Starting phenix.real_space_refine on Mon Mar 11 11:14:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i38_35145/03_2024/8i38_35145.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i38_35145/03_2024/8i38_35145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i38_35145/03_2024/8i38_35145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i38_35145/03_2024/8i38_35145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i38_35145/03_2024/8i38_35145.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i38_35145/03_2024/8i38_35145.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.123 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 5306 2.51 5 N 1354 2.21 5 O 1412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A ASP 231": "OD1" <-> "OD2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 276": "OD1" <-> "OD2" Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 492": "OE1" <-> "OE2" Residue "A PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 598": "OE1" <-> "OE2" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 659": "NH1" <-> "NH2" Residue "B PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 220": "OE1" <-> "OE2" Residue "B ASP 231": "OD1" <-> "OD2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "B PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 276": "OD1" <-> "OD2" Residue "B PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 492": "OE1" <-> "OE2" Residue "B PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 598": "OE1" <-> "OE2" Residue "B GLU 628": "OE1" <-> "OE2" Residue "B PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 659": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8122 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4061 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 17, 'TRANS': 503} Chain breaks: 3 Chain: "B" Number of atoms: 4061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4061 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 17, 'TRANS': 503} Chain breaks: 3 Time building chain proxies: 4.57, per 1000 atoms: 0.56 Number of scatterers: 8122 At special positions: 0 Unit cell: (88.54, 90.404, 122.092, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1412 8.00 N 1354 7.00 C 5306 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: 2.70 Conformation dependent library (CDL) restraints added in 1.4 seconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 52.0% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 106 through 115 Processing helix chain 'A' and resid 156 through 169 removed outlier: 3.719A pdb=" N VAL A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 185 removed outlier: 5.616A pdb=" N ALA A 182 " --> pdb=" O LYS A 178 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 removed outlier: 3.512A pdb=" N SER A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 255 removed outlier: 3.803A pdb=" N ALA A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 294 through 300 removed outlier: 3.547A pdb=" N TYR A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 322 removed outlier: 3.648A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 397 removed outlier: 3.511A pdb=" N LEU A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 removed outlier: 3.713A pdb=" N GLU A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 405' Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.728A pdb=" N ALA A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 438 removed outlier: 3.552A pdb=" N GLY A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 455 removed outlier: 3.626A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 472 Processing helix chain 'A' and resid 477 through 492 removed outlier: 4.383A pdb=" N SER A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 503 Processing helix chain 'A' and resid 512 through 541 removed outlier: 3.938A pdb=" N LEU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 555 removed outlier: 3.513A pdb=" N THR A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 580 through 594 removed outlier: 4.315A pdb=" N TYR A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 605 Processing helix chain 'A' and