Starting phenix.real_space_refine on Tue Nov 19 10:11:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui0_26521/11_2024/7ui0_26521_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui0_26521/11_2024/7ui0_26521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui0_26521/11_2024/7ui0_26521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui0_26521/11_2024/7ui0_26521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui0_26521/11_2024/7ui0_26521_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui0_26521/11_2024/7ui0_26521_neut.cif" } resolution = 3.4 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= 0.001 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 90 5.16 5 C 12123 2.51 5 N 3330 2.21 5 O 3660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 159 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19203 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4660 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 548} Chain breaks: 2 Chain: "I" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 905 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "M" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 104} Restraints were copied for chains: L, N, H, J, C, B Time building chain proxies: 12.15, per 1000 atoms: 0.63 Number of scatterers: 19203 At special positions: 0 Unit cell: (137.775, 138.6, 186.45, 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 90 16.00 O 3660 8.00 N 3330 7.00 C 12123 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 633 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 5.15 Conformation dependent library (CDL) restraints added in 2.6 seconds 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 42 sheets defined 16.3% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 303 through 310 removed outlier: 4.022A pdb=" N GLY A 306 " --> pdb=" O TYR A 303 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS A 308 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 411 through 428 removed outlier: 4.479A pdb=" N LYS A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 543 removed outlier: 4.844A pdb=" N THR A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU A 538 " --> pdb=" O HIS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 removed outlier: 3.937A pdb=" N ILE A 550 " --> pdb=" O ASN A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 660 through 664 Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 701 through 710 Processing helix chain 'A' and resid 711 through 717 Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 303 through 310 removed outlier: 4.022A pdb=" N GLY B 306 " --> pdb=" O TYR B 303 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS B 308 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 411 through 428 removed outlier: 4.479A pdb=" N LYS B 415 " --> pdb=" O ASP B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 543 removed outlier: 4.843A pdb=" N THR B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU B 538 " --> pdb=" O HIS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 removed outlier: 3.938A pdb=" N ILE B 550 " --> pdb=" O ASN B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 660 through 664 Processing helix chain 'B' and resid 690 through 697 Processing helix chain 'B' and resid 701 through 710 Processing helix chain 'B' and resid 711 through 717 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 303 through 310 removed outlier: 4.022A pdb=" N GLY C 306 " --> pdb=" O TYR C 303 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS C 308 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 411 through 428 removed outlier: 4.479A pdb=" N LYS C 415 " --> pdb=" O ASP C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 543 removed outlier: 4.844A pdb=" N THR C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU C 538 " --> pdb=" O HIS C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 removed outlier: 3.937A pdb=" N ILE C 550 " --> pdb=" O ASN C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 660 through 664 Processing helix chain 'C' and resid 690 through 697 Processing helix chain 'C' and resid 701 through 710 Processing helix chain 'C' and resid 711 through 717 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 574 through 576 removed outlier: 7.042A pdb=" N TYR A 114 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 127 Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 152 removed outlier: 6.212A pdb=" N LYS A 151 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LYS A 368 " --> pdb=" O LYS A 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 366 through 372 current: chain 'A' and resid 449 through 457 Processing sheet with id=AA4, first strand: chain 'A' and resid 157 through 175 removed outlier: 8.577A pdb=" N TYR A 164 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LYS A 166 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG A 189 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL A 168 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU A 187 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL A 170 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE A 185 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLN A 172 " --> pdb=" O MET A 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 180 through 191 current: chain 'A' and resid 246 through 248 