Starting phenix.real_space_refine on Sat Feb 17 23:06:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xeu_33159/02_2024/7xeu_33159_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xeu_33159/02_2024/7xeu_33159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xeu_33159/02_2024/7xeu_33159.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xeu_33159/02_2024/7xeu_33159.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xeu_33159/02_2024/7xeu_33159_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xeu_33159/02_2024/7xeu_33159_updated.pdb" } resolution = 2.77 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= 0.000 sd= 0.003 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 108 5.16 5 C 13172 2.51 5 N 3372 2.21 5 O 3440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 140": "OD1" <-> "OD2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 327": "OE1" <-> "OE2" Residue "B GLU 353": "OE1" <-> "OE2" Residue "B TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 594": "OE1" <-> "OE2" Residue "B TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 696": "OE1" <-> "OE2" Residue "C ASP 140": "OD1" <-> "OD2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 284": "OD1" <-> "OD2" Residue "C GLU 353": "OE1" <-> "OE2" Residue "C TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 140": "OD1" <-> "OD2" Residue "D TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 300": "OE1" <-> "OE2" Residue "D TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 665": "OE1" <-> "OE2" Residue "D GLU 696": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20092 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4995 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "B" Number of atoms: 4995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4995 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "C" Number of atoms: 4995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4995 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "D" Number of atoms: 4995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4995 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.03, per 1000 atoms: 0.55 Number of scatterers: 20092 At special positions: 0 Unit cell: (158.184, 157.17, 118.638, 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 108 16.00 O 3440 8.00 N 3372 7.00 C 13172 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: 7.39 Conformation dependent library (CDL) restraints added in 3.3 seconds 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 4 sheets defined 53.6% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.07 Creating SS restraints... Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 84 through 87 Processing helix chain 'A' and resid 90 through 97 removed outlier: 3.599A pdb=" N THR A 97 " --> pdb=" O TYR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 130 through 139 removed outlier: 3.747A pdb=" N LEU A 134 " --> pdb=" O CYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 172 through 180 Processing helix chain 'A' and resid 208 through 215 Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.739A pdb=" N LEU A 225 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 256 through 276 removed outlier: 3.792A pdb=" N ALA A 260 " --> pdb=" O PRO A 256 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 351 through 357 Processing helix chain 'A' and resid 374 through 407 Proline residue: A 386 - end of helix Processing helix chain 'A' and resid 424 through 453 Processing helix chain 'A' and resid 455 through 460 removed outlier: 3.998A pdb=" N ILE A 458 " --> pdb=" O ARG A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 485 Processing helix chain 'A' and resid 492 through 509 removed outlier: 4.308A pdb=" N LEU A 508 " --> pdb=" O TRP A 504 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TYR A 509 " --> pdb=" O LEU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 531 removed outlier: 3.531A pdb=" N TYR A 520 " --> pdb=" O HIS A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 552 Processing helix chain 'A' and resid 588 through 598 removed outlier: 3.929A pdb=" N PHE A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 628 Processing helix chain 'A' and resid 632 through 646 Processing helix chain 'A' and resid 650 through 667 Processing helix chain 'A' and resid 708 through 713 removed outlier: 3.961A pdb=" N LYS A 712 " --> pdb=" O ALA A 708 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR A 713 " --> pdb=" O ALA A 709 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 708 through 713' Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 84 through 87 Processing helix chain 'B' and resid 90 through 97 removed outlier: 3.803A pdb=" N THR B 97 " --> pdb=" O TYR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 172 through 180 Processing helix chain 'B' and resid 208 through 215 Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.700A pdb=" N LEU B 225 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 250 Processing helix chain 'B' and resid 256 through 276 removed outlier: 3.637A pdb=" N ALA B 260 " --> pdb=" O PRO B 256 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 276 " --> pdb=" O MET B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 284 No H-bonds generated for 'chain 'B' and resid 282 through 284' Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 303 through 310 Processing helix chain 'B' and resid 351 through 357 Processing helix chain 'B' and resid 375 through 407 Proline residue: B 386 - end of helix Processing helix chain 'B' and resid 424 through 453 Processing helix chain 'B' and resid 455 through 460 removed outlier: 4.000A pdb=" N ILE B 458 " --> pdb=" O ARG B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 485 Processing helix chain 'B' and resid 492 through 509 removed outlier: 4.222A pdb=" N LEU B 508 " --> pdb=" O TRP B 504 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N TYR B 509 " --> pdb=" O LEU B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 531 removed outlier: 3.532A pdb=" N TYR B 520 " --> pdb=" O HIS B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 552 Processing helix chain 'B' and resid 588 through 598 removed outlier: 3.925A pdb=" N PHE B 598 " --> pdb=" O GLU B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 628 Processing helix chain 'B' and resid 632 through 646 Processing helix chain 'B' and resid 650 through 667 Processing helix chain 'B' and resid 708 through 713 removed outlier: 3.827A pdb=" N LYS B 712 " --> pdb=" O ALA B 708 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR B 713 " --> pdb=" O ALA B 709 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 708 through 713' Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 84 through 87 Processing helix chain 'C' and resid 91 through 97 removed outlier: 3.561A pdb=" N THR C 97 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 130 through 138 removed outlier: 3.662A pdb=" N LEU C 134 " --> pdb=" O CYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 172 through 180 Processing helix chain 'C' and resid 208 through 215 Processing helix chain 'C' and resid 220 through 226 removed outlier: 3.739A pdb=" N LEU C 225 " --> pdb=" O VAL C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 250 Processing helix chain 'C' and resid 256 through 276 removed outlier: 3.692A pdb=" N ALA C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG C 275 " --> pdb=" O GLN C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 284 No H-bonds generated for 'chain 'C' and resid 282 through 284' Processing helix chain 'C' and resid 293 through 300 Processing helix chain 'C' and resid 303 through 310 Processing helix chain 'C' and resid 351 through 357 Processing helix chain 'C' and resid 371 through 407 Proline residue: C 386 - end of helix Processing helix chain 'C' and resid 424 through 453 Processing helix chain 'C' and resid 455 through 460 removed outlier: 3.902A pdb=" N ILE C 458 " --> pdb=" O ARG C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 485 Processing helix chain 'C' and resid 492 through 509 removed outlier: 4.318A pdb=" N LEU C 508 " --> pdb=" O TRP C 504 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TYR C 509 " --> pdb=" O LEU C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 531 removed outlier: 3.517A pdb=" N TYR C 520 " --> pdb=" O HIS C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 552 Processing helix chain 'C' and resid 588 through 598 removed outlier: 3.939A pdb=" N PHE C 598 " --> pdb=" O GLU C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 628 Processing helix chain 'C' and resid 632 through 646 Processing helix chain 'C' and resid 650 through 667 Processing helix chain 'C' and resid 708 through 713 removed outlier: 3.597A pdb=" N THR C 713 " --> pdb=" O ALA C 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 90 through 97 removed outlier: 3.778A pdb=" N THR D 97 " --> pdb=" O TYR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 131 through 138 Processing helix chain 'D' and resid 162 through 168 Processing helix chain 'D' and resid 172 through 180 Processing helix chain 'D' and resid 208 through 215 Processing helix chain 'D' and resid 220 through 226 removed outlier: 3.820A pdb=" N LEU D 225 " --> pdb=" O VAL D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 250 Processing helix chain 'D' and resid 256 through 276 removed outlier: 3.649A pdb=" N ALA D 260 " --> pdb=" O PRO D 256 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG D 275 " --> pdb=" O GLN D 271 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 276 " --> pdb=" O MET D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 284 No H-bonds generated for 'chain 'D' and resid 282 through 284' Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 310 Processing helix chain 'D' and resid 351 through 357 Processing helix chain 'D' and resid 375 through 407 Proline residue: D 386 - end of helix Processing helix chain 'D' and resid 424 through 453 Processing helix chain 'D' and resid 455 through 460 removed outlier: 3.995A pdb=" N ILE D 458 " --> pdb=" O ARG D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 484 Processing helix chain 'D' and resid 492 through 509 removed outlier: 4.319A pdb=" N LEU D 508 " --> pdb=" O TRP D 504 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N TYR D 509 " --> pdb=" O LEU D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 531 removed outlier: 3.535A pdb=" N TYR D 520 " --> pdb=" O HIS D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 552 Processing helix chain 'D' and resid 588 through 598 removed outlier: 3.925A pdb=" N PHE D 598 " --> pdb=" O GLU D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 628 Processing helix chain 'D' and resid 632 through 646 Processing helix chain 'D' and resid 650 through 667 Processing helix chain 'D' and resid 708 through 713 removed outlier: 3.688A pdb=" N THR D 713 " --> pdb=" O ALA D 709 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 324 through 326 Processing sheet with id= B, first strand: chain 'B' and resid 324 through 326 Processing sheet with id= C, first strand: chain 'C' and resid 324 through 326 Processing sheet with id= D, first strand: chain 'D' and resid 324 through 326 867 hydrogen bonds defined for protein. 