resid 643 through 657 removed outlier: 3.678A pdb=" N TYR A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 156 through 169 removed outlier: 3.718A pdb=" N VAL B 164 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 169 " --> pdb=" O ALA B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 185 removed outlier: 5.616A pdb=" N ALA B 182 " --> pdb=" O LYS B 178 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 219 removed outlier: 3.512A pdb=" N SER B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 255 removed outlier: 3.803A pdb=" N ALA B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 273 Processing helix chain 'B' and resid 294 through 300 removed outlier: 3.547A pdb=" N TYR B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 322 removed outlier: 3.648A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP B 318 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 removed outlier: 3.511A pdb=" N LEU B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 removed outlier: 3.713A pdb=" N GLU B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 400 through 405' Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.728A pdb=" N ALA B 417 " --> pdb=" O GLN B 413 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP B 425 " --> pdb=" O CYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 438 removed outlier: 3.553A pdb=" N GLY B 438 " --> pdb=" O HIS B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 455 removed outlier: 3.626A pdb=" N SER B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 462 through 472 Processing helix chain 'B' and resid 477 through 492 removed outlier: 4.383A pdb=" N SER B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU B 492 " --> pdb=" O SER B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 503 Processing helix chain 'B' and resid 512 through 541 removed outlier: 3.937A pdb=" N LEU B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 555 removed outlier: 3.512A pdb=" N THR B 549 " --> pdb=" O LYS B 545 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR B 552 " --> pdb=" O SER B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 580 through 594 removed outlier: 4.315A pdb=" N TYR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS B 585 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 605 Processing helix chain 'B' and resid 643 through 657 removed outlier: 3.678A pdb=" N TYR B 649 " --> pdb=" O MET B 645 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 90 removed outlier: 6.923A pdb=" N THR A 88 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL A 43 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N MET A 90 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS A 41 " --> pdb=" O MET A 90 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ASP A 44 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LYS A 126 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 124 " --> pdb=" O CYS A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 229 removed outlier: 6.142A pdb=" N LEU A 228 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 290 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 85 through 90 removed outlier: 6.923A pdb=" N THR B 88 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL B 43 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N MET B 90 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS B 41 " --> pdb=" O MET B 90 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ASP B 44 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LYS B 126 " --> pdb=" O ASP B 44 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR B 124 " --> pdb=" O CYS B 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 227 through 229 removed outlier: 6.141A pdb=" N LEU B 228 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY B 290 " --> pdb=" O VAL B 278 " (cutoff:3.500A) 316 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1256 1.32 - 1.45: 2324 1.45 - 1.58: 4629 1.58 - 1.71: 3 1.71 - 1.84: 84 Bond restraints: 8296 Sorted by residual: bond pdb=" CA SER A 85 " pdb=" C SER A 85 " ideal model delta sigma weight residual 1.523 1.456 0.067 1.61e-02 3.86e+03 