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 246 through 248 current: chain 'A' and resid 287 through 289 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 294 through 295 current: chain 'A' and resid 340 through 345 Processing sheet with id=AA5, first strand: chain 'A' and resid 206 through 207 Processing sheet with id=AA6, first strand: chain 'A' and resid 210 through 215 Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 380 Processing sheet with id=AA8, first strand: chain 'A' and resid 559 through 563 Processing sheet with id=AA9, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AB1, first strand: chain 'A' and resid 638 through 643 removed outlier: 5.804A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 666 through 667 Processing sheet with id=AB3, first strand: chain 'B' and resid 574 through 576 removed outlier: 7.043A pdb=" N TYR B 114 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 145 through 152 removed outlier: 6.212A pdb=" N LYS B 151 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LYS B 368 " --> pdb=" O LYS B 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 366 through 372 current: chain 'B' and resid 449 through 457 Processing sheet with id=AB5, first strand: chain 'B' and resid 157 through 175 removed outlier: 8.578A pdb=" N TYR B 164 " --> pdb=" O PRO B 191 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LYS B 166 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG B 189 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 168 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU B 187 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL B 170 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE B 185 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLN B 172 " --> pdb=" O MET B 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 180 through 191 current: chain 'B' and resid 246 through 248 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 246 through 248 current: chain 'B' and resid 287 through 289 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 294 through 295 current: chain 'B' and resid 340 through 345 Processing sheet with id=AB6, first strand: chain 'B' and resid 206 through 207 Processing sheet with id=AB7, first strand: chain 'B' and resid 210 through 215 Processing sheet with id=AB8, first strand: chain 'B' and resid 376 through 380 Processing sheet with id=AB9, first strand: chain 'B' and resid 559 through 563 Processing sheet with id=AC1, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AC2, first strand: chain 'B' and resid 638 through 643 removed outlier: 5.803A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 666 through 667 Processing sheet with id=AC4, first strand: chain 'C' and resid 574 through 576 removed outlier: 7.042A pdb=" N TYR C 114 " --> pdb=" O LEU C 623 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 145 through 152 removed outlier: 6.212A pdb=" N LYS C 151 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LYS C 368 " --> pdb=" O LYS C 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 366 through 372 current: chain 'C' and resid 449 through 457 Processing sheet with id=AC6, first strand: chain 'C' and resid 157 through 175 removed outlier: 8.577A pdb=" N TYR C 164 " --> pdb=" O PRO C 191 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LYS C 166 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG C 189 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL C 168 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU C 187 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL C 170 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE C 185 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLN C 172 " --> pdb=" O MET C 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 180 through 191 current: chain 'C' and resid 246 through 248 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 246 through 248 current: chain 'C' and resid 287 through 289 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 294 through 295 current: chain 'C' and resid 340 through 345 Processing sheet with id=AC7, first strand: chain 'C' and resid 206 through 207 Processing sheet with id=AC8, first strand: chain 'C' and resid 210 through 215 Processing sheet with id=AC9, first strand: chain 'C' and resid 376 through 380 Processing sheet with id=AD1, first strand: chain 'C' and resid 559 through 563 Processing sheet with id=AD2, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AD3, first strand: chain 'C' and resid 638 through 643 removed outlier: 5.804A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AD5, first strand: chain 'H' and resid 9 through 12 removed outlier: 5.546A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE H 34 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N MET H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AD7, first strand: chain 'I' and resid 9 through 12 removed outlier: 5.546A pdb=" N GLU I 10 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE I 34 " --> pdb=" O MET I 50 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N MET I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 3 through 5 Processing sheet with id=AD9, first strand: chain 'J' and resid 9 through 12 removed outlier: 5.546A pdb=" N GLU J 10 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE J 34 " --> pdb=" O MET J 50 