2568 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: 5.29 Time building geometry restraints manager: 8.06 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: 6235 1.34 - 1.46: 3735 1.46 - 1.58: 10476 1.58 - 1.69: 2 1.69 - 1.81: 160 Bond restraints: 20608 Sorted by residual: bond pdb=" CG PRO B 146 " pdb=" CD PRO B 146 " ideal model delta sigma weight residual 1.503 1.243 0.260 3.40e-02 8.65e+02 5.83e+01 bond pdb=" CG PRO C 146 " pdb=" CD PRO C 146 " ideal model delta sigma weight residual 1.503 1.248 0.255 3.40e-02 8.65e+02 5.62e+01 bond pdb=" CB PRO B 146 " pdb=" CG PRO B 146 " ideal model delta sigma weight residual 1.492 1.667 -0.175 5.00e-02 4.00e+02 1.22e+01 bond pdb=" CB PRO C 146 " pdb=" CG PRO C 146 " ideal model delta sigma weight residual 1.492 1.662 -0.170 5.00e-02 4.00e+02 1.15e+01 bond pdb=" N PRO C 146 " pdb=" CD PRO C 146 " ideal model delta sigma weight residual 1.473 1.516 -0.043 1.40e-02 5.10e+03 9.38e+00 ... (remaining 20603 not shown) Histogram of bond angle deviations from ideal: 86.56 - 96.71: 6 96.71 - 106.86: 541 106.86 - 117.01: 13862 117.01 - 127.16: 13311 127.16 - 137.31: 268 Bond angle restraints: 27988 Sorted by residual: angle pdb=" N ASN C 143 " pdb=" CA ASN C 143 " pdb=" C ASN C 143 " ideal model delta sigma weight residual 110.13 94.61 15.52 1.15e+00 7.56e-01 1.82e+02 angle pdb=" N ASN A 143 " pdb=" CA ASN A 143 " pdb=" C ASN A 143 " ideal model delta sigma weight residual 110.13 94.68 15.45 1.15e+00 7.56e-01 1.80e+02 angle pdb=" N PRO B 146 " pdb=" CD PRO B 146 " pdb=" CG PRO B 146 " ideal model delta sigma weight residual 103.20 86.56 16.64 1.50e+00 4.44e-01 1.23e+02 angle pdb=" CA PRO C 146 " pdb=" N PRO C 146 " pdb=" CD PRO C 146 " ideal model delta sigma weight residual 112.00 96.74 15.26 1.40e+00 5.10e-01 1.19e+02 angle pdb=" N PRO C 146 " pdb=" CD PRO C 146 " pdb=" CG PRO C 146 " ideal model delta sigma weight residual 103.20 87.27 15.93 1.50e+00 4.44e-01 1.13e+02 ... (remaining 27983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 11104 17.62 - 35.23: 979 35.23 - 52.85: 151 52.85 - 70.47: 38 70.47 - 88.08: 12 Dihedral angle restraints: 12284 sinusoidal: 5116 harmonic: 7168 Sorted by residual: dihedral pdb=" CA ASN A 143 " pdb=" C ASN A 143 " pdb=" N PRO A 144 " pdb=" CA PRO A 144 " ideal model delta harmonic sigma weight residual -180.00 -157.11 -22.89 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" C ILE A 693 " pdb=" N ILE A 693 " pdb=" CA ILE A 693 " pdb=" CB ILE A 693 " ideal model delta harmonic sigma weight residual -122.00 -133.26 11.26 0 2.50e+00 1.60e-01 2.03e+01 dihedral pdb=" CA ASN C 143 " pdb=" C ASN C 143 " pdb=" N PRO C 144 " pdb=" CA PRO C 144 " ideal model delta harmonic sigma weight residual -180.00 -160.16 -19.84 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 12281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2720 0.059 - 0.118: 394 0.118 - 0.177: 35 0.177 - 0.236: 16 0.236 - 0.295: 7 Chirality restraints: 3172 Sorted by residual: chirality pdb=" C13 CLR A 801 " pdb=" C12 CLR A 801 " pdb=" C14 CLR A 801 " pdb=" C17 CLR A 801 " both_signs ideal model delta sigma weight residual False -2.93 -2.64 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C13 CLR D 801 " pdb=" C12 CLR D 801 " pdb=" C14 CLR D 801 " pdb=" C17 CLR D 801 " both_signs ideal model delta sigma weight residual False -2.93 -2.64 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C13 CLR C 801 " pdb=" C12 CLR C 801 " pdb=" C14 CLR C 801 " pdb=" C17 CLR C 801 " both_signs ideal model delta sigma weight residual False -2.93 -2.64 -0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 3169 not shown) Planarity restraints: 3432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 371 " -0.099 5.00e-02 4.00e+02 1.50e-01 3.60e+01 pdb=" N PRO D 372 " 0.259 5.00e-02 4.00e+02 pdb=" CA PRO D 372 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO D 372 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 371 " -0.099 5.00e-02 4.00e+02 1.50e-01 3.58e+01 pdb=" N PRO B 372 " 0.259 5.00e-02 4.00e+02 pdb=" CA PRO B 372 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO B 372 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 371 " -0.099 5.00e-02 4.00e+02 1.50e-01 3.58e+01 pdb=" N PRO A 372 " 0.259 5.00e-02 4.00e+02 pdb=" CA PRO A 372 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO A 372 " -0.070 5.00e-02 4.00e+02 ... (remaining 3429 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 866 2.72 - 3.27: 20472 3.27 - 3.81: 32899 3.81 - 4.36: 38900 4.36 - 4.90: 66780 Nonbonded interactions: 159917 Sorted by model distance: nonbonded pdb=" OH TYR C 539 " pdb=" OG1 THR C 599 " model vdw 2.180 2.440 nonbonded pdb=" OH TYR D 539 " pdb=" OG1 THR D 599 " model vdw 2.203 2.440 nonbonded pdb=" OH TYR B 539 " pdb=" OG1 THR B 599 " model vdw 2.205 2.440 nonbonded pdb=" OH TYR A 539 " pdb=" OG1 THR A 599 " model vdw 2.207 2.440 nonbonded pdb=" N ASN A 143 " pdb=" O ASN A 143 " model vdw 2.234 2.496 ... (remaining 159912 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.650 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: 0.020 Extract box with map and model: 4.290 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 51.220 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.110 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:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 0.260 20608 Z= 0.280 Angle : 0.832 16.638 27988 Z= 0.488 Chirality : 0.045 0.295 3172 Planarity : 0.006 0.150 3432 Dihedral : 13.449 88.084 7660 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.24 % Favored : 95.35 % Rotamer: Outliers : 0.51 % Allowed : 0.55 % Favored : 98.94 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.17), residues: 2432 helix: 1.62 (0.15), residues: 1324 sheet: -1.21 (0.63), residues: 44 loop : -2.40 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 173 HIS 0.009 0.001 HIS C 408 PHE 0.010 0.001 PHE C 76 TYR 0.033 0.001 TYR D 466 ARG 0.004 0.000 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 339 time to evaluate : 2.302 Fit side-chains revert: symmetry clash REVERT: B 165 ILE cc_start: 0.8679 (mt) cc_final: 0.8305 (mm) REVERT: B 230 GLN cc_start: 0.7614 (tt0) cc_final: 0.7397 (tt0) REVERT: B 428 MET cc_start: 0.6660 (mmp) cc_final: 0.6240 (pp-130) REVERT: C 155 GLU cc_start: 0.6868 (tm-30) cc_final: 0.6499 (tp30) REVERT: D 165 ILE cc_start: 0.8533 (mt) cc_final: 0.8286 (mp) REVERT: D 230 GLN cc_start: 0.7828 (tt0) cc_final: 0.7518 (tt0) outliers start: 11 outliers final: 11 residues processed: 347 average time/residue: 1.2801 time to fit residues: 502.2056 Evaluate side-chains 216 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 205 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 469 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.0370 chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 221 optimal weight: 0.1980 overall best weight: 1.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN B 229 HIS C 181 ASN D 408 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 20608 Z= 0.245 Angle : 0.651 12.008 27988 Z= 0.321 Chirality : 0.040 0.254 3172 Planarity : 0.006 0.130 3432 Dihedral : 7.012 92.156 2983 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.24 % Favored : 95.52 % Rotamer: Outliers : 2.53 % Allowed : 10.20 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.17), residues: 2432 helix: 1.70 (0.15), residues: 1348 sheet: -0.14 (0.51), residues: 68 loop : -2.15 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 173 HIS 0.005 0.001 HIS D 408 PHE 0.012 0.001 PHE B 467 TYR 0.021 0.001 TYR B 466 ARG 0.007 0.001 ARG B 682 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 229 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 GLU cc_start: 0.6932 (tp30) cc_final: 0.6396 (tm-30) REVERT: A 272 MET cc_start: 0.8262 (tpp) cc_final: 0.8039 (tpp) REVERT: B 165 ILE cc_start: 0.8679 (mt) cc_final: 0.8312 (mm) REVERT: B 230 GLN cc_start: 0.7571 (tt0) cc_final: 0.7366 (tt0) REVERT: B 250 MET cc_start: 0.8619 (mmm) cc_final: 0.8314 (mmt) REVERT: B 428 MET cc_start: 0.6753 (mmp) cc_final: 0.6238 (pp-130) REVERT: C 155 GLU cc_start: 0.6948 (tm-30) cc_final: 0.6497 (tp30) REVERT: C 250 MET cc_start: 0.8597 (mmm) cc_final: 0.8287 (mmt) REVERT: D 155 GLU cc_start: 0.7057 (tp30) cc_final: 0.6480 (tm-30) REVERT: D 230 GLN cc_start: 0.7733 (tt0) cc_final: 0.7442 (tt0) REVERT: D 272 MET cc_start: 0.8281 (tpp) cc_final: 0.8075 (tpp) outliers start: 55 outliers final: 36 residues processed: 266 average time/residue: 1.0936 time to fit residues: 336.3659 Evaluate side-chains 219 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 183 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 371 GLU Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 529 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 61 optimal weight: 30.0000 chunk 221 optimal weight: 0.7980 chunk 239 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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: 0.8113 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 20608 Z= 0.295 Angle : 0.647 9.381 27988 Z= 0.321 Chirality : 0.040 0.251 3172 Planarity : 0.006 0.125 3432 Dihedral : 6.118 89.494 2962 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.65 % Favored : 95.02 % Rotamer: Outliers : 4.23 % Allowed : 11.72 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.17), residues: 2432 helix: 1.68 (0.14), residues: 1336 sheet: -0.07 (0.51), residues: 68 loop : -2.13 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 173 HIS 0.003 0.001 HIS D 246 PHE 0.015 0.001 PHE B 467 TYR 0.022 0.002 TYR C 466 ARG 0.008 0.001 ARG B 275 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 202 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7352 (mtp85) REVERT: A 250 MET cc_start: 0.8552 (mmm) cc_final: 0.8284 (mmt) REVERT: A 272 MET cc_start: 0.8173 (tpp) cc_final: 0.7933 (tpp) REVERT: B 165 ILE cc_start: 0.8702 (mt) cc_final: 0.8427 (mm) REVERT: B 177 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8446 (tt) REVERT: B 250 MET cc_start: 0.8522 (mmm) cc_final: 