1.72e+01 bond pdb=" CA THR A 88 " pdb=" C THR A 88 " ideal model delta sigma weight residual 1.521 1.467 0.054 1.30e-02 5.92e+03 1.70e+01 bond pdb=" CA SER B 85 " pdb=" C SER B 85 " ideal model delta sigma weight residual 1.523 1.456 0.066 1.61e-02 3.86e+03 1.70e+01 bond pdb=" CA THR B 88 " pdb=" C THR B 88 " ideal model delta sigma weight residual 1.521 1.468 0.053 1.30e-02 5.92e+03 1.65e+01 bond pdb=" N SER A 85 " pdb=" CA SER A 85 " ideal model delta sigma weight residual 1.460 1.404 0.056 1.45e-02 4.76e+03 1.49e+01 ... (remaining 8291 not shown) Histogram of bond angle deviations from ideal: 87.61 - 96.91: 2 96.91 - 106.22: 203 106.22 - 115.52: 5043 115.52 - 124.82: 5850 124.82 - 134.13: 140 Bond angle restraints: 11238 Sorted by residual: angle pdb=" N SER B 85 " pdb=" CA SER B 85 " pdb=" C SER B 85 " ideal model delta sigma weight residual 110.44 87.61 22.83 1.20e+00 6.94e-01 3.62e+02 angle pdb=" N SER A 85 " pdb=" CA SER A 85 " pdb=" C SER A 85 " ideal model delta sigma weight residual 110.44 87.62 22.82 1.20e+00 6.94e-01 3.62e+02 angle pdb=" CA GLU B 599 " pdb=" CB GLU B 599 " pdb=" CG GLU B 599 " ideal model delta sigma weight residual 114.10 128.46 -14.36 2.00e+00 2.50e-01 5.15e+01 angle pdb=" CA GLU A 599 " pdb=" CB GLU A 599 " pdb=" CG GLU A 599 " ideal model delta sigma weight residual 114.10 128.42 -14.32 2.00e+00 2.50e-01 5.13e+01 angle pdb=" N VAL B 87 " pdb=" CA VAL B 87 " pdb=" C VAL B 87 " ideal model delta sigma weight residual 109.34 124.15 -14.81 2.08e+00 2.31e-01 5.07e+01 ... (remaining 11233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 4437 16.60 - 33.20: 347 33.20 - 49.80: 62 49.80 - 66.40: 18 66.40 - 83.00: 4 Dihedral angle restraints: 4868 sinusoidal: 1892 harmonic: 2976 Sorted by residual: dihedral pdb=" C VAL A 87 " pdb=" N VAL A 87 " pdb=" CA VAL A 87 " pdb=" CB VAL A 87 " ideal model delta harmonic sigma weight residual -122.00 -149.46 27.46 0 2.50e+00 1.60e-01 1.21e+02 dihedral pdb=" C VAL B 87 " pdb=" N VAL B 87 " pdb=" CA VAL B 87 " pdb=" CB VAL B 87 " ideal model delta harmonic sigma weight residual -122.00 -149.40 27.40 0 2.50e+00 1.60e-01 1.20e+02 dihedral pdb=" N VAL A 87 " pdb=" C VAL A 87 " pdb=" CA VAL A 87 " pdb=" CB VAL A 87 " ideal model delta harmonic sigma weight residual 123.40 148.99 -25.59 0 2.50e+00 1.60e-01 1.05e+02 ... (remaining 4865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.229: 1322 0.229 - 0.458: 4 0.458 - 0.687: 0 0.687 - 0.916: 0 0.916 - 1.145: 2 Chirality restraints: 1328 Sorted by residual: chirality pdb=" CA VAL A 87 " pdb=" N VAL A 87 " pdb=" C VAL A 87 " pdb=" CB VAL A 87 " both_signs ideal model delta sigma weight residual False 2.44 1.30 1.14 2.00e-01 2.50e+01 3.28e+01 chirality pdb=" CA VAL B 87 " pdb=" N VAL B 87 " pdb=" C VAL B 87 " pdb=" CB VAL B 87 " both_signs ideal model delta sigma weight residual False 2.44 1.30 1.14 2.00e-01 2.50e+01 3.27e+01 chirality pdb=" CB THR A 142 " pdb=" CA THR A 142 " pdb=" OG1 THR A 142 " pdb=" CG2 THR A 142 " both_signs ideal model delta sigma weight residual False 2.55 2.19 0.36 2.00e-01 2.50e+01 3.26e+00 ... (remaining 1325 not shown) Planarity restraints: 1378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 459 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO A 460 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 460 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 460 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 459 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO B 460 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 460 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 460 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 84 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.43e+00 pdb=" C LEU B 84 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU B 84 " 0.014 2.00e-02 2.50e+03 pdb=" N SER B 85 " 0.012 2.00e-02 2.50e+03 ... (remaining 1375 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 71 2.56 - 3.15: 5824 3.15 - 3.73: 12120 3.73 - 4.32: 17946 4.32 - 4.90: 29069 Nonbonded interactions: 65030 Sorted by model distance: nonbonded pdb=" O GLY A 631 " pdb=" OD1 ASP A 632 " model vdw 1.981 3.040 