Starting phenix.real_space_refine on Sun Feb 18 07:41:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yih_33859/02_2024/7yih_33859.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yih_33859/02_2024/7yih_33859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yih_33859/02_2024/7yih_33859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yih_33859/02_2024/7yih_33859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yih_33859/02_2024/7yih_33859.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yih_33859/02_2024/7yih_33859.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.041 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 K 5 8.98 5 S 128 5.16 5 C 13796 2.51 5 N 3544 2.21 5 O 3848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 339": "OD1" <-> "OD2" Residue "A TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A ASP 575": "OD1" <-> "OD2" Residue "A TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 687": "OE1" <-> "OE2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 339": "OD1" <-> "OD2" Residue "B TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 374": "OE1" <-> "OE2" Residue "B ASP 575": "OD1" <-> "OD2" Residue "B TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 687": "OE1" <-> "OE2" Residue "C PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 339": "OD1" <-> "OD2" Residue "C TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 374": "OE1" <-> "OE2" Residue "C ASP 575": "OD1" <-> "OD2" Residue "C TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 687": "OE1" <-> "OE2" Residue "D PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 339": "OD1" <-> "OD2" Residue "D TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 374": "OE1" <-> "OE2" Residue "D ASP 575": "OD1" <-> "OD2" Residue "D TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 687": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21321 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "B" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "C" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "D" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' K': 5} Classifications: {'undetermined': 5, 'water': 1} Link IDs: {None: 5} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 10.47, per 1000 atoms: 0.49 Number of scatterers: 21321 At special positions: 0 Unit cell: (158.763, 158.763, 129.897, 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) K 5 19.00 S 128 16.00 O 3848 8.00 N 3544 7.00 C 13796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.73 Conformation dependent library (CDL) restraints added in 3.9 seconds 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5048 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 46.4% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.858A pdb=" N THR A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 211 through 238 removed outlier: 3.628A pdb=" N THR A 215 " --> pdb=" O CYS A 211 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 244 through 265 removed outlier: 3.827A pdb=" N LEU A 248 " --> pdb=" O ASN A 244 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 280 through 301 removed outlier: 6.284A pdb=" N VAL A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 328 removed outlier: 3.633A pdb=" N VAL A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 338 Processing helix chain 'A' and resid 345 through 375 removed outlier: 3.514A pdb=" N VAL A 375 " --> pdb=" O GLY A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 397 Processing helix chain 'A' and resid 414 through 431 Processing helix chain 'A' and resid 442 through 495 removed outlier: 3.823A pdb=" N LYS A 446 " --> pdb=" O THR A 442 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N MET A 474 " --> pdb=" O ILE A 470 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR A 475 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN A 477 " --> pdb=" O GLN A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 516 Processing helix chain 'A' and resid 520 through 527 removed outlier: 3.874A pdb=" N VAL A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 542 removed outlier: 3.551A pdb=" N ARG A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 563 Processing helix chain 'A' and resid 646 through 653 removed outlier: 3.665A pdb=" N LEU A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 664 removed outlier: 3.756A pdb=" N ASN A 658 " --> pdb=" O THR A 654 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 150 through 154 removed outlier: 3.858A pdb=" N THR B 153 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 211 through 238 removed outlier: 3.628A pdb=" N THR B 215 " --> pdb=" O CYS B 211 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 244 through 265 removed outlier: 3.827A pdb=" N LEU B 248 " --> pdb=" O ASN B 244 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 