Starting phenix.real_space_refine (version: 1.21rc1) on Sun Jul 9 23:25:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xeu_33159/07_2023/7xeu_33159_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xeu_33159/07_2023/7xeu_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_33159/07_2023/7xeu_33159.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xeu_33159/07_2023/7xeu_33159.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xeu_33159/07_2023/7xeu_33159_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xeu_33159/07_2023/7xeu_33159_updated.pdb" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 9.72, per 1000 atoms: 0.48 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: 9.32 Conformation dependent library (CDL) restraints added in 3.1 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: 2.19 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: 5.64 Time building geometry restraints manager: 9.87 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: 10908 17.62 - 35.23: 975 35.23 - 52.85: 135 52.85 - 70.47: 30 70.47 - 88.08: 12 Dihedral angle restraints: 12060 sinusoidal: 4892 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 12057 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: 0.640 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: 5.060 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 51.900 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.120 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: 72.220 ------------------------------------------------------------------------------- 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 : 13.228 88.084 7436 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 % 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 *********************** 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 : 2.399 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 11 residues processed: 347 average time/residue: 1.2996 time to fit residues: 510.5341 Evaluate side-chains 217 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 206 time to evaluate : 2.175 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 5 average time/residue: 1.1469 time to fit residues: 9.7088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.087 20608 Z= 0.242 Angle : 0.657 12.400 27988 Z= 0.323 Chirality : 0.040 0.246 3172 Planarity : 0.006 0.127 3432 Dihedral : 4.740 58.271 2732 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.19 % Favored : 95.56 % Rotamer Outliers : 2.80 % 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: 0.19 (0.17), residues: 2432 helix: 1.69 (0.15), residues: 1348 sheet: -0.13 (0.51), residues: 68 loop : -2.15 (0.18), residues: 1016 *********************** 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 291 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 230 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 39 residues processed: 273 average time/residue: 1.1454 time to fit residues: 360.7192 Evaluate side-chains 223 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 184 time to evaluate : 2.276 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 28 residues processed: 11 average time/residue: 0.5949 time to fit residues: 11.3994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 0.0570 chunk 68 optimal weight: 8.9990 chunk 184 optimal weight: 0.0670 chunk 150 optimal weight: 1.9990 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: 0.9980 chunk 75 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 overall best weight: 0.7838 ------------------------------------------------------------------------------- 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: 0.8035 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.081 20608 Z= 0.179 Angle : 0.583 9.384 27988 Z= 0.288 Chirality : 0.038 0.244 3172 Planarity : 0.005 0.121 3432 Dihedral : 4.649 59.554 2732 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.95 % Favored : 95.85 % Rotamer Outliers : 3.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.83 (0.15), residues: 1348 sheet: 0.16 (0.53), residues: 68 loop : -2.05 (0.18), residues: 1016 *********************** 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 288 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 208 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 39 residues processed: 263 average time/residue: 1.1136 time to fit residues: 339.1722 Evaluate side-chains 225 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 186 time to evaluate : 2.318 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 27 residues processed: 15 average time/residue: 0.4886 time to fit residues: 13.0483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 222 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 634 ASN D 634 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 20608 Z= 0.246 Angle : 0.600 9.563 27988 Z= 0.295 Chirality : 0.039 0.251 3172 Planarity : 0.006 0.118 3432 Dihedral : 4.722 59.997 2732 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.48 % Favored : 95.35 % Rotamer Outliers : 3.49 % 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: 0.37 (0.17), residues: 2432 helix: 1.82 (0.14), residues: 1336 sheet: 0.31 (0.54), residues: 68 loop : -2.01 (0.19), residues: 1028 *********************** 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 281 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 205 time to evaluate : 2.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 41 residues processed: 259 average time/residue: 1.0738 time to fit residues: 324.4417 Evaluate side-chains 220 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 179 time to evaluate : 2.398 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 29 residues processed: 14 average time/residue: 0.5293 time to fit residues: 13.0173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 3 optimal weight: 0.9980 chunk 175 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 201 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 120 optimal weight: 9.9990 chunk 211 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1948 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= 0.214 Angle : 0.600 19.398 27988 Z= 0.287 Chirality : 0.039 0.301 3172 Planarity : 0.006 0.177 3432 Dihedral : 4.621 59.504 2732 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.11 % Favored : 95.72 % Rotamer Outliers : 3.