nonbonded pdb=" O GLY B 631 " pdb=" OD1 ASP B 632 " model vdw 1.981 3.040 nonbonded pdb=" OH TYR A 47 " pdb=" CG2 VAL A 49 " model vdw 2.089 3.460 nonbonded pdb=" OH TYR B 47 " pdb=" CG2 VAL B 49 " model vdw 2.090 3.460 nonbonded pdb=" O MET B 645 " pdb=" CD2 TYR B 649 " model vdw 2.143 3.340 ... (remaining 65025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 5.070 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.720 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 8296 Z= 0.372 Angle : 1.197 22.833 11238 Z= 0.719 Chirality : 0.071 1.145 1328 Planarity : 0.007 0.053 1378 Dihedral : 12.795 83.001 2960 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.77 % Favored : 91.03 % Rotamer: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Cbeta Deviations : 0.42 % 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: -6.34 (0.17), residues: 1026 helix: -4.65 (0.09), residues: 602 sheet: -3.32 (0.52), residues: 70 loop : -3.07 (0.27), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 425 HIS 0.005 0.002 HIS A 395 PHE 0.014 0.002 PHE A 308 TYR 0.011 0.002 TYR B 594 ARG 0.004 0.001 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.861 Fit side-chains REVERT: A 219 HIS cc_start: 0.6604 (m170) cc_final: 0.5250 (t-90) REVERT: A 220 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7008 (mp0) REVERT: B 220 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7218 (mp0) REVERT: B 232 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7523 (mp0) REVERT: B 244 ARG cc_start: 0.5489 (mtm180) cc_final: 0.5076 (mtm180) outliers start: 0 outliers final: 1 residues processed: 141 average time/residue: 1.1257 time to fit residues: 168.7047 Evaluate side-chains 104 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 632 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 0.0770 chunk 94 optimal weight: 0.6980 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN A 395 HIS A 403 HIS B 266 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8296 Z= 0.220 Angle : 0.643 6.679 11238 Z= 0.328 Chirality : 0.041 0.132 1328 Planarity : 0.005 0.042 1378 Dihedral : 5.894 47.881 1130 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.21 % Favored : 92.59 % Rotamer: Outliers : 3.29 % Allowed : 11.68 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.55 (0.22), residues: 1026 helix: -3.01 (0.16), residues: 624 sheet: -2.87 (0.57), residues: 70 loop : -2.58 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 426 HIS 0.008 0.001 HIS A 395 PHE 0.010 0.001 PHE A 308 TYR 0.017 0.002 TYR B 47 ARG 0.003 0.000 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 0.801 Fit side-chains REVERT: A 90 MET cc_start: 0.5927 (OUTLIER) cc_final: 0.4670 (mpp) REVERT: A 219 HIS cc_start: 0.6670 (m170) cc_final: 0.5440 (t70) REVERT: A 220 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7353 (mm-30) REVERT: A 424 MET cc_start: 0.7501 (mmm) cc_final: 0.7296 (mmm) REVERT: B 219 HIS cc_start: 0.6861 (m170) cc_final: 0.5338 (t70) REVERT: B 220 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7440 (mm-30) REVERT: B 232 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7425 (mp0) REVERT: B 244 ARG cc_start: 0.4957 (mtm180) cc_final: 0.4689 (mtm180) REVERT: B 274 MET cc_start: 0.4540 (OUTLIER) cc_final: 0.4197 (mpt) outliers start: 29 outliers final: 7 residues processed: 124 average time/residue: 1.1033 time to fit residues: 146.1405 Evaluate side-chains 106 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 571 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 93 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8296 Z= 0.214 Angle : 0.595 8.192 11238 Z= 0.301 Chirality : 0.041 0.136 1328 Planarity : 0.004 0.043 1378 Dihedral : 5.232 21.894 1128 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.12 % Favored : 92.69 % Rotamer: Outliers : 4.08 % Allowed : 13.38 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.24), residues: 1026 helix: -2.09 (0.19), residues: 636 sheet: -2.54 (0.59), residues: 70 loop : -2.44 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 425 HIS 0.005 0.001 HIS B 484 PHE 0.010 0.001 PHE A 387 TYR 0.018 0.002 TYR A 649 ARG 0.002 0.000 