280 through 301 removed outlier: 6.285A pdb=" N VAL B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 328 removed outlier: 3.633A pdb=" N VAL B 325 " --> pdb=" O SER B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 338 Processing helix chain 'B' and resid 345 through 375 removed outlier: 3.514A pdb=" N VAL B 375 " --> pdb=" O GLY B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 397 Processing helix chain 'B' and resid 414 through 431 Processing helix chain 'B' and resid 442 through 495 removed outlier: 3.823A pdb=" N LYS B 446 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N MET B 474 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR B 475 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN B 477 " --> pdb=" O GLN B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 516 Processing helix chain 'B' and resid 520 through 527 removed outlier: 3.874A pdb=" N VAL B 524 " --> pdb=" O ASP B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 542 removed outlier: 3.551A pdb=" N ARG B 542 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 563 Processing helix chain 'B' and resid 646 through 653 removed outlier: 3.665A pdb=" N LEU B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 664 removed outlier: 3.756A pdb=" N ASN B 658 " --> pdb=" O THR B 654 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER B 659 " --> pdb=" O ALA B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 692 Processing helix chain 'C' and resid 83 through 88 Processing helix chain 'C' and resid 150 through 154 removed outlier: 3.858A pdb=" N THR C 153 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 183 through 187 Processing helix chain 'C' and resid 211 through 238 removed outlier: 3.628A pdb=" N THR C 215 " --> pdb=" O CYS C 211 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 244 through 265 removed outlier: 3.827A pdb=" N LEU C 248 " --> pdb=" O ASN C 244 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 280 through 301 removed outlier: 6.285A pdb=" N VAL C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE C 295 " --> pdb=" O THR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 328 removed outlier: 3.633A pdb=" N VAL C 325 " --> pdb=" O SER C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 338 Processing helix chain 'C' and resid 345 through 375 removed outlier: 3.514A pdb=" N VAL C 375 " --> pdb=" O GLY C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 397 Processing helix chain 'C' and resid 414 through 431 Processing helix chain 'C' and resid 442 through 495 removed outlier: 3.823A pdb=" N LYS C 446 " --> pdb=" O THR C 442 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET C 447 " --> pdb=" O ASP C 443 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N MET C 474 " --> pdb=" O ILE C 470 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR C 475 " --> pdb=" O PHE C 471 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN C 477 " --> pdb=" O GLN C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 516 Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.874A pdb=" N VAL C 524 " --> pdb=" O ASP C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 542 removed outlier: 3.551A pdb=" N ARG C 542 " --> pdb=" O VAL C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 563 Processing helix chain 'C' and resid 646 through 653 removed outlier: 3.665A pdb=" N LEU C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 664 removed outlier: 3.756A pdb=" N ASN C 658 " --> pdb=" O THR C 654 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER C 659 " --> pdb=" O ALA C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 692 Processing helix chain 'D' and resid 83 through 88 Processing helix chain 'D' and resid 150 through 154 removed outlier: 3.858A pdb=" N THR D 153 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'D' and resid 211 through 238 removed outlier: 3.628A pdb=" N THR D 215 " --> pdb=" O CYS D 211 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 244 through 265 removed outlier: 3.827A pdb=" N LEU D 248 " --> pdb=" O ASN D 244 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 280 through 301 removed outlier: 6.285A pdb=" N VAL D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE D 295 " --> pdb=" O THR D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 328 removed outlier: 3.633A pdb=" N VAL D 325 " --> pdb=" O SER D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 338 Processing helix chain 'D' and resid 345 through 375 removed outlier: 3.514A pdb=" N VAL D 375 " --> pdb=" O GLY D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 397 Processing helix chain 'D' and resid 414 through 431 Processing helix chain 'D' and resid 442 through 495 removed outlier: 3.823A pdb=" N LYS D 446 " --> pdb=" O THR D 442 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET D 447 " --> pdb=" O ASP D 443 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N MET D 474 " --> pdb=" O ILE D 470 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR D 475 " --> pdb=" O PHE D 471 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN D 477 " --> pdb=" O GLN D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 516 Processing helix chain 'D' and resid 520 through 527 removed outlier: 3.874A pdb=" N VAL D 524 " --> pdb=" O ASP D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 542 removed outlier: 3.551A pdb=" N ARG D 542 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 563 Processing helix chain 'D' and resid 646 through 653 removed outlier: 3.665A pdb=" N LEU D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 664 removed outlier: 3.756A pdb=" N ASN D 658 " --> pdb=" O THR D 654 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER D 659 " --> pdb=" O ALA D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 692 Processing sheet with id=AA1, first strand: chain 'A' and resid 270 through 271 removed outlier: 4.075A pdb=" N PHE A 270 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 567 through 571 removed outlier: 3.661A pdb=" N SER A 592 " --> pdb=" O ASP A 637 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N HIS A 639 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL A 590 " --> pdb=" O HIS A 639 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 602 through 607 removed outlier: 3.636A pdb=" N GLU A 602 " --> pdb=" O GLN A 599 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL A 597 " --> pdb=" O VAL A 604 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE A 606 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU A 595 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 596 " --> pdb=" O ARG A 631 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 270 through 271 removed outlier: 4.075A pdb=" N PHE B 270 " --> pdb=" O ILE B 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 567 through 571 removed outlier: 3.663A pdb=" N SER B 592 " --> pdb=" O ASP B 637 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N HIS B 639 " --> pdb=" O VAL B 590 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL B 590 " --> pdb=" O HIS B 639 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 602 through 607 removed outlier: 3.636A pdb=" N GLU B 602 " --> pdb=" O GLN B 599 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL B 597 " --> pdb=" O VAL B 604 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE B 606 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU B 595 " --> pdb=" O ILE B 606 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 596 " --> pdb=" O ARG B 631 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 270 through 271 removed outlier: 4.075A pdb=" N PHE C 270 " --> pdb=" O ILE C 278 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 567 through 571 removed outlier: 3.663A pdb=" N SER C 592 " --> pdb=" O ASP C 637 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N HIS C 639 " --> pdb=" O VAL C 590 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL C 590 " --> pdb=" O HIS C 639 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 602 through 607 removed outlier: 3.636A pdb=" N GLU C 602 " --> pdb=" O GLN C 599 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL C 597 " --> pdb=" O VAL C 604 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE C 606 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU C 595 " --> pdb=" O ILE C 606 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 596 " --> pdb=" O ARG C 631 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 270 through 271 removed outlier: 4.075A pdb=" N PHE D 270 " --> pdb=" O ILE D 278 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 567 through 571 removed outlier: 3.661A pdb=" N SER D 592 " --> pdb=" O ASP D 637 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N HIS D 639 " --> pdb=" O VAL D 590 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL D 590 " --> pdb=" O HIS D 639 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 602 through 607 removed outlier: 3.636A pdb=" N GLU D 602 " --> pdb=" O GLN D 599 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL D 597 " --> pdb=" O VAL D 604 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE D 606 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU D 595 " --> pdb=" O ILE D 606 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU D 596 " --> pdb=" O ARG D 631 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2484 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: 6.77 Time building geometry restraints manager: 8.