0.8226 (mmt) REVERT: B 428 MET cc_start: 0.6733 (mmp) cc_final: 0.6205 (pp-130) REVERT: C 155 GLU cc_start: 0.6915 (tm-30) cc_final: 0.6469 (tp30) REVERT: C 167 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8268 (mp) REVERT: C 188 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7194 (mtp85) REVERT: C 250 MET cc_start: 0.8489 (mmm) cc_final: 0.8270 (mmt) REVERT: C 280 VAL cc_start: 0.8830 (p) cc_final: 0.8596 (m) REVERT: D 188 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7346 (mtp85) REVERT: D 230 GLN cc_start: 0.7595 (tt0) cc_final: 0.7255 (tt0) REVERT: D 272 MET cc_start: 0.8261 (tpp) cc_final: 0.7996 (tpp) outliers start: 92 outliers final: 51 residues processed: 267 average time/residue: 1.1081 time to fit residues: 342.6676 Evaluate side-chains 243 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 187 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 372 PRO Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 711 GLU Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 281 GLN Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 372 PRO Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 695 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 10.0000 chunk 166 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 222 optimal weight: 0.7980 chunk 235 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 211 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN B 634 ASN D 634 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 20608 Z= 0.213 Angle : 0.585 9.381 27988 Z= 0.289 Chirality : 0.038 0.245 3172 Planarity : 0.005 0.124 3432 Dihedral : 5.344 90.896 2959 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.44 % Favored : 95.39 % Rotamer: Outliers : 3.91 % Allowed : 13.56 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.18), residues: 2432 helix: 1.81 (0.15), residues: 1336 sheet: 0.22 (0.53), residues: 68 loop : -2.01 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 504 HIS 0.002 0.001 HIS D 308 PHE 0.011 0.001 PHE D 389 TYR 0.023 0.001 TYR C 466 ARG 0.006 0.000 ARG D 383 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 208 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 MET cc_start: 0.8485 (mmm) cc_final: 0.8224 (mmm) REVERT: A 272 MET cc_start: 0.8161 (tpp) cc_final: 0.7898 (tpp) REVERT: A 280 VAL cc_start: 0.8744 (p) cc_final: 0.8543 (m) REVERT: A 677 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7243 (mmt-90) REVERT: B 165 ILE cc_start: 0.8740 (mt) cc_final: 0.8391 (mm) REVERT: B 180 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6682 (pm20) REVERT: B 250 MET cc_start: 0.8506 (mmm) cc_final: 0.8279 (mmt) REVERT: B 428 MET cc_start: 0.6736 (mmp) cc_final: 0.6199 (pp-130) REVERT: C 155 GLU cc_start: 0.6866 (tm-30) cc_final: 0.6421 (tp30) REVERT: C 165 ILE cc_start: 0.8518 (mp) cc_final: 0.8255 (mm) REVERT: C 167 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8250 (mp) REVERT: C 188 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7241 (mtp85) REVERT: C 250 MET cc_start: 0.8490 (mmm) cc_final: 0.8250 (mmm) REVERT: C 280 VAL cc_start: 0.8809 (p) cc_final: 0.8584 (m) REVERT: D 188 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7341 (mtp85) REVERT: D 230 GLN cc_start: 0.7516 (tt0) cc_final: 0.7145 (tt0) REVERT: D 272 MET cc_start: 0.8224 (tpp) cc_final: 0.7985 (tpp) outliers start: 85 outliers final: 41 residues processed: 272 average time/residue: 1.0996 time to fit residues: 345.2805 Evaluate side-chains 234 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 188 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 281 GLN Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 281 GLN Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 695 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 175 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 201 optimal weight: 7.9990 chunk 163 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 120 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 433 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 20608 Z= 0.206 Angle : 0.581 9.318 27988 Z= 0.287 Chirality : 0.039 0.245 3172 Planarity : 0.005 0.119 3432 Dihedral : 5.204 91.500 2959 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.28 % Favored : 95.56 % Rotamer: Outliers : 3.91 % Allowed : 14.29 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.18), residues: 2432 helix: 1.82 (0.15), residues: 1336 sheet: 0.34 (0.54), residues: 68 loop : -1.95 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 173 HIS 0.002 0.001 HIS D 308 PHE 0.011 0.001 PHE C 389 TYR 0.025 0.001 TYR C 466 ARG 0.010 0.000 ARG B 682 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 199 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7248 (mtp85) REVERT: A 250 MET cc_start: 0.8499 (mmm) cc_final: 0.8233 (mmm) REVERT: A 272 MET cc_start: 0.8148 (tpp) cc_final: 0.7939 (tpp) REVERT: A 677 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7219 (mmt-90) REVERT: A 701 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7118 (ttm-80) REVERT: B 165 ILE cc_start: 0.8725 (mt) cc_final: 0.8373 (mm) REVERT: B 250 MET cc_start: 0.8474 (mmm) cc_final: 0.8245 (mmm) REVERT: B 428 MET cc_start: 0.6746 (mmp) cc_final: 0.6206 (pp-130) REVERT: C 155 GLU cc_start: 0.6866 (tm-30) cc_final: 0.6027 (tp30) REVERT: C 165 ILE cc_start: 0.8513 (mt) cc_final: 