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 101 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.5969 (OUTLIER) cc_final: 0.4838 (mpp) REVERT: A 219 HIS cc_start: 0.6647 (m170) cc_final: 0.5335 (t70) REVERT: A 220 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7383 (mm-30) REVERT: A 279 LEU cc_start: 0.7198 (tt) cc_final: 0.6988 (tp) REVERT: A 645 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.6927 (mtt) REVERT: B 193 LYS cc_start: 0.8219 (tttm) cc_final: 0.7810 (mmpt) REVERT: B 219 HIS cc_start: 0.6778 (m170) cc_final: 0.5346 (t70) REVERT: B 220 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7470 (mm-30) REVERT: B 232 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7532 (mp0) REVERT: B 274 MET cc_start: 0.4765 (OUTLIER) cc_final: 0.4514 (mmt) REVERT: B 387 PHE cc_start: 0.7143 (m-80) cc_final: 0.6890 (m-80) REVERT: B 645 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.6966 (mtt) outliers start: 36 outliers final: 10 residues processed: 117 average time/residue: 1.1857 time to fit residues: 147.5992 Evaluate side-chains 110 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 645 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 49 optimal weight: 0.0270 chunk 10 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 94 optimal weight: 0.5980 chunk 100 optimal weight: 9.9990 chunk 89 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 GLN B 273 GLN B 413 GLN B 454 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8296 Z= 0.178 Angle : 0.557 7.111 11238 Z= 0.281 Chirality : 0.040 0.137 1328 Planarity : 0.004 0.041 1378 Dihedral : 4.922 23.950 1128 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.50 % Favored : 92.30 % Rotamer: Outliers : 3.40 % Allowed : 14.97 % Favored : 81.63 % 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: -2.69 (0.26), residues: 1026 helix: -1.41 (0.20), residues: 618 sheet: -2.42 (0.60), residues: 70 loop : -2.02 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 425 HIS 0.004 0.001 HIS B 484 PHE 0.014 0.001 PHE A 406 TYR 0.011 0.001 TYR A 649 ARG 0.002 0.000 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 101 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.6205 (OUTLIER) cc_final: 0.5012 (mpp) REVERT: A 97 MET cc_start: 0.6280 (OUTLIER) cc_final: 0.6037 (tpt) REVERT: A 205 ARG cc_start: 0.7873 (mmm-85) cc_final: 0.7616 (mmm-85) REVERT: A 219 HIS cc_start: 0.6598 (m170) cc_final: 0.5338 (t70) REVERT: A 220 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7486 (mm-30) REVERT: A 645 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6978 (mtt) REVERT: B 205 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7517 (mmm-85) REVERT: B 219 HIS cc_start: 0.6720 (m170) cc_final: 0.5312 (t70) REVERT: B 220 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7427 (mm-30) REVERT: B 232 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7566 (mp0) REVERT: B 274 MET cc_start: 0.4678 (OUTLIER) cc_final: 0.4434 (mmt) REVERT: B 645 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.6980 (mtt) outliers start: 30 outliers final: 9 residues processed: 113 average time/residue: 1.2354 time to fit residues: 148.4406 Evaluate side-chains 109 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 645 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 51 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN B 266 GLN B 413 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8296 Z= 0.270 Angle : 0.612 6.475 11238 Z= 0.306 Chirality : 0.043 0.141 1328 Planarity : 0.004 0.042 1378 Dihedral : 5.036 22.788 1128 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.09 % Favored : 91.72 % Rotamer: Outliers : 3.06 % Allowed : 15.65 % Favored : 81.29 % 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: -2.53 (0.26), residues: 1026 helix: -1.33 (0.20), residues: 618 sheet: -2.43 (0.60), residues: 70 loop : -1.85 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 425 HIS 0.005 0.001 HIS A 484 PHE 0.012 0.001 PHE B 406 TYR 0.013 0.002 TYR A 649 ARG 0.003 0.000 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.6311 (OUTLIER) cc_final: 0.5480 (mpp) REVERT: A 95 GLU cc_start: 