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6656 1.34 - 1.46: 4337 1.46 - 1.58: 10619 1.58 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 21804 Sorted by residual: bond pdb=" N TRP B 38 " pdb=" CA TRP B 38 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.41e-02 5.03e+03 3.70e+00 bond pdb=" N TRP C 38 " pdb=" CA TRP C 38 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.41e-02 5.03e+03 3.70e+00 bond pdb=" N TRP D 38 " pdb=" CA TRP D 38 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.41e-02 5.03e+03 3.70e+00 bond pdb=" N TRP A 38 " pdb=" CA TRP A 38 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.41e-02 5.03e+03 3.70e+00 bond pdb=" N VAL C 36 " pdb=" CA VAL C 36 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.25e-02 6.40e+03 3.12e+00 ... (remaining 21799 not shown) Histogram of bond angle deviations from ideal: 98.86 - 105.95: 356 105.95 - 113.05: 11920 113.05 - 120.15: 8010 120.15 - 127.24: 9054 127.24 - 134.34: 244 Bond angle restraints: 29584 Sorted by residual: angle pdb=" N PRO A 39 " pdb=" CA PRO A 39 " pdb=" C PRO A 39 " ideal model delta sigma weight residual 112.47 124.04 -11.57 2.06e+00 2.36e-01 3.15e+01 angle pdb=" N PRO D 39 " pdb=" CA PRO D 39 " pdb=" C PRO D 39 " ideal model delta sigma weight residual 112.47 124.04 -11.57 2.06e+00 2.36e-01 3.15e+01 angle pdb=" N PRO B 39 " pdb=" CA PRO B 39 " pdb=" C PRO B 39 " ideal model delta sigma weight residual 112.47 124.04 -11.57 2.06e+00 2.36e-01 3.15e+01 angle pdb=" N PRO C 39 " pdb=" CA PRO C 39 " pdb=" C PRO C 39 " ideal model delta sigma weight residual 112.47 124.04 -11.57 2.06e+00 2.36e-01 3.15e+01 angle pdb=" CA PRO A 549 " pdb=" N PRO A 549 " pdb=" CD PRO A 549 " ideal model delta sigma weight residual 112.00 104.71 7.29 1.40e+00 5.10e-01 2.71e+01 ... (remaining 29579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11627 17.95 - 35.91: 1105 35.91 - 53.86: 160 53.86 - 71.81: 24 71.81 - 89.77: 16 Dihedral angle restraints: 12932 sinusoidal: 5144 harmonic: 7788 Sorted by residual: dihedral pdb=" CA PRO C 39 " pdb=" C PRO C 39 " pdb=" N VAL C 40 " pdb=" CA VAL C 40 " ideal model delta harmonic sigma weight residual 180.00 146.66 33.34 0 5.00e+00 4.00e-02 4.45e+01 dihedral pdb=" CA PRO B 39 " pdb=" C PRO B 39 " pdb=" N VAL B 40 " pdb=" CA VAL B 40 " ideal model delta harmonic sigma weight residual 180.00 146.66 33.34 0 5.00e+00 4.00e-02 4.45e+01 dihedral pdb=" CA PRO A 39 " pdb=" C PRO A 39 " pdb=" N VAL A 40 " pdb=" CA VAL A 40 " ideal model delta harmonic sigma weight residual 180.00 146.66 33.34 0 5.00e+00 4.00e-02 4.45e+01 ... (remaining 12929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3116 0.077 - 0.154: 276 0.154 - 0.231: 8 0.231 - 0.308: 0 0.308 - 0.384: 4 Chirality restraints: 3404 Sorted by residual: chirality pdb=" CA PRO A 39 " pdb=" N PRO A 39 " pdb=" C PRO A 39 " pdb=" CB PRO A 39 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA PRO B 39 " pdb=" N PRO B 39 " pdb=" C PRO B 39 " pdb=" CB PRO B 39 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA PRO D 39 " pdb=" N PRO D 39 " pdb=" C PRO D 39 " pdb=" CB PRO D 39 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.38 2.00e-01 2.50e+01 3.69e+00 ... (remaining 3401 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 548 " 0.108 5.00e-02 4.00e+02 1.59e-01 4.06e+01 pdb=" N PRO C 549 " -0.275 5.00e-02 4.00e+02 pdb=" CA PRO C 549 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO C 549 " 0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 548 " -0.108 5.00e-02 4.00e+02 1.59e-01 4.06e+01 pdb=" N PRO D 549 " 0.275 5.00e-02 4.00e+02 pdb=" CA PRO D 549 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO D 549 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 548 " -0.108 5.00e-02 4.00e+02 1.59e-01 4.06e+01 pdb=" N PRO A 549 " 0.275 5.00e-02 4.00e+02 pdb=" CA PRO A 549 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO A 549 " -0.078 5.00e-02 4.00e+02 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.68: 480 2.68 - 3.30: 24200 3.30 - 3.91: 40714 3.91 - 4.53: 52640 4.53 - 5.14: 83488 Nonbonded interactions: 201522 Sorted by model distance: nonbonded pdb=" O ARG A 677 " pdb=" N TRP D 38 " model vdw 2.066 2.520 nonbonded pdb=" N TRP A 38 " pdb=" O ARG B 677 " model vdw 2.066 2.520 nonbonded pdb=" N TRP C 38 " pdb=" O ARG D 677 " model vdw 2.066 2.520 nonbonded pdb=" N TRP B 38 " pdb=" O ARG C 677 " model vdw 2.066 2.520 nonbonded pdb=" N VAL B 36 " pdb=" O LYS C 678 " model vdw 2.233 2.520 ... (remaining 201517 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 11 through 692) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.520 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: 14.670 Check model and map are aligned: 0.300 Set scattering table: 0.210 Process input model: 54.990 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 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 : 0.004 0.079 21804 Z= 0.230 Angle : 0.783 11.808 29584 Z= 0.436 Chirality : 0.047 0.384 3404 Planarity : 0.008 0.159 3668 Dihedral : 14.228 