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N MET J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.893A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AE4, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.893A pdb=" N LEU M 33 " --> pdb=" O SER M 49 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AE6, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.892A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1578 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: 7.39 Time building geometry restraints manager: 5.88 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: 4418 1.46 - 1.58: 8895 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 19683 Sorted by residual: bond pdb=" CZ ARG B 624 " pdb=" NH2 ARG B 624 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.59e+00 bond pdb=" CZ ARG A 624 " pdb=" NH2 ARG A 624 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.47e+00 bond pdb=" CZ ARG C 624 " pdb=" NH2 ARG C 624 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.38e+00 bond pdb=" CZ ARG C 588 " pdb=" NH2 ARG C 588 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.13e+00 bond pdb=" CZ ARG A 588 " pdb=" NH2 ARG A 588 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.74e+00 ... (remaining 19678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 26023 2.30 - 4.59: 689 4.59 - 6.89: 30 6.89 - 9.19: 3 9.19 - 11.48: 3 Bond angle restraints: 26748 Sorted by residual: angle pdb=" CB HIS B 637 " pdb=" CG HIS B 637 " pdb=" CD2 HIS B 637 " ideal model delta sigma weight residual 131.20 125.37 5.83 1.30e+00 5.92e-01 2.01e+01 angle pdb=" CB HIS A 637 " pdb=" CG HIS A 637 " pdb=" CD2 HIS A 637 " ideal model delta sigma weight residual 131.20 125.37 5.83 1.30e+00 5.92e-01 2.01e+01 angle pdb=" CB HIS C 637 " pdb=" CG HIS C 637 " pdb=" CD2 HIS C 637 " ideal model delta sigma weight residual 131.20 125.39 5.81 1.30e+00 5.92e-01 2.00e+01 angle pdb=" CB MET I 81 " pdb=" CG MET I 81 " pdb=" SD MET I 81 " ideal model delta sigma weight residual 112.70 101.22 11.48 3.00e+00 1.11e-01 1.47e+01 angle pdb=" CB MET J 81 " pdb=" CG MET J 81 " pdb=" SD MET J 81 " ideal model delta sigma weight residual 112.70 101.24 11.46 3.00e+00 1.11e-01 1.46e+01 ... (remaining 26743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 10474 17.61 - 35.22: 936 35.22 - 52.83: 149 52.83 - 70.43: 42 70.43 - 88.04: 12 Dihedral angle restraints: 11613 sinusoidal: 4569 harmonic: 7044 Sorted by residual: dihedral pdb=" CA SER J 101 " pdb=" C SER J 101 " pdb=" N SER J 102 " pdb=" CA SER J 102 " ideal model delta harmonic sigma weight residual 180.00 156.32 23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA SER I 101 " pdb=" C SER I 101 " pdb=" N SER I 102 " pdb=" CA SER I 102 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA SER H 101 " pdb=" C SER H 101 " pdb=" N SER H 102 " pdb=" CA SER H 102 " ideal model delta harmonic sigma weight residual 180.00 156.37 23.63 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 11610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2258 0.053 - 0.106: 545 0.106 - 0.159: 83 0.159 - 0.212: 15 0.212 - 0.265: 6 Chirality restraints: 2907 Sorted by residual: chirality pdb=" CA TYR A 653 " pdb=" N TYR A 653 " pdb=" C TYR A 653 " pdb=" CB TYR A 653 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA TYR B 653 " pdb=" N TYR B 653 " pdb=" C TYR B 653 " pdb=" CB TYR B 653 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA TYR C 653 " pdb=" N TYR C 653 " pdb=" C TYR C 653 " pdb=" CB TYR C 653 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 2904 not shown) Planarity restraints: 3456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 653 " -0.066 2.00e-02 2.50e+03 3.43e-02 2.35e+01 pdb=" CG TYR C 653 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR C 653 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR C 653 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR C 653 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR C 653 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 653 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR C 653 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 653 " -0.066 2.00e-02 2.50e+03 3.42e-02 2.34e+01 pdb=" CG TYR A 653 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 653 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR A 653 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR A 653 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 653 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 653 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 653 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 653 " -0.065 2.00e-02 2.50e+03 3.42e-02 2.33e+01 pdb=" CG TYR B 653 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 653 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR B 653 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR B 653 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR B 653 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 653 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR B 653 " -0.041 2.00e-02 2.50e+03 ... (remaining 3453 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 311 2.60 - 3.18: 16905 3.18 - 3.75: 29308 3.75 - 4.33: 41168 4.33 - 4.90: 68598 Nonbonded interactions: 156290 Sorted by model distance: nonbonded pdb=" SG CYS C 133 " pdb=" SG CYS C 529 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS B 