0.6020 (mt-10) cc_final: 0.4517 (mp0) REVERT: A 211 GLU cc_start: 0.6349 (mt-10) cc_final: 0.5891 (mt-10) REVERT: A 219 HIS cc_start: 0.6731 (m170) cc_final: 0.5291 (t-170) REVERT: A 220 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7633 (mm-30) REVERT: A 645 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.7026 (mtt) REVERT: B 40 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.5976 (tp) REVERT: B 193 LYS cc_start: 0.8266 (tttm) cc_final: 0.7879 (mmpt) REVERT: B 219 HIS cc_start: 0.6801 (m170) cc_final: 0.5344 (t70) REVERT: B 220 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7610 (mm-30) REVERT: B 232 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7557 (mp0) REVERT: B 576 MET cc_start: 0.6869 (OUTLIER) cc_final: 0.6545 (tpp) REVERT: B 645 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.7045 (mtt) outliers start: 27 outliers final: 8 residues processed: 111 average time/residue: 1.2317 time to fit residues: 145.1710 Evaluate side-chains 104 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 645 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 97 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8296 Z= 0.268 Angle : 0.600 6.246 11238 Z= 0.300 Chirality : 0.043 0.147 1328 Planarity : 0.004 0.041 1378 Dihedral : 4.998 23.332 1128 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.09 % Favored : 91.72 % Rotamer: Outliers : 3.74 % Allowed : 16.78 % Favored : 79.48 % 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: -2.44 (0.26), residues: 1026 helix: -1.29 (0.20), residues: 616 sheet: -1.89 (0.54), residues: 90 loop : -1.81 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 425 HIS 0.005 0.001 HIS A 484 PHE 0.012 0.001 PHE B 387 TYR 0.012 0.002 TYR B 649 ARG 0.002 0.000 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 89 time to evaluate : 0.850 Fit side-chains REVERT: A 90 MET cc_start: 0.6463 (OUTLIER) cc_final: 0.5567 (mpp) REVERT: A 95 GLU cc_start: 0.6033 (mt-10) cc_final: 0.4515 (mp0) REVERT: A 97 MET cc_start: 0.6215 (OUTLIER) cc_final: 0.5718 (tpt) REVERT: A 211 GLU cc_start: 0.6334 (mt-10) cc_final: 0.5848 (mt-10) REVERT: A 219 HIS cc_start: 0.6772 (m170) cc_final: 0.5323 (t-170) REVERT: A 220 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7588 (mm-30) REVERT: A 274 MET cc_start: 0.4692 (mpm) cc_final: 0.4474 (mpp) REVERT: A 280 LEU cc_start: 0.6086 (OUTLIER) cc_final: 0.5518 (mt) REVERT: A 645 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.7053 (mtt) REVERT: B 40 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.6189 (tp) REVERT: B 193 LYS cc_start: 0.8321 (tttm) cc_final: 0.7901 (mmpt) REVERT: B 205 ARG cc_start: 0.7720 (mmm-85) cc_final: 0.7459 (mmm-85) REVERT: B 219 HIS cc_start: 0.6794 (m170) cc_final: 0.5343 (t-170) REVERT: B 220 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7668 (mm-30) REVERT: B 258 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7838 (mttm) REVERT: B 576 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6563 (tpp) REVERT: B 645 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.7042 (mtt) outliers start: 33 outliers final: 8 residues processed: 107 average time/residue: 1.1917 time to fit residues: 135.8082 Evaluate side-chains 101 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 645 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 84 optimal weight: 0.3980 chunk 100 optimal weight: 8.9990 chunk 62 optimal weight: 0.0670 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8296 Z= 0.191 Angle : 0.559 6.525 11238 Z= 0.279 Chirality : 0.041 0.139 1328 Planarity : 0.004 0.042 1378 Dihedral : 4.800 23.421 1128 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.99 % Favored : 91.81 % Rotamer: Outliers : 3.51 % Allowed : 17.46 % Favored : 79.02 % 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: -2.05 (0.26), residues: 1026 helix: -0.98 (0.21), residues: 622 sheet: -1.75 (0.63), residues: 60 loop : -1.72 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 425 HIS 0.004 0.001 HIS A 484 PHE 0.015 0.001 PHE B 406 TYR 0.008 0.001 TYR A 649 ARG 0.002 0.000 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 90 time to evaluate : 0.891 Fit