89.766 7884 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 1.07 % Allowed : 13.91 % Favored : 85.02 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.16), residues: 2616 helix: 0.17 (0.15), residues: 1184 sheet: 0.42 (0.91), residues: 48 loop : -3.85 (0.14), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 38 HIS 0.005 0.001 HIS C 570 PHE 0.011 0.001 PHE C 293 TYR 0.014 0.002 TYR A 42 ARG 0.007 0.001 ARG D 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 3.153 Fit side-chains REVERT: A 394 LEU cc_start: 0.8471 (tp) cc_final: 0.8191 (tp) REVERT: B 394 LEU cc_start: 0.8462 (tp) cc_final: 0.8181 (tp) REVERT: C 394 LEU cc_start: 0.8479 (tp) cc_final: 0.8230 (tp) REVERT: D 394 LEU cc_start: 0.8484 (tp) cc_final: 0.8197 (tp) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.3060 time to fit residues: 121.2446 Evaluate side-chains 200 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 206 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 chunk 154 optimal weight: 0.8980 chunk 239 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 HIS ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 HIS ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21804 Z= 0.318 Angle : 0.766 11.783 29584 Z= 0.412 Chirality : 0.048 0.385 3404 Planarity : 0.007 0.101 3668 Dihedral : 6.098 31.069 2864 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 1.07 % Allowed : 14.37 % Favored : 84.56 % Rotamer: Outliers : 0.84 % Allowed : 10.76 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.16), residues: 2616 helix: 0.36 (0.15), residues: 1184 sheet: -2.14 (0.54), residues: 112 loop : -4.02 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 38 HIS 0.006 0.001 HIS B 539 PHE 0.012 0.002 PHE D 464 TYR 0.017 0.002 TYR B 419 ARG 0.003 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 232 time to evaluate : 2.508 Fit side-chains REVERT: A 55 ARG cc_start: 0.4159 (mpt180) cc_final: 0.2940 (mpt180) REVERT: A 394 LEU cc_start: 0.8473 (tp) cc_final: 0.8257 (tp) REVERT: B 55 ARG cc_start: 0.4171 (mpt180) cc_final: 0.2951 (mpt180) REVERT: B 394 LEU cc_start: 0.8464 (tp) cc_final: 0.8249 (tp) REVERT: C 55 ARG cc_start: 0.4165 (mpt180) cc_final: 0.2947 (mpt180) REVERT: C 394 LEU cc_start: 0.8488 (tp) cc_final: 0.8269 (tp) REVERT: D 55 ARG cc_start: 0.4160 (mpt180) cc_final: 0.2942 (mpt180) REVERT: D 394 LEU cc_start: 0.8489 (tp) cc_final: 0.8268 (tp) outliers start: 20 outliers final: 16 residues processed: 240 average time/residue: 0.3147 time to fit residues: 120.9657 Evaluate side-chains 208 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 192 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 558 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 240 optimal weight: 0.6980 chunk 259 optimal weight: 0.9990 chunk 213 optimal weight: 0.6980 chunk 238 optimal weight: 0.3980 chunk 81 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 570 HIS B 118 HIS B 570 HIS C 118 HIS C 570 HIS D 118 HIS D 570 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21804 Z= 0.268 Angle : 0.732 11.545 29584 Z= 0.390 Chirality : 0.046 0.382 3404 Planarity : 0.006 0.095 3668 Dihedral : 6.001 30.369 2864 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 1.07 % Allowed : 14.45 % Favored : 84.48 % Rotamer: Outliers : 2.27 % Allowed : 15.71 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.16), residues: 2616 helix: 0.47 (0.15), residues: 1184 sheet: -1.97 (0.47), residues: 132 loop : -4.00 (0.15), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 38 HIS 0.006 0.001 HIS D 539 PHE 0.015 0.002 PHE C 28 TYR 0.015 0.001 TYR C 368 ARG 0.003 0.000 ARG D 327 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 240 time to evaluate : 2.574 Fit side-chains REVERT: A 55 ARG cc_start: 0.4282 (mpt180) cc_final: 0.3193 (mmt-90) REVERT: A 394 LEU cc_start: 0.8427 (tp) cc_final: 0.8226 (tp) REVERT: A 671 ARG cc_start: 0.6775 (tpt170) cc_final: 0.6457 (tpt170) REVERT: B 55 ARG cc_start: 0.4292 (mpt180) cc_final: 0.3205 (mmt-90) REVERT: B 394 LEU cc_start: 0.8417 (tp) cc_final: 0.8217 (tp) REVERT: B 671 ARG cc_start: 0.6771 (tpt170) cc_final: 0.6463 (tpt170) REVERT: C 55 ARG cc_start: 0.4286 (mpt180) cc_final: 0.3203 (mmt-90) REVERT: C 394 LEU cc_start: 0.8437 (tp) cc_final: 0.8233 (tp) REVERT: C 671 ARG cc_start: 0.6769 (tpt170) cc_final: 0.6458 (tpt170) REVERT: D 55 ARG cc_start: 0.4285 (mpt180) cc_final: 0.3198 (mmt-90) REVERT: D 394 LEU cc_start: 0.8443 (tp) cc_final: 0.8237 (tp) REVERT: D 671 ARG cc_start: 0.6776 (tpt170) cc_final: 0.6464 (tpt170) outliers start: 54 outliers final: 42 residues processed: 278 average time/residue: 0.3035 time to fit residues: 134.9937 Evaluate side-chains 250 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 208 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 670 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 