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.18), residues: 2432 helix: 1.82 (0.14), residues: 1340 sheet: 0.43 (0.55), residues: 68 loop : -1.92 (0.19), residues: 1024 *********************** 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 281 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 204 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 41 residues processed: 258 average time/residue: 1.1885 time to fit residues: 352.1952 Evaluate side-chains 225 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 184 time to evaluate : 2.289 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 30 residues processed: 14 average time/residue: 0.5106 time to fit residues: 12.4509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 0.2980 chunk 212 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN C 186 HIS C 433 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 20608 Z= 0.249 Angle : 0.615 13.159 27988 Z= 0.296 Chirality : 0.039 0.250 3172 Planarity : 0.006 0.156 3432 Dihedral : 4.583 56.644 2732 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.69 % Favored : 95.15 % Rotamer Outliers : 3.12 % 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: 0.42 (0.18), residues: 2432 helix: 1.76 (0.14), residues: 1344 sheet: 0.44 (0.55), residues: 68 loop : -1.89 (0.19), residues: 1020 *********************** 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 263 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 195 time to evaluate : 2.223 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 40 residues processed: 243 average time/residue: 1.1056 time to fit residues: 312.1406 Evaluate side-chains 220 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 180 time to evaluate : 2.291 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 30 residues processed: 11 average time/residue: 0.4486 time to fit residues: 9.7767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 134 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 198 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 235 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2217 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= 0.167 Angle : 0.592 23.173 27988 Z= 0.279 Chirality : 0.038 0.357 3172 Planarity : 0.006 0.186 3432 Dihedral : 4.435 53.697 2732 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.40 % Favored : 95.48 % Rotamer Outliers : 2.76 % 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: 0.55 (0.18), residues: 2432 helix: 1.94 (0.15), residues: 1344 sheet: 0.58 (0.56), residues: 68 loop : -1.94 (0.19), residues: 1020 *********************** 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 253 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 193 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 37 residues processed: 238 average time/residue: 1.0887 time to fit residues: 301.8656 Evaluate side-chains 218 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 181 time to evaluate : 2.211 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 32 residues processed: 7 average time/residue: 0.2056 time to fit residues: 5.4747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 184 optimal weight: 0.3980 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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: 0.8090 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 20608 Z= 0.188 Angle : 0.591 16.169 27988 Z= 0.284 Chirality : 0.038 0.257 3172 Planarity : 0.006 0.161 3432 Dihedral : 4.359 49.880 2732 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.73 % Favored : 95.15 % Rotamer Outliers : 2.44 % 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: 0.48 (0.18), residues: 2432 helix: 1.87 (0.15), residues: 1348 sheet: 0.63 (0.56), residues: 68 loop : -1.97 (0.19), residues: 1016 *********************** 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 243 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 190 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 35 residues processed: 230 average time/residue: 1.0997 time to fit residues: 292.7407 Evaluate side-chains 218 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 183 time to evaluate : 2.180 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 32 residues processed: 6 average time/residue: 0.4348 time to fit residues: 6.4438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 95 optimal weight: 0.1980 chunk 172 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 198 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN D 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2458 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= 0.242 Angle : 0.624 13.376 27988 Z= 0.298 Chirality : 0.039 0.225 3172 Planarity : 0.006 0.149 3432 Dihedral : 4.363 42.629 2732 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.44 % Favored : 95.44 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % 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: 0.42 (0.18), residues: 2432 helix: 1.78 (0.15), residues: 1348 sheet: 0.64 (0.56), residues: 68 loop : -1.95 (0.19), residues: 1016 *********************** 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 236 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 189 time to evaluate : 2.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 31 residues processed: 227 average time/residue: 1.1118 time to fit residues: 293.7886 Evaluate side-chains 212 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 2.416 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 30 residues processed: 3 average time/residue: 0.2170 time to fit residues: 4.3834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 4.9990 chunk 231 optimal weight: 7.9990 chunk 141 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 243 optimal weight: 1.9990 chunk 223 optimal weight: 0.8980 chunk 193 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** D 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 20608 Z= 0.207 Angle : 0.606 13.480 27988 Z= 0.290 Chirality : 0.038 0.227 3172 Planarity : 0.006 0.140 3432 Dihedral : 4.279 37.260 2732 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.56 % Favored : 95.31 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % 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: 1.72 (0.14), residues: 1368 sheet: 0.65 (0.56), residues: 68 loop : -2.04 (0.19), residues: 996 ********************** 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 222 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 182 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 36 residues processed: 217 average time/residue: 1.1193 time to fit residues: 282.4511 Evaluate side-chains 213 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 177 time to evaluate : 2.201 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 34 residues processed: 7 average time/residue: 0.2359 time to fit residues: 5.7293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 0.9990 chunk 206 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 28 optimal weight: 0.0070 chunk 53 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 199 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.8006 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.158076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.104479 restraints weight = 28670.348| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.56 r_work: 0.3183 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.066 20608 Z= 0.159 Angle : 0.585 13.834 27988 Z= 0.279 Chirality : 0.038 0.275 3172 Planarity : 0.006 0.134 3432 Dihedral : 4.123 36.846 2732 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.28 % Favored : 95.60 % Rotamer Outliers : 1.70 % 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: 0.45 (0.18), residues: 2432 helix: 1.80 (0.15), residues: 1368 sheet: 0.70 (0.56), residues: 68 loop : -2.02 (0.19), residues: 996 =============================================================================== Job complete usr+sys time: 6499.38 seconds wall clock time: 116 minutes 31.87 seconds (6991.87 seconds total)