side-chains REVERT: A 90 MET cc_start: 0.6489 (OUTLIER) cc_final: 0.5572 (mpp) REVERT: A 95 GLU cc_start: 0.6031 (mt-10) cc_final: 0.4520 (mp0) REVERT: A 97 MET cc_start: 0.6273 (OUTLIER) cc_final: 0.5809 (tpt) REVERT: A 193 LYS cc_start: 0.8163 (ttpp) cc_final: 0.7831 (mmpt) REVERT: A 208 SER cc_start: 0.6449 (OUTLIER) cc_final: 0.6207 (p) REVERT: A 211 GLU cc_start: 0.6192 (mt-10) cc_final: 0.5829 (mt-10) REVERT: A 219 HIS cc_start: 0.6648 (m170) cc_final: 0.5320 (t70) REVERT: A 220 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7542 (mm-30) REVERT: A 274 MET cc_start: 0.4674 (mpm) cc_final: 0.4458 (mpp) REVERT: A 645 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.7090 (mtt) REVERT: B 97 MET cc_start: 0.6217 (tpp) cc_final: 0.5772 (tpt) REVERT: B 193 LYS cc_start: 0.8344 (tttm) cc_final: 0.7905 (mmpt) REVERT: B 205 ARG cc_start: 0.7710 (mmm-85) cc_final: 0.7425 (mmm-85) REVERT: B 219 HIS cc_start: 0.6701 (m170) cc_final: 0.5327 (t-170) REVERT: B 220 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7503 (mm-30) REVERT: B 576 MET cc_start: 0.6891 (OUTLIER) cc_final: 0.6545 (tpp) REVERT: B 645 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.7085 (mtt) outliers start: 31 outliers final: 10 residues processed: 104 average time/residue: 1.1327 time to fit residues: 125.8602 Evaluate side-chains 102 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 645 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 49 optimal weight: 0.1980 chunk 9 optimal weight: 0.1980 chunk 78 optimal weight: 0.0000 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8296 Z= 0.139 Angle : 0.555 9.313 11238 Z= 0.271 Chirality : 0.040 0.145 1328 Planarity : 0.003 0.041 1378 Dihedral : 4.546 24.079 1128 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.50 % Favored : 92.30 % Rotamer: Outliers : 2.83 % Allowed : 18.25 % Favored : 78.91 % 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: -1.60 (0.27), residues: 1026 helix: -0.56 (0.21), residues: 612 sheet: -1.59 (0.64), residues: 60 loop : -1.65 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 425 HIS 0.004 0.001 HIS A 484 PHE 0.012 0.001 PHE B 406 TYR 0.006 0.001 TYR A 649 ARG 0.002 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 0.916 Fit side-chains REVERT: A 90 MET cc_start: 0.6438 (OUTLIER) cc_final: 0.5520 (mpp) REVERT: A 95 GLU cc_start: 0.5916 (mt-10) cc_final: 0.4551 (mp0) REVERT: A 97 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.5866 (tpt) REVERT: A 193 LYS cc_start: 0.8150 (ttpp) cc_final: 0.7792 (mmpt) REVERT: A 195 GLU cc_start: 0.6212 (tt0) cc_final: 0.5948 (tt0) REVERT: A 211 GLU cc_start: 0.6055 (mt-10) cc_final: 0.5713 (mt-10) REVERT: A 220 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7433 (mm-30) REVERT: B 97 MET cc_start: 0.6259 (OUTLIER) cc_final: 0.5783 (tpt) REVERT: B 188 GLU cc_start: 0.6579 (tt0) cc_final: 0.6326 (tt0) REVERT: B 205 ARG cc_start: 0.7764 (mmm-85) cc_final: 0.7472 (mmm-85) REVERT: B 220 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7467 (mm-30) REVERT: B 576 MET cc_start: 0.6891 (OUTLIER) cc_final: 0.6531 (tpp) outliers start: 25 outliers final: 12 residues processed: 105 average time/residue: 1.1551 time to fit residues: 129.4034 Evaluate side-chains 100 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 576 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 60 optimal weight: 0.0570 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 484 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8296 Z= 0.161 Angle : 0.565 9.068 11238 Z= 0.274 Chirality : 0.041 0.144 1328 Planarity : 0.003 0.043 1378 Dihedral : 4.510 23.874 1128 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.21 % Favored : 92.59 % Rotamer: Outliers : 2.27 % Allowed : 19.39 % Favored : 78.34 % 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: -1.35 (0.27), residues: 1026 helix: -0.35 (0.21), residues: 612 sheet: -1.42 (0.66), residues: 60 loop : -1.59 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 425 HIS 0.004 0.001 HIS A 484 PHE 0.007 0.001 PHE A 646 TYR 0.006 0.001 TYR B 480 ARG 0.002 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.843 Fit side-chains