0.9980 chunk 180 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 241 optimal weight: 6.9990 chunk 255 optimal weight: 0.0670 chunk 125 optimal weight: 0.3980 chunk 228 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 HIS ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21804 Z= 0.192 Angle : 0.683 11.271 29584 Z= 0.364 Chirality : 0.045 0.385 3404 Planarity : 0.006 0.092 3668 Dihedral : 5.853 29.582 2864 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 1.07 % Allowed : 13.91 % Favored : 85.02 % Rotamer: Outliers : 2.02 % Allowed : 17.56 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.17), residues: 2616 helix: 0.67 (0.15), residues: 1192 sheet: -1.65 (0.49), residues: 132 loop : -3.87 (0.15), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 38 HIS 0.005 0.001 HIS A 539 PHE 0.013 0.001 PHE A 28 TYR 0.015 0.001 TYR B 368 ARG 0.002 0.000 ARG D 327 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 226 time to evaluate : 2.428 Fit side-chains REVERT: A 55 ARG cc_start: 0.3947 (mpt180) cc_final: 0.2847 (mmt-90) REVERT: A 394 LEU cc_start: 0.8383 (tp) cc_final: 0.8166 (tp) REVERT: B 55 ARG cc_start: 0.3953 (mpt180) cc_final: 0.2852 (mmt-90) REVERT: B 394 LEU cc_start: 0.8388 (tp) cc_final: 0.8165 (tp) REVERT: C 55 ARG cc_start: 0.3952 (mpt180) cc_final: 0.2853 (mmt-90) REVERT: C 394 LEU cc_start: 0.8399 (tp) cc_final: 0.8169 (tp) REVERT: D 55 ARG cc_start: 0.3949 (mpt180) cc_final: 0.2849 (mmt-90) REVERT: D 394 LEU cc_start: 0.8411 (tp) cc_final: 0.8180 (tp) outliers start: 48 outliers final: 20 residues processed: 258 average time/residue: 0.3267 time to fit residues: 131.4987 Evaluate side-chains 216 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 196 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 0.0060 chunk 144 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 217 optimal weight: 0.5980 chunk 176 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 229 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21804 Z= 0.219 Angle : 0.685 11.280 29584 Z= 0.367 Chirality : 0.045 0.379 3404 Planarity : 0.005 0.092 3668 Dihedral : 5.839 29.631 2864 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 1.07 % Allowed : 14.45 % Favored : 84.48 % Rotamer: Outliers : 2.44 % Allowed : 17.23 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.17), residues: 2616 helix: 0.82 (0.15), residues: 1172 sheet: -1.39 (0.57), residues: 104 loop : -3.70 (0.15), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 38 HIS 0.005 0.001 HIS B 539 PHE 0.013 0.001 PHE D 28 TYR 0.014 0.001 TYR C 368 ARG 0.002 0.000 ARG B 671 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 204 time to evaluate : 2.626 Fit side-chains REVERT: A 55 ARG cc_start: 0.3844 (mpt180) cc_final: 0.2673 (mmt-90) REVERT: A 394 LEU cc_start: 0.8419 (tp) cc_final: 0.8217 (tp) REVERT: B 55 ARG cc_start: 0.3849 (mpt180) cc_final: 0.2682 (mmt-90) REVERT: B 394 LEU cc_start: 0.8411 (tp) cc_final: 0.8179 (tp) REVERT: C 55 ARG cc_start: 0.3848 (mpt180) cc_final: 0.2675 (mmt-90) REVERT: C 394 LEU cc_start: 0.8427 (tp) cc_final: 0.8190 (tp) REVERT: D 55 ARG cc_start: 0.3844 (mpt180) cc_final: 0.2672 (mmt-90) REVERT: D 394 LEU cc_start: 0.8434 (tp) cc_final: 0.8199 (tp) outliers start: 58 outliers final: 38 residues processed: 254 average time/residue: 0.2964 time to fit residues: 121.9197 Evaluate side-chains 232 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 194 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 670 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 0.0570 chunk 229 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 255 optimal weight: 0.2980 chunk 212 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 overall best weight: 0.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21804 Z= 0.189 Angle : 0.663 10.890 29584 Z= 0.355 Chirality : 0.044 0.371 3404 Planarity : 0.005 0.089 3668 Dihedral : 5.720 29.244 2864 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 1.07 % Allowed : 12.84 % Favored : 86.09 % Rotamer: Outliers : 3.24 % Allowed : 16.93 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.17), residues: 2616 helix: 0.97 (0.15), residues: 1172 sheet: -1.20 (0.58), residues: 104 loop : -3.61 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 38 HIS 0.005 0.001 HIS B 539 PHE 0.013 0.001 PHE A 28 TYR 0.014 0.001 TYR D 368 ARG 0.003 0.000 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 196 time to evaluate : 2.611 Fit side-chains REVERT: A 55 ARG cc_start: 0.3777 (mpt180) cc_final: 0.2511 (mmt-90) REVERT: A 394 LEU cc_start: 0.8381 (tp) cc_final: 0.8149 (tp) REVERT: B 55 ARG cc_start: 0.3782 (mpt180) cc_final: 0.2518 (mmt-90) REVERT: B 394 LEU cc_start: 0.8373 (tp) cc_final: 0.8143 (tp) REVERT: C 55 ARG cc_start: 0.3777 (mpt180) cc_final: 0.2510 (mmt-90) REVERT: C 394 LEU cc_start: 0.8390 (tp) cc_final: 0.8152 (tp) REVERT: D 55 ARG cc_start: 0.3777 (mpt180) cc_final: 0.2505 (mmt-90) REVERT: D 394 LEU cc_start: 0.8398 (tp) cc_final: 0.8162 (tp) outliers start: 77 outliers final: 61 residues processed: 253 average time/residue: 0.2978 time to fit residues: 122.5211 Evaluate side-chains 249 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 188 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 670 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 186 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 215 optimal weight: 0.0570 chunk 142 optimal weight: 0.0570 chunk 254 optimal weight: 0.7980 chunk 159 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21804 Z= 0.185 Angle : 0.659 10.961 29584 Z= 0.353 Chirality : 0.043 0.371 3404 Planarity : 0.005 0.086 3668 Dihedral : 5.696 30.047 2864 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 1.07 % Allowed : 13.38 % Favored : 85.55 % Rotamer: Outliers : 2.61 % Allowed : 18.11 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.80 (0.17), residues: 2616 helix: 1.07 (0.15), residues: 1172 sheet: -1.22 (0.58), residues: 104 loop : -3.54 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 38 HIS 0.005 0.001 HIS A 539 PHE 0.013 0.001 PHE C 652 TYR 0.014 0.001 TYR C 368 ARG 0.002 0.000 ARG C 671 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 200 time to evaluate : 2.378 Fit side-chains REVERT: A 55 ARG cc_start: 0.3696 (mpt180) cc_final: 0.2587 (mmt-90) REVERT: A 394 LEU cc_start: 0.8368 (tp) cc_final: 0.8139 (tp) REVERT: A 427 MET cc_start: 0.8462 (mmt) cc_final: 0.8247 (mmt) REVERT: B 55 ARG cc_start: 0.3700 (mpt180) cc_final: 0.2590 (mmt-90) REVERT: B 394 LEU cc_start: 0.8362 (tp) cc_final: 0.8134 (tp) REVERT: B 427 MET cc_start: 0.8451 (mmt) cc_final: 0.8238 (mmt) REVERT: C 55 ARG cc_start: 0.3698 (mpt180) cc_final: 0.2588 (mmt-90) REVERT: C 394 LEU cc_start: 0.8388 (tp) cc_final: 0.8154 (tp) REVERT: C 427 MET cc_start: 0.8471 (mmt) cc_final: 0.8258 (mmt) REVERT: D 55 ARG cc_start: 0.3693 (mpt180) cc_final: 0.2582 (mmt-90) REVERT: D 394 LEU cc_start: 0.8385 (tp) cc_final: 0.8152 (tp) REVERT: D 427 MET cc_start: 0.8484 (mmt) cc_final: 0.8264 (mmt) outliers start: 62 outliers final: 50 residues processed: 242 average time/residue: 0.2902 time to fit residues: 113.9578 Evaluate side-chains 242 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 192 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 670 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.0980 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 49 optimal weight: 0.0770 chunk 161 optimal weight: 4.9990 chunk 173 optimal weight: 0.6980 chunk 125 optimal weight: 0.0060 chunk 23 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21804 Z= 0.186 Angle : 0.659 11.104 29584 Z= 0.354 Chirality : 0.044 0.372 3404 Planarity : 0.005 0.083 3668 Dihedral : 5.631 29.520 2864 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 1.07 % Allowed : 12.23 % Favored : 86.70 % Rotamer: Outliers : 2.77 % Allowed : 18.99 % Favored : 78.24 % 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: -1.72 (0.17), residues: 2616 helix: 1.11 (0.15), residues: 1184 sheet: -1.18 (0.58), residues: 104 loop : -3.50 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 38 HIS 0.005 0.001 HIS B 539 PHE 0.011 0.001 PHE B 28 TYR 0.013 0.001 TYR D 368 ARG 0.005 0.000 ARG B 677 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 198 time to evaluate : 2.528 Fit side-chains REVERT: A 55 ARG cc_start: 0.3798 (mpt180) cc_final: 0.2847 (mmt-90) REVERT: A 394 LEU cc_start: 0.8372 (tp) cc_final: 0.8136 (tp) REVERT: A 427 MET cc_start: 0.8556 (mmt) cc_final: 0.8313 (mmt) REVERT: B 55 ARG cc_start: 0.3799 (mpt180) cc_final: 0.2853 (mmt-90) REVERT: B 394 LEU cc_start: 0.8366 (tp) cc_final: 0.8130 (tp) REVERT: B 427 MET cc_start: 0.8549 (mmt) cc_final: 0.8309 (mmt) REVERT: C 55 ARG cc_start: 0.3795 (mpt180) cc_final: 0.2848 (mmt-90) REVERT: C 394 LEU cc_start: 0.8392 (tp) cc_final: 0.8151 (tp) REVERT: C 427 MET cc_start: 0.8566 (mmt) cc_final: 0.8325 (mmt) REVERT: D 55 ARG cc_start: 0.3793 (mpt180) cc_final: 0.2842 (mmt-90) REVERT: D 394 LEU cc_start: 0.8390 (tp) cc_final: 0.8150 (tp) REVERT: D 427 MET cc_start: 0.8578 (mmt) cc_final: 0.8332 (mmt) outliers start: 66 outliers final: 62 residues processed: 242 average time/residue: 0.2896 time to fit residues: 115.1186 Evaluate side-chains 254 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 192 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 670 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 142 optimal weight: 0.0570 chunk 103 optimal weight: 0.9990 chunk 186 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 214 optimal weight: 0.0870 chunk 224 optimal weight: 5.9990 chunk 236 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 HIS B 91 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 