133 " pdb=" SG CYS B 529 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS C 116 " pdb=" SG CYS C 573 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS B 116 " pdb=" SG CYS B 573 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS C 207 " pdb=" SG CYS C 271 " model vdw 2.030 3.760 ... (remaining 156285 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 45.750 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 : 0.008 0.049 19683 Z= 0.503 Angle : 0.812 11.484 26748 Z= 0.486 Chirality : 0.049 0.265 2907 Planarity : 0.006 0.091 3456 Dihedral : 13.944 88.042 7086 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.17), residues: 2385 helix: 0.48 (0.29), residues: 309 sheet: -1.10 (0.17), residues: 798 loop : -1.08 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 110 HIS 0.017 0.002 HIS C 637 PHE 0.039 0.003 PHE A 641 TYR 0.066 0.002 TYR C 653 ARG 0.006 0.001 ARG C 627 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 2.247 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: B 187 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7736 (mt-10) REVERT: B 419 ASP cc_start: 0.7559 (t70) cc_final: 0.7267 (t0) REVERT: C 297 MET cc_start: 0.8598 (ptm) cc_final: 0.8384 (ptp) REVERT: H 36 TRP cc_start: 0.7374 (m100) cc_final: 0.7052 (m100) REVERT: H 95 TYR cc_start: 0.6671 (m-80) cc_final: 0.6430 (m-80) REVERT: I 10 GLU cc_start: 0.6858 (mm-30) cc_final: 0.6629 (mm-30) REVERT: J 36 TRP cc_start: 0.7687 (m100) cc_final: 0.7235 (m100) REVERT: J 95 TYR cc_start: 0.6871 (m-80) cc_final: 0.6423 (m-80) REVERT: J 112 GLN cc_start: 0.6577 (pm20) cc_final: 0.6182 (pm20) REVERT: L 91 TYR cc_start: 0.8351 (p90) cc_final: 0.8131 (p90) REVERT: M 37 GLN cc_start: 0.7054 (tt0) cc_final: 0.6386 (tm-30) REVERT: M 91 TYR cc_start: 0.8425 (p90) cc_final: 0.8046 (p90) REVERT: N 37 GLN cc_start: 0.6862 (tt0) cc_final: 0.6459 (tt0) REVERT: N 79 GLN cc_start: 0.6698 (pt0) cc_final: 0.6481 (pt0) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.3258 time to fit residues: 154.5357 Evaluate side-chains 237 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN A 534 HIS B 216 ASN B 458 ASN B 507 GLN B 534 HIS C 129 GLN C 216 ASN C 217 ASN C 534 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 5 GLN ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN M 28 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19683 Z= 0.206 Angle : 0.593 9.243 26748 Z= 0.312 Chirality : 0.044 0.183 2907 Planarity : 0.004 0.039 3456 Dihedral : 5.071 22.535 2688 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.21 % Allowed : 8.15 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.17), residues: 2385 helix: 0.99 (0.30), residues: 315 sheet: -0.95 (0.17), residues: 801 loop : -1.03 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 36 HIS 0.011 0.001 HIS B 534 PHE 0.013 0.002 PHE A 287 TYR 0.026 0.002 TYR A 653 ARG 0.005 0.001 ARG B 627 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 260 time to evaluate : 2.461 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 520 MET cc_start: 0.8111 (mmp) cc_final: 0.7899 (mmp) REVERT: B 194 PHE cc_start: 0.7585 (m-80) cc_final: 0.7310 (m-80) REVERT: B 230 THR cc_start: 0.8794 (t) cc_final: 0.8515 (p) REVERT: B 419 ASP cc_start: 0.7679 (t70) cc_final: 0.7409 (t0) REVERT: B 520 MET cc_start: 0.8306 (mmp) cc_final: 0.8067 (mmp) REVERT: C 456 LEU cc_start: 0.9093 (tp) cc_final: 0.8744 (tt) REVERT: C 677 MET cc_start: 0.8469 (mmt) cc_final: 0.7645 (mmm) REVERT: H 3 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8008 (tm-30) REVERT: H 47 TRP cc_start: 0.8132 (t60) cc_final: 0.7671 (t60) REVERT: H 59 HIS cc_start: 0.7627 (m-70) cc_final: 0.7128 (m-70) REVERT: H 112 GLN cc_start: 0.7187 (pm20) cc_final: 0.6802 (pm20) REVERT: I 10 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6671 (mm-30) REVERT: I 36 TRP cc_start: 0.7602 (m100) cc_final: 0.7375 (m-10) REVERT: I 59 HIS cc_start: 0.7753 (m-70) cc_final: 0.7524 (m-70) REVERT: I 61 ASN cc_start: 0.6412 (t0) cc_final: 0.6001 (t0) REVERT: I 65 LYS cc_start: 0.8404 (mmtt) cc_final: 0.8177 (mmtt) REVERT: J 3 GLN cc_start: 0.8330 (tm-30) cc_final: 0.8096 (tm-30) REVERT: J 47 TRP cc_start: 0.7753 (t60) cc_final: 0.7413 (t60) REVERT: J 51 ILE cc_start: 0.9053 (tt) cc_final: 0.8808 (tp) REVERT: J 73 ASP cc_start: 0.8300 (t0) cc_final: 0.6706 (p0) REVERT: J 80 TYR cc_start: 0.7721 (m-80) cc_final: 0.6975 (m-10) REVERT: L 79 GLN cc_start: 0.7589 (pt0) cc_final: 0.7364 (tm-30) REVERT: L 91 TYR cc_start: 0.8376 (p90) cc_final: 0.8079 (p90) REVERT: M 37 GLN cc_start: 0.6941 (tt0) cc_final: 0.6657 (tm-30) REVERT: M 87 TYR cc_start: 0.7433 (m-80) cc_final: 0.7229 (m-10) REVERT: M 91 TYR cc_start: 0.8466 (p90) cc_final: 0.8156 (p90) REVERT: N 30 ASN cc_start: 0.8875 (t0) cc_final: 0.8660 (t0) REVERT: N 37 GLN cc_start: 0.6932 (tt0) cc_final: 0.6591 (tt0) REVERT: N 69 LYS cc_start: 0.7559 (mtpp) cc_final: 0.7332 (mtpp) outliers start: 25 outliers final: 16 residues processed: 274 average time/residue: 0.3130 time to fit residues: 133.7096 Evaluate side-chains 239 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 223 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 106 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 119 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 179 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 215 optimal weight: 20.0000 chunk 232 optimal