REVERT: A 90 MET cc_start: 0.6345 (OUTLIER) cc_final: 0.5618 (mpp) REVERT: A 95 GLU cc_start: 0.5851 (mt-10) cc_final: 0.4509 (mp0) REVERT: A 97 MET cc_start: 0.6391 (OUTLIER) cc_final: 0.5968 (tpt) REVERT: A 211 GLU cc_start: 0.6173 (mt-10) cc_final: 0.5850 (mt-10) REVERT: A 220 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7448 (mm-30) REVERT: B 97 MET cc_start: 0.6231 (OUTLIER) cc_final: 0.5802 (tpt) REVERT: B 205 ARG cc_start: 0.7782 (mmm-85) cc_final: 0.7511 (mmm-85) REVERT: B 220 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7409 (mm-30) REVERT: B 274 MET cc_start: 0.4356 (mmt) cc_final: 0.4063 (mpm) REVERT: B 576 MET cc_start: 0.6876 (OUTLIER) cc_final: 0.6488 (tpp) outliers start: 20 outliers final: 13 residues processed: 102 average time/residue: 1.3019 time to fit residues: 141.8386 Evaluate side-chains 104 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 576 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.5980 chunk 68 optimal weight: 0.4980 chunk 103 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 8 optimal weight: 0.0270 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8296 Z= 0.152 Angle : 0.565 8.880 11238 Z= 0.274 Chirality : 0.041 0.146 1328 Planarity : 0.003 0.043 1378 Dihedral : 4.450 24.172 1128 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.31 % Favored : 92.50 % Rotamer: Outliers : 2.04 % Allowed : 20.52 % Favored : 77.44 % 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: -1.11 (0.27), residues: 1026 helix: -0.14 (0.22), residues: 612 sheet: -1.26 (0.67), residues: 60 loop : -1.54 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 425 HIS 0.003 0.001 HIS A 484 PHE 0.023 0.001 PHE B 406 TYR 0.007 0.001 TYR B 480 ARG 0.002 0.000 ARG A 244 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 0.920 Fit side-chains REVERT: A 90 MET cc_start: 0.6364 (OUTLIER) cc_final: 0.5693 (mpp) REVERT: A 95 GLU cc_start: 0.5880 (mt-10) cc_final: 0.4526 (mp0) REVERT: A 97 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.5863 (tpt) REVERT: A 195 GLU cc_start: 0.6316 (tt0) cc_final: 0.6062 (tt0) REVERT: A 211 GLU cc_start: 0.6152 (mt-10) cc_final: 0.5863 (mt-10) REVERT: A 220 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7414 (mm-30) REVERT: A 310 MET cc_start: 0.6298 (ttm) cc_final: 0.6090 (ttm) REVERT: B 40 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.6076 (tp) REVERT: B 97 MET cc_start: 0.6241 (OUTLIER) cc_final: 0.5818 (tpt) REVERT: B 188 GLU cc_start: 0.6614 (tt0) cc_final: 0.6378 (tt0) REVERT: B 205 ARG cc_start: 0.7776 (mmm-85) cc_final: 0.7501 (mmm-85) REVERT: B 220 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7486 (mm-30) REVERT: B 274 MET cc_start: 0.4381 (mmt) cc_final: 0.4096 (mpm) REVERT: B 576 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6433 (tpp) outliers start: 18 outliers final: 11 residues processed: 102 average time/residue: 1.2717 time to fit residues: 137.6335 Evaluate side-chains 102 residues out of total 882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 576 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 484 HIS ** 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 = 0.4207 r_free = 0.4207 target = 0.194663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.128878 restraints weight = 7649.060| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.81 r_work: 0.3324 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8296 Z= 0.245 Angle : 0.617 8.813 11238 Z= 0.299 Chirality : 0.043 0.140 1328 Planarity : 0.004 0.042 1378 Dihedral : 4.682 23.831 1128 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.31 % Favored : 92.50 % Rotamer: Outliers : 2.15 % Allowed : 19.95 % Favored : 77.89 % 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: -1.33 (0.27), residues: 1026 helix: -0.38 (0.21), residues: 624 sheet: -0.97 (0.57), residues: 80 loop : -1.61 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 425 HIS 0.004 0.001 HIS A 484 PHE 0.020 0.001 PHE A 406 TYR 0.008 0.001 TYR B 649 ARG 0.003 0.000 ARG B 410 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3111.61 seconds wall clock time: 56 minutes 2.93 seconds (3362.93 seconds total)