LYS cc_start: 0.6307 (mmtt) cc_final: 0.4961 (mtmm) REVERT: D 316 PHE cc_start: 0.8594 (m-80) cc_final: 0.8354 (m-10) REVERT: D 452 GLN cc_start: 0.7814 (tp-100) cc_final: 0.7417 (tm-30) REVERT: D 477 LYS cc_start: 0.7933 (tttm) cc_final: 0.7501 (tppt) REVERT: D 513 ASP cc_start: 0.8169 (t0) cc_final: 0.7903 (t0) REVERT: D 537 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7494 (mp) outliers start: 35 outliers final: 19 residues processed: 189 average time/residue: 1.2286 time to fit residues: 257.3096 Evaluate side-chains 192 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 169 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 537 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 135 optimal weight: 0.4980 chunk 156 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15112 Z= 0.166 Angle : 0.487 9.621 20499 Z= 0.257 Chirality : 0.040 0.170 2332 Planarity : 0.003 0.041 2538 Dihedral : 3.802 17.308 2064 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.79 % Allowed : 17.47 % Favored : 80.74 % 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: 1.94 (0.20), residues: 1798 helix: 2.02 (0.15), residues: 1120 sheet: -0.09 (0.66), residues: 50 loop : 0.13 (0.27), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 373 HIS 0.003 0.001 HIS D 365 PHE 0.012 0.001 PHE C 301 TYR 0.016 0.001 TYR A 297 ARG 0.007 0.000 ARG A 603 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 1.762 Fit side-chains REVERT: A 219 LEU cc_start: 0.7891 (tt) cc_final: 0.7335 (tp) REVERT: A 302 ARG cc_start: 0.7642 (mtm-85) cc_final: 0.7338 (mtp-110) REVERT: A 425 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6373 (mp-120) REVERT: A 458 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8153 (pttm) REVERT: A 556 LYS cc_start: 0.7919 (ptpp) cc_final: 0.7508 (pmtt) REVERT: A 599 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.5351 (mp0) REVERT: B 418 ASP cc_start: 0.7946 (m-30) cc_final: 0.7589 (m-30) REVERT: B 425 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.6746 (mp-120) REVERT: B 559 LYS cc_start: 0.8269 (mtpp) cc_final: 0.7704 (mmtt) REVERT: C 193 ASP cc_start: 0.7712 (t0) cc_final: 0.7261 (t0) REVERT: C 272 GLU cc_start: 0.5724 (tt0) cc_final: 0.4954 (mp0) REVERT: C 514 ASP cc_start: 0.7551 (m-30) cc_final: 0.7165 (m-30) REVERT: C 537 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7751 (mp-120) REVERT: C 542 SER cc_start: 0.8251 (p) cc_final: 0.7991 (m) REVERT: C 559 LYS cc_start: 0.6413 (mmtt) cc_final: 0.5127 (mtmm) REVERT: D 316 PHE cc_start: 0.8584 (m-80) cc_final: 0.8353 (m-10) REVERT: D 452 GLN cc_start: 0.7779 (tp-100) cc_final: 0.7412 (tm-30) REVERT: D 477 LYS cc_start: 0.7910 (tttm) cc_final: 0.7471 (tppt) REVERT: D 513 ASP cc_start: 0.8159 (t0) cc_final: 0.7894 (t0) REVERT: D 537 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7496 (mp) REVERT: D 593 ILE cc_start: 0.8994 (tp) cc_final: 0.8581 (mt) outliers start: 29 outliers final: 15 residues processed: 181 average time/residue: 1.1707 time to fit residues: 234.8957 Evaluate side-chains 182 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 537 GLN Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 537 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 165 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15112 Z= 0.245 Angle : 0.519 10.165 20499 Z= 0.273 Chirality : 0.042 0.184 2332 Planarity : 0.004 0.040 2538 Dihedral : 3.887 17.782 2064 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.79 % Allowed : 17.53 % Favored : 80.68 % 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: 1.85 (0.20), residues: 1798 helix: 1.96 (0.15), residues: 1118 sheet: -0.16 (0.66), residues: 50 loop : 0.08 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 373 HIS 0.004 0.001 HIS D 365 PHE 0.016 0.001 PHE B 192 TYR 0.017 0.001 TYR A 297 ARG 0.007 0.000 ARG B 499 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 165 time to evaluate : 1.882 Fit side-chains revert: symmetry clash REVERT: A 219 LEU cc_start: 0.7992 (tt) cc_final: 0.7438 (tp) REVERT: A 302 ARG cc_start: 0.7679 (mtm-85) cc_final: 0.7352 (mtp-110) REVERT: A 425 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.6376 (mp-120) REVERT: A 455 GLU cc_start: 0.7887 (mp0) cc_final: 0.7618 (mp0) REVERT: A 458 LYS cc_start: 0.8669 (ttpp) cc_final: 0.8156 (pttm) REVERT: A 556 LYS cc_start: 0.7909 (ptpp) cc_final: 0.7517 (pmtt) REVERT: A 599 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.5316 (mp0) REVERT: B 418 ASP cc_start: 0.7943 (m-30) cc_final: 0.7547 (m-30) REVERT: B 425 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.6746 (mp-120) REVERT: B 559 LYS cc_start: 0.8300 (mtpp) cc_final: 0.7729 (mmtt) REVERT: C 193 ASP cc_start: 0.7819 (t0) cc_final: 0.7352 (t0) REVERT: C 272 GLU cc_start: 0.5728 (tt0) cc_final: 0.4926 (mp0) REVERT: C 537 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7807 (mp-120) REVERT: C 542 SER cc_start: 0.8273 (p) cc_final: 0.7986 (m) REVERT: C 559 LYS cc_start: 0.6409 (mmtt) cc_final: 0.5214 (mtmm) REVERT: D 316 PHE cc_start: 0.8527 (m-80) cc_final: 0.8269 (m-10) REVERT: D 452 GLN cc_start: 0.7826 (tp-100) cc_final: 0.7428 (tm-30) REVERT: D 477 LYS cc_start: 0.7926 (tttm) cc_final: 0.7470 (tppt) REVERT: D 513 ASP cc_start: 0.8185 (t0) cc_final: 0.7932 (t0) REVERT: D 537 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7562 (mp) outliers start: 29 outliers final: 17 residues processed: 182 average time/residue: 1.1674 time to fit residues: 235.6528 Evaluate side-chains 183 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 537 GLN Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 537 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 103 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 142 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 chunk 151 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 GLN C 248 GLN C 407 ASN ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15112 Z= 0.173 Angle : 0.491 10.791 20499 Z= 0.259 Chirality : 0.040 0.237 2332 Planarity : 0.003 0.037 2538 Dihedral : 3.806 19.562 2064 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.60 % Allowed : 17.78 % Favored : 80.62 % 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: 1.96 (0.20), residues: 1798 helix: 2.04 (0.15), residues: 1118 sheet: -0.12 (0.67), residues: 50 loop : 0.16 (0.27), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 171 HIS 0.004 0.001 HIS D 365 PHE 0.012 0.001 PHE C 301 TYR 0.016 0.001 TYR A 297 ARG 0.008 0.000 ARG B 499 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 168 time to evaluate : 1.923 Fit side-chains revert: symmetry clash REVERT: A 219 LEU cc_start: 0.7841 (tt) cc_final: 0.7297 (tp) REVERT: A 302 ARG cc_start: 0.7628 (mtm-85) cc_final: 0.7332 (mtp-110) REVERT: A 425 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.6410 (mp-120) REVERT: A 458 LYS cc_start: 0.8672 (ttpp) cc_final: 0.8149 (pttm) REVERT: A 556 LYS cc_start: 0.7939 (ptpp) cc_final: 0.7549 (pmtt) REVERT: A 599 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.5333 (mp0) REVERT: B 418 ASP cc_start: 0.7940 (m-30) cc_final: 0.7602 (m-30) REVERT: B 425 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.6637 (mp-120) REVERT: C 272 GLU cc_start: 0.5739 (tt0) cc_final: 0.4953 (mp0) REVERT: C 514 ASP cc_start: 0.7594 (m-30) cc_final: 0.7223 (m-30) REVERT: C 542 SER cc_start: 0.8289 (p) cc_final: 0.8007 (m) REVERT: C 559 LYS cc_start: 0.6450 (mmtt) cc_final: 0.5260 (mtmm) REVERT: D 316 PHE cc_start: 0.8515 (m-80) cc_final: 0.8260 (m-10) REVERT: D 452 GLN cc_start: 0.7815 (tp-100) cc_final: 0.7403 (tm-30) REVERT: D 477 LYS cc_start: 0.7905 (tttm) cc_final: 0.7479 (tppt) REVERT: D 513 ASP cc_start: 0.8162 (t0) cc_final: 0.7902 (t0) REVERT: D 537 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7511 (mp) REVERT: D 593 ILE cc_start: 0.9014 (tp) cc_final: 0.8597 (mt) outliers start: 26 outliers final: 18 residues processed: 183 average time/residue: 1.1785 time to fit residues: 239.6007 Evaluate side-chains 181 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 159 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 537 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 43 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 GLN C 248 GLN ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.123959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.101572 restraints weight = 32569.141| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.61 r_work: 0.3103 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15112 Z= 0.200 Angle : 0.507 11.602 20499 Z= 0.266 Chirality : 0.041 0.233 2332 Planarity : 0.003 0.038 2538 Dihedral : 3.818 20.877 2064 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.60 % Allowed : 18.02 % Favored : 80.37 % 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: 1.93 (0.20), residues: 1798 helix: 2.02 (0.15), residues: 1120 sheet: -0.12 (0.67), residues: 50 loop : 0.12 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 171 HIS 0.004 0.001 HIS D 365 PHE 0.014 0.001 PHE B 192 TYR 0.016 0.001 TYR A 297 ARG 0.008 0.000 ARG D 643 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5043.01 seconds wall clock time: 90 minutes 21.86 seconds (5421.86 seconds total)