weight: 10.0000 chunk 192 optimal weight: 20.0000 chunk 213 optimal weight: 20.0000 chunk 73 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN B 507 GLN C 217 ASN J 5 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 19683 Z= 0.510 Angle : 0.694 12.137 26748 Z= 0.368 Chirality : 0.046 0.186 2907 Planarity : 0.005 0.053 3456 Dihedral : 5.325 24.007 2688 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.17 % Allowed : 11.38 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.16), residues: 2385 helix: 0.65 (0.29), residues: 312 sheet: -1.40 (0.17), residues: 822 loop : -0.95 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 36 HIS 0.011 0.001 HIS A 516 PHE 0.023 0.002 PHE B 294 TYR 0.038 0.002 TYR A 653 ARG 0.006 0.001 ARG C 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8031 (mpp) REVERT: H 36 TRP cc_start: 0.7078 (m100) cc_final: 0.6849 (m-10) REVERT: H 47 TRP cc_start: 0.8278 (t60) cc_final: 0.7935 (t60) REVERT: H 112 GLN cc_start: 0.6720 (pm20) cc_final: 0.6504 (pm20) REVERT: I 65 LYS cc_start: 0.8502 (mmtt) cc_final: 0.8264 (mmtp) REVERT: J 3 GLN cc_start: 0.8358 (tm-30) cc_final: 0.8046 (tm-30) REVERT: J 27 TYR cc_start: 0.6671 (p90) cc_final: 0.6273 (p90) REVERT: J 95 TYR cc_start: 0.6687 (m-80) cc_final: 0.6413 (m-80) REVERT: L 79 GLN cc_start: 0.7682 (pt0) cc_final: 0.7433 (tm-30) REVERT: L 91 TYR cc_start: 0.8420 (p90) cc_final: 0.8002 (p90) REVERT: M 37 GLN cc_start: 0.7072 (tt0) cc_final: 0.6493 (tt0) REVERT: M 91 TYR cc_start: 0.8488 (p90) cc_final: 0.8137 (p90) REVERT: N 37 GLN cc_start: 0.7058 (tt0) cc_final: 0.6600 (tt0) REVERT: N 61 ARG cc_start: 0.7527 (ptt180) cc_final: 0.7185 (ptt90) REVERT: N 69 LYS cc_start: 0.7745 (mtpp) cc_final: 0.7527 (mtpp) REVERT: N 87 TYR cc_start: 0.7528 (m-10) cc_final: 0.7205 (m-10) outliers start: 45 outliers final: 21 residues processed: 247 average time/residue: 0.3044 time to fit residues: 118.4976 Evaluate side-chains 230 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 106 TRP Chi-restraints excluded: chain J residue 110 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 20.0000 chunk 162 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 23 optimal weight: 0.0070 chunk 102 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 216 optimal weight: 9.9990 chunk 229 optimal weight: 20.0000 chunk 113 optimal weight: 0.7980 chunk 205 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 5 GLN ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN N 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 19683 Z= 0.202 Angle : 0.558 9.816 26748 Z= 0.295 Chirality : 0.042 0.197 2907 Planarity : 0.004 0.042 3456 Dihedral : 4.845 20.632 2688 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.93 % Allowed : 12.74 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.17), residues: 2385 helix: 1.41 (0.30), residues: 297 sheet: -1.18 (0.17), residues: 831 loop : -0.92 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 47 HIS 0.005 0.001 HIS A 516 PHE 0.016 0.001 PHE C 194 TYR 0.030 0.001 TYR A 653 ARG 0.005 0.000 ARG N 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 225 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 CYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8133 (p) REVERT: C 177 HIS cc_start: 0.7776 (p90) cc_final: 0.7550 (p90) REVERT: C 178 ARG cc_start: 0.7896 (mtt90) cc_final: 0.7661 (mtt90) REVERT: C 232 MET cc_start: 0.8569 (mmt) cc_final: 0.8162 (mmt) REVERT: H 3 GLN cc_start: 0.8425 (tm-30) cc_final: 0.8207 (tm-30) REVERT: H 47 TRP cc_start: 0.8231 (t60) cc_final: 0.7857 (t60) REVERT: H 59 HIS cc_start: 0.7679 (m-70) cc_final: 0.7256 (m-70) REVERT: I 5 GLN cc_start: 0.8866 (mt0) cc_final: 0.8636 (tp40) REVERT: I 10 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6364 (mm-30) REVERT: I 36 TRP cc_start: 0.7193 (m-10) cc_final: 0.6764 (m-10) REVERT: I 59 HIS cc_start: 0.7810 (m-70) cc_final: 0.7422 (m-70) REVERT: J 36 TRP cc_start: 0.6695 (m-10) cc_final: 0.6478 (m-10) REVERT: J 73 ASP cc_start: 0.8039 (t0) cc_final: 0.6333 (p0) REVERT: J 80 TYR cc_start: 0.8014 (m-80) cc_final: 0.6712 (m-10) REVERT: L 61 ARG cc_start: 0.7762 (ptt180) cc_final: 0.7370 (ptt90) REVERT: L 79 GLN cc_start: 0.7581 (pt0) cc_final: 0.7357 (tm-30) REVERT: L 87 TYR cc_start: 0.7401 (m-10) cc_final: 0.7163 (m-10) REVERT: L 91 TYR cc_start: 0.8373 (p90) cc_final: 0.8145 (p90) REVERT: M 37 GLN cc_start: 0.7095 (tt0) cc_final: 0.6527 (tt0) REVERT: M 61 ARG cc_start: 0.8014 (ptt180) cc_final: 0.7660 (ptt180) REVERT: M 91 TYR cc_start: 0.8471 (p90) cc_final: 0.8135 (p90) REVERT: N 27 ASP cc_start: 0.8784 (t0) cc_final: 0.7913 (m-30) REVERT: N 61 ARG cc_start: 0.7535 (ptt180) cc_final: 0.7088 (ptt90) REVERT: N 69 LYS cc_start: 0.7793 (mtpp) cc_final: 0.7571 (mtpp) REVERT: N 79 GLN cc_start: 0.7721 (pt0) cc_final: 0.7453 (pp30) REVERT: N 87 TYR cc_start: 0.7500 (m-10) cc_final: 0.7247 (m-10) outliers start: 40 outliers final: 19 residues processed: 257 average time/residue: 0.3121 time to fit residues: 124.9356 Evaluate side-chains 228 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 2.