0.8247 (mm) REVERT: C 167 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8366 (mp) REVERT: C 188 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7266 (mtp85) REVERT: C 250 MET cc_start: 0.8461 (mmm) cc_final: 0.8223 (mmm) REVERT: C 280 VAL cc_start: 0.8795 (p) cc_final: 0.8574 (m) REVERT: C 512 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7714 (ptp-170) REVERT: D 188 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7313 (mtp85) REVERT: D 230 GLN cc_start: 0.7507 (tt0) cc_final: 0.7081 (tt0) REVERT: D 272 MET cc_start: 0.8237 (tpp) cc_final: 0.8031 (tpp) outliers start: 85 outliers final: 47 residues processed: 263 average time/residue: 1.1201 time to fit residues: 340.5031 Evaluate side-chains 234 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 180 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 281 GLN Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 674 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 4.9990 chunk 212 optimal weight: 0.0970 chunk 46 optimal weight: 0.7980 chunk 138 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 236 optimal weight: 0.9990 chunk 195 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 123 optimal weight: 0.2980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN C 122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 20608 Z= 0.158 Angle : 0.588 22.100 27988 Z= 0.278 Chirality : 0.038 0.319 3172 Planarity : 0.006 0.187 3432 Dihedral : 5.093 96.424 2959 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.24 % Favored : 95.60 % Rotamer: Outliers : 3.58 % Allowed : 15.40 % Favored : 81.02 % 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: 0.51 (0.18), residues: 2432 helix: 1.90 (0.15), residues: 1340 sheet: 0.45 (0.55), residues: 68 loop : -1.94 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 173 HIS 0.002 0.000 HIS D 308 PHE 0.008 0.001 PHE C 389 TYR 0.025 0.001 TYR A 466 ARG 0.011 0.000 ARG B 275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 196 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7240 (mtp85) REVERT: A 250 MET cc_start: 0.8458 (mmm) cc_final: 0.8202 (mmm) REVERT: A 512 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7687 (ptp-170) REVERT: B 88 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7971 (p) REVERT: B 94 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7227 (pp) REVERT: B 165 ILE cc_start: 0.8671 (mt) cc_final: 0.8291 (mm) REVERT: B 180 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6963 (pm20) REVERT: B 188 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.6933 (mpp80) REVERT: B 250 MET cc_start: 0.8456 (mmm) cc_final: 0.8234 (mmm) REVERT: B 428 MET cc_start: 0.6743 (mmp) cc_final: 0.6181 (pp-130) REVERT: B 488 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6451 (tm-30) REVERT: C 155 GLU cc_start: 0.6340 (tm-30) cc_final: 0.5940 (tp30) REVERT: C 165 ILE cc_start: 0.8510 (mt) cc_final: 0.8245 (mm) REVERT: C 188 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7298 (mtp85) REVERT: C 250 MET cc_start: 0.8433 (mmm) cc_final: 0.8197 (mmm) REVERT: C 272 MET cc_start: 0.8340 (tpp) cc_final: 0.8098 (tpp) REVERT: C 512 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7653 (ptp-170) REVERT: D 88 THR cc_start: 0.8241 (OUTLIER) cc_final: 0.7956 (p) REVERT: D 165 ILE cc_start: 0.8483 (mt) cc_final: 0.8072 (mm) REVERT: D 188 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7384 (mtp85) outliers start: 78 outliers final: 33 residues processed: 251 average time/residue: 1.1412 time to fit residues: 331.0188 Evaluate side-chains 228 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 185 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 666 MET Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 674 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 chunk 134 optimal weight: 20.0000 chunk 172 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 198 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20608 Z= 0.201 Angle : 0.594 14.876 27988 Z= 0.287 Chirality : 0.038 0.239 3172 Planarity : 0.006 0.161 3432 Dihedral : 4.619 32.622 2956 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.52 % Favored : 95.35 % Rotamer: Outliers : 3.26 % Allowed : 15.81 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.18), residues: 2432 helix: 1.91 (0.15), residues: 1340 sheet: 0.53 (0.56), residues: 68 loop : -1.95 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 173 HIS 0.003 0.001 HIS B 164 PHE 0.012 0.001 PHE D 389 TYR 0.027 0.001 TYR A 466 ARG 0.012 0.000 ARG D 275 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 196 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7235 (mtp85) REVERT: A 250 MET cc_start: 0.8447 (mmm) cc_final: 0.8183 (mmm) REVERT: A 272 MET cc_start: 0.8246 (tpp) cc_final: 0.7747 (tpp) REVERT: A 276 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8513 (mm) REVERT: A 512 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7687 (ptp-170) REVERT: A 677 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7196 (mmt-90) REVERT: B 88 THR cc_start: 0.8239 (OUTLIER) cc_final: 0.7993 (p) REVERT: B 94 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7247 (pp) REVERT: B 155 GLU cc_start: 0.6869 (tp30) cc_final: 0.6666 (tp30) REVERT: B 180 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6976 (pm20) REVERT: B 188 