HIS C 91 ASN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 HIS D 91 ASN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21804 Z= 0.182 Angle : 0.649 10.892 29584 Z= 0.348 Chirality : 0.043 0.367 3404 Planarity : 0.005 0.080 3668 Dihedral : 5.607 29.142 2864 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 1.07 % Allowed : 13.00 % Favored : 85.93 % Rotamer: Outliers : 3.03 % Allowed : 18.66 % Favored : 78.32 % 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: -1.65 (0.17), residues: 2616 helix: 1.18 (0.15), residues: 1176 sheet: -1.10 (0.52), residues: 124 loop : -3.49 (0.16), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 38 HIS 0.005 0.001 HIS A 539 PHE 0.032 0.001 PHE B 28 TYR 0.013 0.001 TYR D 368 ARG 0.003 0.000 ARG D 677 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 204 time to evaluate : 2.355 Fit side-chains REVERT: A 55 ARG cc_start: 0.3734 (mpt180) cc_final: 0.2834 (mmt-90) REVERT: A 394 LEU cc_start: 0.8373 (tp) cc_final: 0.8132 (tp) REVERT: A 427 MET cc_start: 0.8517 (mmt) cc_final: 0.8290 (mmt) REVERT: B 55 ARG cc_start: 0.3738 (mpt180) cc_final: 0.2838 (mmt-90) REVERT: B 394 LEU cc_start: 0.8366 (tp) cc_final: 0.8124 (tp) REVERT: B 427 MET cc_start: 0.8510 (mmt) cc_final: 0.8282 (mmt) REVERT: C 55 ARG cc_start: 0.3735 (mpt180) cc_final: 0.2836 (mmt-90) REVERT: C 394 LEU cc_start: 0.8392 (tp) cc_final: 0.8149 (tp) REVERT: C 427 MET cc_start: 0.8526 (mmt) cc_final: 0.8299 (mmt) REVERT: D 55 ARG cc_start: 0.3733 (mpt180) cc_final: 0.2815 (mmt-90) REVERT: D 394 LEU cc_start: 0.8393 (tp) cc_final: 0.8149 (tp) REVERT: D 427 MET cc_start: 0.8541 (mmt) cc_final: 0.8308 (mmt) outliers start: 72 outliers final: 65 residues processed: 248 average time/residue: 0.2818 time to fit residues: 114.0635 Evaluate side-chains 269 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 204 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 670 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 174 optimal weight: 0.7980 chunk 263 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 21804 Z= 0.411 Angle : 0.798 12.129 29584 Z= 0.431 Chirality : 0.050 0.334 3404 Planarity : 0.005 0.067 3668 Dihedral : 6.105 27.633 2864 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.92 % Allowed : 14.37 % Favored : 84.71 % Rotamer: Outliers : 2.90 % Allowed : 18.78 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.17), residues: 2616 helix: 0.76 (0.15), residues: 1172 sheet: -1.44 (0.57), residues: 104 loop : -3.64 (0.15), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 217 HIS 0.006 0.001 HIS D 539 PHE 0.017 0.002 PHE D 464 TYR 0.022 0.002 TYR B 460 ARG 0.004 0.001 ARG D 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 215 time to evaluate : 2.455 Fit side-chains REVERT: A 55 ARG cc_start: 0.4532 (mpt180) cc_final: 0.2924 (mmt-90) REVERT: B 55 ARG cc_start: 0.4534 (mpt180) cc_final: 0.2930 (mmt-90) REVERT: C 55 ARG cc_start: 0.4525 (mpt180) cc_final: 0.2925 (mmt-90) REVERT: D 55 ARG cc_start: 0.4502 (mpt180) cc_final: 0.2905 (mmt-90) outliers start: 69 outliers final: 61 residues processed: 262 average time/residue: 0.2843 time to fit residues: 121.7498 Evaluate side-chains 263 residues out of total 2380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 202 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 670 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 2.9990 chunk 64 optimal weight: 0.0670 chunk 193 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 58 optimal weight: 0.0040 chunk 209 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 184 optimal weight: 0.0770 overall best weight: 0.3488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.226939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.204196 restraints weight = 28148.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.202985 restraints weight = 42083.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.199476 restraints weight = 35107.302| |-----------------------------------------------------------------------------| r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21804 Z= 0.175 Angle : 0.655 9.851 29584 Z= 0.351 Chirality : 0.043 0.291 3404 Planarity : 0.005 0.066 3668 Dihedral : 5.731 27.828 2864 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.92 % Allowed : 13.04 % Favored : 86.05 % Rotamer: Outliers : 1.93 % Allowed : 20.29 % Favored : 77.77 % 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: -1.86 (0.17), residues: 2616 helix: 1.02 (0.15), residues: 1164 sheet: -2.25 (0.49), residues: 136 loop : -3.46 (0.16), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 217 HIS 0.006 0.001 HIS A 539 PHE 0.013 0.001 PHE C 652 TYR 0.013 0.001 TYR A 368 ARG 0.004 0.000 ARG C 671 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3560.32 seconds wall clock time: 66 minutes 41.57 seconds (4001.57 seconds total)