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 106 TRP Chi-restraints excluded: chain M residue 4 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 170 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 205 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN N 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 19683 Z= 0.490 Angle : 0.657 9.961 26748 Z= 0.348 Chirality : 0.045 0.166 2907 Planarity : 0.005 0.047 3456 Dihedral : 5.122 21.400 2688 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.60 % Allowed : 14.33 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.17), residues: 2385 helix: 0.72 (0.29), residues: 315 sheet: -1.53 (0.16), residues: 861 loop : -0.81 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 36 HIS 0.010 0.001 HIS A 516 PHE 0.027 0.002 PHE C 194 TYR 0.043 0.002 TYR A 653 ARG 0.003 0.000 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 216 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 421 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8122 (mpp) REVERT: B 412 CYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8167 (p) REVERT: B 534 HIS cc_start: 0.8820 (OUTLIER) cc_final: 0.8066 (t-90) REVERT: C 421 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8202 (mpp) REVERT: H 47 TRP cc_start: 0.8281 (t60) cc_final: 0.7948 (t60) REVERT: H 112 GLN cc_start: 0.6741 (pm20) cc_final: 0.6343 (pm20) REVERT: I 5 GLN cc_start: 0.8902 (mt0) cc_final: 0.8651 (tp40) REVERT: I 10 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6420 (mm-30) REVERT: I 36 TRP cc_start: 0.6914 (m-10) cc_final: 0.6710 (m-10) REVERT: I 61 ASN cc_start: 0.6427 (t0) cc_final: 0.5816 (t0) REVERT: I 95 TYR cc_start: 0.6706 (m-80) cc_final: 0.6386 (m-80) REVERT: J 73 ASP cc_start: 0.8102 (t0) cc_final: 0.6380 (p0) REVERT: J 80 TYR cc_start: 0.7885 (m-80) cc_final: 0.6832 (m-10) REVERT: L 79 GLN cc_start: 0.7496 (pt0) cc_final: 0.7247 (tm-30) REVERT: L 91 TYR cc_start: 0.8430 (p90) cc_final: 0.7899 (p90) REVERT: M 37 GLN cc_start: 0.7137 (tt0) cc_final: 0.6573 (tm-30) REVERT: M 61 ARG cc_start: 0.8084 (ptt180) cc_final: 0.7779 (ptt180) REVERT: M 91 TYR cc_start: 0.8489 (p90) cc_final: 0.8191 (p90) REVERT: N 61 ARG cc_start: 0.7602 (ptt180) cc_final: 0.7155 (ptt90) REVERT: N 79 GLN cc_start: 0.7696 (pt0) cc_final: 0.7036 (pp30) outliers start: 54 outliers final: 36 residues processed: 251 average time/residue: 0.3065 time to fit residues: 121.0076 Evaluate side-chains 243 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 106 TRP Chi-restraints excluded: chain M residue 4 MET Chi-restraints excluded: chain N residue 4 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 3.9990 chunk 206 optimal weight: 30.0000 chunk 45 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 229 optimal weight: 20.0000 chunk 190 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19683 Z= 0.228 Angle : 0.563 10.835 26748 Z= 0.299 Chirality : 0.042 0.169 2907 Planarity : 0.004 0.039 3456 Dihedral : 4.812 20.007 2688 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.46 % Allowed : 14.91 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.17), residues: 2385 helix: 1.37 (0.30), residues: 297 sheet: -1.35 (0.16), residues: 864 loop : -0.84 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 36 HIS 0.005 0.001 HIS A 516 PHE 0.021 0.001 PHE C 194 TYR 0.035 0.001 TYR A 653 ARG 0.002 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 218 time to evaluate : 2.479 Fit side-chains REVERT: A 421 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8096 (mpp) REVERT: B 412 CYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8246 (p) REVERT: B 534 HIS cc_start: 0.8721 (OUTLIER) cc_final: 0.7899 (t-90) REVERT: C 421 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8219 (mpp) REVERT: C 534 HIS cc_start: 0.8752 (OUTLIER) cc_final: 0.7647 (t-90) REVERT: H 6 GLN cc_start: 0.6094 (mp10) cc_final: 0.5892 (mp10) REVERT: H 36 TRP cc_start: 0.5903 (OUTLIER) cc_final: 0.5434 (m-10) REVERT: H 59 HIS cc_start: 0.7787 (m-70) cc_final: 0.7406 (m-70) REVERT: H 95 TYR cc_start: 0.6495 (m-80) cc_final: 0.5644 (m-80) REVERT: H 109 TYR cc_start: 0.8446 (m-80) cc_final: 0.8177 (m-80) REVERT: I 10 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6383 (mm-30) REVERT: I 59 HIS cc_start: 0.7690 (m-70) cc_final: 0.7357 (m-70) REVERT: I 61 ASN cc_start: 0.6248 (t0) cc_final: 0.5794 (t0) REVERT: I 95 TYR cc_start: 0.6675 (m-80) cc_final: 0.6399 (m-80) REVERT: J 5 GLN cc_start: 0.9005 (mt0) cc_final: 0.8679 (tp40) REVERT: J 73 ASP cc_start: 0.8096 (t0) cc_final: 0.6453 (p0) REVERT: J 80 TYR cc_start: 0.7839 (m-80) cc_final: 0.6849 (m-10) REVERT: L 37 GLN cc_start: 0.7206 (tt0) cc_final: 0.6632 (tm-30) REVERT: L 61 ARG cc_start: 0.7814 (ptt180) cc_final: 0.7363 (ptt90) REVERT: M 37 GLN cc_start: 0.7129 (tt0) cc_final: 0.6765 (tm-30) REVERT: M 61 ARG cc_start: 0.8053 (ptt180) cc_final: 0.7745 (ptt180) REVERT: M 87 TYR cc_start: 0.7393 (m-80) cc_final: 0.7190 (m-10) REVERT: M 91 TYR cc_start: 0.8470 (p90) cc_final: 0.8198 (p90) REVERT: N 27 ASP cc_start: 0.8588 (t0) cc_final: 0.7830 (m-30) REVERT: N 37 GLN cc_start: 0.6998 (tt0) cc_final: 0.6528 (tt0) REVERT: N 61 ARG cc_start: 0.7654 (ptt180) cc_final: 0.7173 (ptt90) REVERT: N 79 GLN cc_start: 0.7662 (pt0) cc_final: 0.7024 (pp30) outliers start: 51 outliers final: 30 residues processed: 253 average time/residue: 0.3074 time to fit residues: 121.4121 Evaluate side-chains 245 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 106 TRP Chi-restraints excluded: chain M residue 4 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 129 optimal weight: 8.9990 chunk 193 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 228 