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.6927 (mpp80) REVERT: B 250 MET cc_start: 0.8439 (mmm) cc_final: 0.8210 (mmm) REVERT: B 428 MET cc_start: 0.6788 (mmp) cc_final: 0.6181 (pp-130) REVERT: B 488 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6501 (tm-30) REVERT: C 155 GLU cc_start: 0.6341 (tm-30) cc_final: 0.5936 (tp30) REVERT: C 188 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7519 (mpp80) REVERT: C 250 MET cc_start: 0.8446 (mmm) cc_final: 0.8207 (mmm) REVERT: C 272 MET cc_start: 0.8369 (tpp) cc_final: 0.8024 (tpp) REVERT: C 512 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7684 (ptp-170) REVERT: D 88 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.7965 (p) REVERT: D 188 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7353 (mtp85) outliers start: 71 outliers final: 43 residues processed: 247 average time/residue: 1.1385 time to fit residues: 324.1648 Evaluate side-chains 238 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 183 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 281 GLN Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 674 ARG Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 149 optimal weight: 0.0870 chunk 160 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN C 186 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20608 Z= 0.197 Angle : 0.593 11.768 27988 Z= 0.287 Chirality : 0.038 0.239 3172 Planarity : 0.006 0.149 3432 Dihedral : 4.598 34.227 2956 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.56 % Favored : 95.31 % Rotamer: Outliers : 3.40 % Allowed : 15.81 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.18), residues: 2432 helix: 1.88 (0.15), residues: 1352 sheet: 0.55 (0.56), residues: 68 loop : -1.94 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 173 HIS 0.009 0.001 HIS A 229 PHE 0.011 0.001 PHE D 389 TYR 0.029 0.001 TYR A 466 ARG 0.012 0.000 ARG B 682 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 192 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 THR cc_start: 0.8275 (m) cc_final: 0.8029 (p) REVERT: A 188 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7173 (mtp85) REVERT: A 250 MET cc_start: 0.8480 (mmm) cc_final: 0.8206 (mmm) REVERT: A 272 MET cc_start: 0.8283 (tpp) cc_final: 0.7725 (tpp) REVERT: A 276 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8487 (mm) REVERT: A 512 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7622 (ptp-170) REVERT: A 677 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7198 (mmt-90) REVERT: B 88 THR cc_start: 0.8240 (OUTLIER) cc_final: 0.7995 (p) REVERT: B 94 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7182 (pp) REVERT: B 188 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.6953 (mpp80) REVERT: B 250 MET cc_start: 0.8468 (mmm) cc_final: 0.8224 (mmm) REVERT: B 428 MET cc_start: 0.6773 (mmp) cc_final: 0.6165 (pp-130) REVERT: B 488 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6515 (tm-30) REVERT: C 155 GLU cc_start: 0.6354 (tm-30) cc_final: 0.5939 (tp30) REVERT: C 188 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7451 (mpp80) REVERT: C 250 MET cc_start: 0.8446 (mmm) cc_final: 0.8193 (mmm) REVERT: C 272 MET cc_start: 0.8381 (tpp) cc_final: 0.8009 (tpp) REVERT: C 280 VAL cc_start: 0.8795 (p) cc_final: 0.8587 (m) REVERT: C 512 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7661 (ptp-170) REVERT: D 88 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.7972 (p) REVERT: D 188 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7418 (mtp85) outliers start: 74 outliers final: 41 residues processed: 250 average time/residue: 1.1662 time to fit residues: 336.2802 Evaluate side-chains 239 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 187 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 674 ARG Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 1.9990 chunk 225 optimal weight: 0.7980 chunk 205 optimal weight: 0.7980 chunk 219 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 95 optimal weight: 0.0980 chunk 172 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 198 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 218 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 20608 Z= 0.159 Angle : 0.577 13.351 27988 Z= 0.278 Chirality : 0.037 0.229 3172 Planarity : 0.006 0.141 3432 Dihedral : 4.481 34.252 2956 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.15 % Favored : 95.72 % Rotamer: Outliers : 2.53 % Allowed : 16.59 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.18), residues: 2432 helix: 1.87 (0.15), residues: 1376 sheet: 0.63 (0.56), residues: 68 loop : -2.02 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 173 HIS 0.002 0.000 HIS A 160 PHE 0.010 0.001 PHE D 462 TYR 0.028 0.001 TYR C 466 ARG 0.013 0.000 ARG D 682 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 209 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 THR cc_start: 0.8238 (m) cc_final: 0.8002 (p) REVERT: A 188 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7196 (mtp85) REVERT: A 272 MET cc_start: 0.8221 (tpp) cc_final: 0.7653 (tpp) REVERT: A 276 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8496 (mm) REVERT: A 512 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7580 (ptp-170) REVERT: B 88 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7991 (p) REVERT: B 94 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7179 (pp) REVERT: B 188 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.6935 (mpp80) REVERT: B 428 MET cc_start: 0.6770 (mmp) cc_final: 0.6161 (pp-130) REVERT: B 488 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6505 (tm-30) REVERT: C 155 GLU cc_start: 0.6335 (tm-30) cc_final: 0.5934 (tp30) REVERT: C 272 MET cc_start: 0.8350 (tpp) cc_final: 0.7956 (tpp) REVERT: C 280 VAL cc_start: 0.8761 (p) cc_final: 0.8549 (m) REVERT: C 456 LEU cc_start: 0.8206 (pt) cc_final: 0.7991 (tp) REVERT: C 512 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7622 (ptp-170) REVERT: D 88 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.7974 (p) REVERT: D 155 GLU cc_start: 0.6492 (tp30) cc_final: 0.5982 (tm-30) REVERT: D 188 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7371 (mtp85) outliers start: 55 outliers final: 27 residues processed: 250 average time/residue: 1.2064 time to fit residues: 346.6452 Evaluate side-chains 228 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 192 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 674 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 3.9990 chunk 231 optimal weight: 7.9990 chunk 141 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 243 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 193 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 chunk 118 optimal weight: 9.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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: 0.8120 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20608 Z= 0.268 Angle : 0.643 10.834 27988 Z= 0.311 Chirality : 0.040 0.251 3172 Planarity : 0.006 0.143 3432 Dihedral : 4.673 36.880 2956 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.52 % Favored : 95.35 % Rotamer: Outliers : 2.25 % Allowed : 17.14 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.18), residues: 2432 helix: 1.71 (0.14), residues: 1376 sheet: 0.66 (0.57), residues: 68 loop : -2.01 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 173 HIS 0.014 0.001 HIS A 229 PHE 0.016 0.001 PHE C 389 TYR 0.030 0.002 TYR C 466 ARG 0.014 0.000 ARG D 275 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 181 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 THR cc_start: 0.8225 (m) cc_final: 0.7942 (p) REVERT: A 188 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7159 (mtp85) REVERT: A 230 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7499 (tm-30) REVERT: A 272 MET cc_start: 0.8244 (tpp) cc_final: 0.7742 (tpp) REVERT: A 512 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7673 (ptp-170) REVERT: A 682 ARG cc_start: 0.6882 (ttp-110) cc_final: 0.6414 (ptm-80) REVERT: A 701 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7090 (ttm-80) REVERT: B 88 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.8010 (p) REVERT: B 94 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7134 (pp) REVERT: B 188 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.6983 (mpp80) REVERT: B 229 HIS cc_start: 0.6703 (OUTLIER) cc_final: 0.6462 (m90) REVERT: B 428 MET cc_start: 0.6848 (mmp) cc_final: 0.6189 (pp-130) REVERT: B 488 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6460 (tm-30) REVERT: B 674 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6583 (mpt180) REVERT: C 155 GLU cc_start: 0.6433 (tm-30) cc_final: 0.5934 (tp30) REVERT: C 272 MET cc_start: 0.8314 (tpp) cc_final: 0.7898 (tpp) REVERT: C 280 VAL cc_start: 0.8763 (p) cc_final: 0.8553 (m) REVERT: C 456 LEU cc_start: 0.8274 (pt) cc_final: 0.8024 (tp) REVERT: C 512 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7633 (ptp-170) REVERT: D 88 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.8011 (p) REVERT: D 165 ILE cc_start: 0.8371 (mt) cc_final: 0.8063 (mm) REVERT: D 188 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7386 (mtp85) outliers start: 49 outliers final: 30 residues processed: 223 average time/residue: 1.1800 time to fit residues: 307.2251 Evaluate side-chains 219 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 177 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 229 HIS Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 674 ARG Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 674 ARG Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 2.9990 chunk 206 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 193 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.156887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.103353 restraints weight = 28648.056| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.56 r_work: 0.3167 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 20608 Z= 0.186 Angle : 0.609 12.851 27988 Z= 0.291 Chirality : 0.038 0.237 3172 Planarity : 0.005 0.138 3432 Dihedral : 4.535 36.134 2956 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.03 % Favored : 95.85 % Rotamer: Outliers : 1.84 % Allowed : 17.78 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.18), residues: 2432 helix: 1.81 (0.15), residues: 1364 sheet: 0.69 (0.56), residues: 68 loop : -2.02 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 707 HIS 0.003 0.001 HIS D 160 PHE 0.011 0.001 PHE A 389 TYR 0.027 0.001 TYR C 466 ARG 0.013 0.000 ARG D 275 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6788.95 seconds wall clock time: 121 minutes 52.28 seconds (7312.28 seconds total)