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19683 Z= 0.346 Angle : 0.599 10.247 26748 Z= 0.317 Chirality : 0.043 0.177 2907 Planarity : 0.004 0.046 3456 Dihedral : 4.872 20.287 2688 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.65 % Allowed : 15.48 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.17), residues: 2385 helix: 1.30 (0.30), residues: 297 sheet: -1.45 (0.16), residues: 873 loop : -0.83 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP I 36 HIS 0.007 0.001 HIS A 516 PHE 0.020 0.002 PHE A 294 TYR 0.034 0.001 TYR A 653 ARG 0.007 0.000 ARG B 627 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 214 time to evaluate : 2.140 Fit side-chains REVERT: A 421 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8100 (mpp) REVERT: B 412 CYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8302 (p) REVERT: B 534 HIS cc_start: 0.8780 (OUTLIER) cc_final: 0.7970 (t-90) REVERT: C 177 HIS cc_start: 0.7894 (p90) cc_final: 0.7683 (p90) REVERT: C 421 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8212 (mpp) REVERT: C 534 HIS cc_start: 0.8765 (OUTLIER) cc_final: 0.7686 (t-90) REVERT: H 3 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7823 (tm-30) REVERT: I 10 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6376 (mm-30) REVERT: I 95 TYR cc_start: 0.6727 (m-80) cc_final: 0.6510 (m-80) REVERT: J 5 GLN cc_start: 0.8984 (mt0) cc_final: 0.8563 (tp40) REVERT: J 6 GLN cc_start: 0.6053 (mp10) cc_final: 0.5195 (mp-120) REVERT: J 73 ASP cc_start: 0.8123 (t0) cc_final: 0.7739 (t0) REVERT: J 80 TYR cc_start: 0.7764 (m-80) cc_final: 0.7251 (m-10) REVERT: L 37 GLN cc_start: 0.7307 (tt0) cc_final: 0.6712 (tm-30) REVERT: M 37 GLN cc_start: 0.7097 (tt0) cc_final: 0.6732 (tm-30) REVERT: M 61 ARG cc_start: 0.8065 (ptt180) cc_final: 0.7746 (ptt180) REVERT: M 91 TYR cc_start: 0.8486 (p90) cc_final: 0.8204 (p90) REVERT: N 27 ASP cc_start: 0.8588 (t0) cc_final: 0.7814 (m-30) REVERT: N 37 GLN cc_start: 0.7103 (tt0) cc_final: 0.6617 (tt0) REVERT: N 61 ARG cc_start: 0.7635 (ptt180) cc_final: 0.7097 (ptt90) outliers start: 55 outliers final: 38 residues processed: 247 average time/residue: 0.3256 time to fit residues: 126.4694 Evaluate side-chains 249 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 206 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 106 TRP Chi-restraints excluded: chain M residue 4 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 207 optimal weight: 20.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 ASN ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN N 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19683 Z= 0.181 Angle : 0.550 11.580 26748 Z= 0.290 Chirality : 0.042 0.151 2907 Planarity : 0.004 0.038 3456 Dihedral : 4.574 18.682 2688 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.27 % Allowed : 16.11 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.17), residues: 2385 helix: 1.57 (0.30), residues: 297 sheet: -1.26 (0.16), residues: 876 loop : -0.79 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP H 36 HIS 0.004 0.001 HIS A 637 PHE 0.014 0.001 PHE C 194 TYR 0.029 0.001 TYR A 653 ARG 0.007 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 222 time to evaluate : 2.187 Fit side-chains REVERT: A 421 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8148 (mpp) REVERT: B 534 HIS cc_start: 0.8691 (OUTLIER) cc_final: 0.7802 (t-90) REVERT: B 587 MET cc_start: 0.8876 (mtp) cc_final: 0.8070 (ttm) REVERT: C 384 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.7855 (m-80) REVERT: C 534 HIS cc_start: 0.8682 (OUTLIER) cc_final: 0.7547 (t-90) REVERT: H 59 HIS cc_start: 0.7771 (m-70) cc_final: 0.7515 (m-70) REVERT: I 10 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6338 (mm-30) REVERT: I 59 HIS cc_start: 0.7647 (m-70) cc_final: 0.7402 (m-70) REVERT: I 61 ASN cc_start: 0.6311 (t0) cc_final: 0.5736 (t0) REVERT: I 95 TYR cc_start: 0.6633 (m-80) cc_final: 0.6417 (m-80) REVERT: I 112 GLN cc_start: 0.7030 (pm20) cc_final: 0.6652 (pm20) REVERT: J 70 LEU cc_start: 0.9433 (mp) cc_final: 0.8753 (tt) REVERT: J 73 ASP cc_start: 0.8161 (t0) cc_final: 0.7867 (t0) REVERT: J 80 TYR cc_start: 0.7530 (m-80) cc_final: 0.7213 (m-10) REVERT: L 3 GLN cc_start: 0.8845 (tp40) cc_final: 0.8022 (pp30) REVERT: L 37 GLN cc_start: 0.7175 (tt0) cc_final: 0.6572 (tm-30) REVERT: M 91 TYR cc_start: 0.8473 (p90) cc_final: 0.8174 (p90) REVERT: N 3 GLN cc_start: 0.8875 (mm110) cc_final: 0.8236 (pp30) REVERT: N 27 ASP cc_start: 0.8514 (t0) cc_final: 0.7821 (m-30) REVERT: N 37 GLN cc_start: 0.7092 (tt0) cc_final: 0.6635 (tt0) REVERT: N 61 ARG cc_start: 0.7618 (ptt180) cc_final: 0.7043 (ptt90) outliers start: 47 outliers final: 31 residues processed: 255 average time/residue: 0.3107 time to fit residues: 123.9034 Evaluate side-chains 242 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 384 PHE Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 106 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 212 optimal weight: 20.0000 chunk 128 optimal weight: 0.0670 chunk 92 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 192 optimal weight: 30.0000 chunk 201 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 225 optimal weight: 5.9990 overall best weight: 1.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 5 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19683 Z= 0.180 Angle : 0.541 11.114 26748 Z= 0.284 Chirality : 0.041 0.152 2907 Planarity : 0.004 0.040 3456 Dihedral : 4.493 18.185 2688 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.98 % Allowed : 16.30 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.95 (0.17), residues: 2385 helix: 1.68 (0.30), residues: 297 sheet: -1.05 (0.16), residues: 843 loop : -0.81 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP I 36 HIS 0.004 0.001 HIS B 311 PHE 0.015 0.001 PHE C 194 TYR 0.031 0.001 TYR A 653 ARG 0.008 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 1.679 Fit side-chains revert: symmetry clash REVERT: A 421 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8162 (mpp) REVERT: B 534 HIS cc_start: 0.8652 (OUTLIER) cc_final: 0.7719 (t-90) REVERT: B 587 MET cc_start: 0.8874 (mtp) cc_final: 0.8131 (ttm) REVERT: C 384 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.7907 (m-80) REVERT: C 421 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8277 (mpp) REVERT: C 534 HIS cc_start: 0.8624 (OUTLIER) cc_final: 0.7463 (t-90) REVERT: H 59 HIS cc_start: 0.7849 (m-70) cc_final: 0.7574 (m-70) REVERT: H 112 GLN cc_start: 0.7296 (pm20) cc_final: 0.7081 (pm20) REVERT: I 10 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6298 (mm-30) REVERT: I 27 TYR cc_start: 0.6467 (p90) cc_final: 0.6046 (p90) REVERT: I 59 HIS cc_start: 0.7647 (m-70) cc_final: 0.7395 (m-70) REVERT: I 95 TYR cc_start: 0.6597 (m-80) cc_final: 0.6384 (m-80) REVERT: I 112 GLN cc_start: 0.6944 (pm20) cc_final: 0.6655 (pm20) REVERT: J 6 GLN cc_start: 0.5984 (mp10) cc_final: 0.5384 (mp-120) REVERT: J 59 HIS cc_start: 0.7931 (m-70) cc_final: 0.7558 (m-70) REVERT: J 73 ASP cc_start: 0.8223 (t0) cc_final: 0.7962 (t0) REVERT: J 80 TYR cc_start: 0.7449 (m-80) cc_final: 0.7212 (m-10) REVERT: L 3 GLN cc_start: 0.8824 (tp40) cc_final: 0.8566 (mm-40) REVERT: L 37 GLN cc_start: 0.7206 (tt0) cc_final: 0.6612 (tm-30) REVERT: L 79 GLN cc_start: 0.6446 (pp30) cc_final: 0.6239 (pp30) REVERT: M 61 ARG cc_start: 0.7941 (ptt180) cc_final: 0.7496 (ptt180) REVERT: M 91 TYR cc_start: 0.8481 (p90) cc_final: 0.8251 (p90) REVERT: N 2 ILE cc_start: 0.7453 (OUTLIER) cc_final: 0.6792 (mp) REVERT: N 3 GLN cc_start: 0.8892 (mm110) cc_final: 0.8226 (pp30) REVERT: N 27 ASP cc_start: 0.8443 (t0) cc_final: 0.7848 (m-30) REVERT: N 37 GLN cc_start: 0.7117 (tt0) cc_final: 0.6670 (tt0) REVERT: N 61 ARG cc_start: 0.7558 (ptt180) cc_final: 0.6990 (ptt90) outliers start: 41 outliers final: 29 residues processed: 249 average time/residue: 0.2313 time to fit residues: 90.7915 Evaluate side-chains 247 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 384 PHE Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 106 TRP Chi-restraints excluded: chain N residue 2 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 236 optimal weight: 9.9990 chunk 217 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 200 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19683 Z= 0.321 Angle : 0.588 10.732 26748 Z= 0.310 Chirality : 0.043 0.151 2907 Planarity : 0.004 0.043 3456 Dihedral : 4.693 19.153 2688 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.88 % Allowed : 16.59 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.17), residues: 2385 helix: 1.52 (0.30), residues: 297 sheet: -1.33 (0.16), residues: 879 loop : -0.72 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP H 36 HIS 0.007 0.001 HIS A 516 PHE 0.023 0.001 PHE A 294 TYR 0.045 0.001 TYR A 653 ARG 0.007 0.000 ARG C 178 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 2.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 421 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8130 (mpp) REVERT: B 534 HIS cc_start: 0.8739 (OUTLIER) cc_final: 0.7856 (t-90) REVERT: B 587 MET cc_start: 0.8952 (mtp) cc_final: 0.8198 (ttm) REVERT: C 421 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8213 (mpp) REVERT: C 534 HIS cc_start: 0.8752 (OUTLIER) cc_final: 0.7627 (t-90) REVERT: H 59 HIS cc_start: 0.7934 (m-70) cc_final: 0.7558 (m-70) REVERT: H 112 GLN cc_start: 0.7298 (pm20) cc_final: 0.7039 (pm20) REVERT: I 10 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6285 (mm-30) REVERT: I 112 GLN cc_start: 0.6934 (pm20) cc_final: 0.6669 (pm20) REVERT: J 73 ASP cc_start: 0.8244 (t0) cc_final: 0.7998 (t0) REVERT: J 80 TYR cc_start: 0.7513 (m-80) cc_final: 0.7298 (m-10) REVERT: L 3 GLN cc_start: 0.8793 (tp40) cc_final: 0.8023 (pp30) REVERT: L 79 GLN cc_start: 0.6447 (pp30) cc_final: 0.6225 (pp30) REVERT: M 91 TYR cc_start: 0.8487 (p90) cc_final: 0.8236 (p90) REVERT: N 2 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.6813 (mp) REVERT: N 3 GLN cc_start: 0.8905 (mm110) cc_final: 0.8211 (pp30) REVERT: N 27 ASP cc_start: 0.8463 (t0) cc_final: 0.7773 (m-30) REVERT: N 37 GLN cc_start: 0.7151 (tt0) cc_final: 0.6741 (tm-30) REVERT: N 61 ARG cc_start: 0.7552 (ptt180) cc_final: 0.7041 (ptt90) REVERT: N 79 GLN cc_start: 0.6687 (pp30) cc_final: 0.6430 (pp30) outliers start: 39 outliers final: 29 residues processed: 243 average time/residue: 0.2680 time to fit residues: 103.6251 Evaluate side-chains 244 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 210 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 106 TRP Chi-restraints excluded: chain N residue 2 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 188 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 193 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: