Starting phenix.real_space_refine on Sun Aug 4 12:37:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh2_23334/08_2024/7lh2_23334.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh2_23334/08_2024/7lh2_23334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh2_23334/08_2024/7lh2_23334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh2_23334/08_2024/7lh2_23334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh2_23334/08_2024/7lh2_23334.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lh2_23334/08_2024/7lh2_23334.cif" } resolution = 3.43 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= 0.005 sd= 0.025 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 48 5.16 5 C 6930 2.51 5 N 1690 2.21 5 O 1860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 31": "NH1" <-> "NH2" Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A ARG 130": "NH1" <-> "NH2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 686": "OD1" <-> "OD2" Residue "A ARG 689": "NH1" <-> "NH2" Residue "A GLU 694": "OE1" <-> "OE2" Residue "B ARG 31": "NH1" <-> "NH2" Residue "B PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B ARG 502": "NH1" <-> "NH2" Residue "B TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 558": "NH1" <-> "NH2" Residue "B TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 686": "OD1" <-> "OD2" Residue "B ARG 689": "NH1" <-> "NH2" Residue "B GLU 694": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10528 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5226 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 34, 'TRANS': 645} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 5226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5226 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 34, 'TRANS': 645} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'CLR': 1, 'SAL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'CLR': 1, 'SAL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.34, per 1000 atoms: 0.60 Number of scatterers: 10528 At special positions: 0 Unit cell: (102.16, 120.379, 113.872, 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 48 16.00 O 1860 8.00 N 1690 7.00 C 6930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.38 Conformation dependent library (CDL) restraints added in 2.1 seconds 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2512 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 5 sheets defined 69.6% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 43 through 48 removed outlier: 3.592A pdb=" N LYS A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 48' Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 75 through 105 removed outlier: 5.451A pdb=" N LEU A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLY A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 109 through 115 removed outlier: 3.768A pdb=" N LEU A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 removed outlier: 3.664A pdb=" N PHE A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 152 Processing helix chain 'A' and resid 168 through 196 Processing helix chain 'A' and resid 197 through 205 removed outlier: 3.982A pdb=" N PHE A 200 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 202 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE A 203 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 254 through 257 Processing helix chain 'A' and resid 258 through 282 Processing helix chain 'A' and resid 291 through 308 removed outlier: 3.614A pdb=" N PHE A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.845A pdb=" N TYR A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 366 removed outlier: 6.494A pdb=" N VAL A 341 " --> pdb=" O HIS A 337 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ASP A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 Processing helix chain 'A' and resid 396 through 406 Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 436 through 448 removed outlier: 3.783A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 456 through 465 removed outlier: 3.549A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 481 Processing helix chain 'A' and resid 483 through 505 removed outlier: 3.866A pdb=" N LEU A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 560 removed outlier: 3.670A pdb=" N THR A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 579 Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 653 through 670 removed outlier: 3.747A pdb=" N VAL A 670 " --> pdb=" O GLU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 690 Processing helix chain 'A' and resid 695 through 702 removed outlier: 3.928A pdb=" N GLU A 700 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 725 removed outlier: 4.045A pdb=" N SER A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 30 Processing helix chain 'B' and resid 43 through 48 removed outlier: 3.592A pdb=" N LYS B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 48' Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 75 through 105 removed outlier: 5.451A pdb=" N LEU B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLY B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) Proline residue: B 96 - end of helix Processing helix chain 'B' and resid 109 through 115 removed outlier: 3.769A pdb=" N LEU B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 127 removed outlier: 3.665A pdb=" N PHE B 125 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 152 Processing helix chain 'B' and resid 168 through 196 Processing helix chain 'B' and resid 197 through 205 removed outlier: 3.982A pdb=" N PHE B 200 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 202 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE B 203 " --> pdb=" O PHE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 225 Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'B' and resid 241 through 253 Processing helix chain 'B' and resid 254 through 257 Processing helix chain 'B' and resid 258 through 282 Processing helix chain 'B' and resid 291 through 308 removed outlier: 3.614A pdb=" N PHE B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.846A pdb=" N TYR B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 366 removed outlier: 6.493A pdb=" N VAL B 341 " --> pdb=" O HIS B 337 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ASP B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 396 through 406 Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 436 through 448 removed outlier: 3.783A pdb=" N LEU B 440 " --> pdb=" O PRO B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 456 through 465 removed outlier: 3.548A pdb=" N PHE B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 481 Processing helix chain 'B' and resid 483 through 505 removed outlier: 3.866A pdb=" N LEU B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 560 removed outlier: 3.670A pdb=" N THR B 560 " --> pdb=" O LEU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 579 Processing helix chain 'B' and resid 626 through 631 Processing helix chain 'B' and resid 653 through 670 removed outlier: 3.747A pdb=" N VAL B 670 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 690 Processing helix chain 'B' and resid 695 through 702 removed outlier: 3.928A pdb=" N GLU B 700 " --> pdb=" O ALA B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 725 removed outlier: 4.044A pdb=" N SER B 725 " --> pdb=" O GLU B 721 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 135 removed outlier: 3.587A pdb=" N SER A 394 " --> pdb=" O GLY A 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.891A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N LYS A 513 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 12.029A pdb=" N ILE A 535 " --> pdb=" O LYS A 513 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS A 536 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASP A 645 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE A 538 " --> pdb=" O ASP A 645 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL A 642 " --> pdb=" O TYR A 675 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ALA A 677 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU A 644 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 134 through 135 removed outlier: 3.588A pdb=" N SER B 394 " --> pdb=" O GLY B 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.891A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N LYS B 513 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 12.029A pdb=" N ILE B 535 " --> pdb=" O LYS B 513 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LYS B 536 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASP B 645 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE B 538 " --> pdb=" O ASP B 645 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL B 642 " --> pdb=" O TYR B 675 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ALA B 677 " --> pdb=" O VAL B 642 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU B 644 " --> pdb=" O ALA B 677 " (cutoff:3.500A) 646 hydrogen bonds defined for protein. 1878 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: 3.05 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3242 1.34 - 1.46: 2346 1.46 - 1.58: 5104 1.58 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 10770 Sorted by residual: bond pdb=" C1 SAL A 801 " pdb=" C2 SAL A 801 " ideal model delta sigma weight residual 1.409 1.484 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C1 SAL B 801 " pdb=" C2 SAL B 801 " ideal model delta sigma weight residual 1.409 1.484 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" N VAL B 402 " pdb=" CA VAL B 402 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.49e+00 bond pdb=" N SER B 398 " pdb=" CA SER B 398 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.19e-02 7.06e+03 6.66e+00 bond pdb=" N GLN B 403 " pdb=" CA GLN B 403 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.83e+00 ... (remaining 10765 not shown) Histogram of bond angle deviations from ideal: 99.01 - 106.00: 294 106.00 - 113.00: 5913 113.00 - 120.00: 3689 120.00 - 126.99: 4658 126.99 - 133.99: 100 Bond angle restraints: 14654 Sorted by residual: angle pdb=" O VAL B 402 " pdb=" C VAL B 402 " pdb=" N GLN B 403 " ideal model delta sigma weight residual 121.87 124.67 -2.80 9.70e-01 1.06e+00 8.32e+00 angle pdb=" CA LEU A 448 " pdb=" CB LEU A 448 " pdb=" CG LEU A 448 " ideal model delta sigma weight residual 116.30 125.79 -9.49 3.50e+00 8.16e-02 7.36e+00 angle pdb=" CA LEU B 448 " pdb=" CB LEU B 448 " pdb=" CG LEU B 448 " ideal model delta sigma weight residual 116.30 125.74 -9.44 3.50e+00 8.16e-02 7.27e+00 angle pdb=" CA SER B 398 " pdb=" C SER B 398 " pdb=" O SER B 398 " ideal model delta sigma weight residual 120.82 118.04 2.78 1.05e+00 9.07e-01 7.00e+00 angle pdb=" CA ARG B 399 " pdb=" C ARG B 399 " pdb=" O ARG B 399 " ideal model delta sigma weight residual 120.55 117.84 2.71 1.06e+00 8.90e-01 6.52e+00 ... (remaining 14649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 5809 16.06 - 32.13: 527 32.13 - 48.19: 100 48.19 - 64.25: 22 64.25 - 80.32: 12 Dihedral angle restraints: 6470 sinusoidal: 2546 harmonic: 3924 Sorted by residual: dihedral pdb=" CA PHE A 23 " pdb=" C PHE A 23 " pdb=" N SER A 24 " pdb=" CA SER A 24 " ideal model delta harmonic sigma weight residual 180.00 160.58 19.42 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA PHE B 23 " pdb=" C PHE B 23 " pdb=" N SER B 24 " pdb=" CA SER B 24 " ideal model delta harmonic sigma weight residual 180.00 160.58 19.42 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ASP B 686 " pdb=" CB ASP B 686 " pdb=" CG ASP B 686 " pdb=" OD1 ASP B 686 " ideal model delta sinusoidal sigma weight residual -30.00 -87.57 57.57 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 6467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1174 0.039 - 0.077: 427 0.077 - 0.116: 123 0.116 - 0.154: 16 0.154 - 0.193: 4 Chirality restraints: 1744 Sorted by residual: chirality pdb=" CG LEU A 193 " pdb=" CB LEU A 193 " pdb=" CD1 LEU A 193 " pdb=" CD2 LEU A 193 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" CG LEU B 193 " pdb=" CB LEU B 193 " pdb=" CD1 LEU B 193 " pdb=" CD2 LEU B 193 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CA VAL B 402 " pdb=" N VAL B 402 " pdb=" C VAL B 402 " pdb=" CB VAL B 402 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.28e-01 ... (remaining 1741 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 633 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO B 634 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 634 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 634 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 633 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO A 634 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 634 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 634 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 198 " 0.015 2.00e-02 2.50e+03 1.47e-02 3.78e+00 pdb=" CG PHE B 198 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 198 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 198 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 198 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 198 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 198 " 0.000 2.00e-02 2.50e+03 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 64 2.60 - 3.18: 9454 3.18 - 3.75: 16149 3.75 - 4.33: 21547 4.33 - 4.90: 36174 Nonbonded interactions: 83388 Sorted by model distance: nonbonded pdb=" OG SER A 398 " pdb=" O2' SAL A 801 " model vdw 2.030 3.040 nonbonded pdb=" OG SER B 86 " pdb=" O GLN B 403 " model vdw 2.164 3.040 nonbonded pdb=" OD2 ASP A 83 " pdb=" OG1 THR A 410 " model vdw 2.223 3.040 nonbonded pdb=" OD2 ASP B 83 " pdb=" OG1 THR B 410 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR B 503 " pdb=" OH TYR B 545 " model vdw 2.226 3.040 ... (remaining 83383 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.000 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.290 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.003 0.075 10770 Z= 0.198 Angle : 0.558 9.493 14654 Z= 0.304 Chirality : 0.043 0.193 1744 Planarity : 0.004 0.053 1812 Dihedral : 13.017 80.315 3958 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.18 % Allowed : 0.53 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.24), residues: 1352 helix: 1.34 (0.18), residues: 894 sheet: 1.90 (0.69), residues: 52 loop : -1.07 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 472 HIS 0.002 0.001 HIS A 25 PHE 0.034 0.001 PHE B 198 TYR 0.014 0.001 TYR B 237 ARG 0.008 0.001 ARG B 572 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 1.192 Fit side-chains REVERT: A 545 TYR cc_start: 0.8268 (p90) cc_final: 0.7954 (p90) outliers start: 2 outliers final: 2 residues processed: 146 average time/residue: 0.1816 time to fit residues: 40.6981 Evaluate side-chains 105 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain B residue 453 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 0.2980 chunk 35 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10770 Z= 0.171 Angle : 0.533 11.041 14654 Z= 0.263 Chirality : 0.042 0.128 1744 Planarity : 0.004 0.050 1812 Dihedral : 4.935 42.852 1594 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.15 % Allowed : 7.67 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.24), residues: 1352 helix: 1.60 (0.18), residues: 896 sheet: 2.11 (0.70), residues: 52 loop : -1.03 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 699 HIS 0.006 0.001 HIS A 704 PHE 0.021 0.001 PHE A 198 TYR 0.012 0.001 TYR A 237 ARG 0.004 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 1.212 Fit side-chains REVERT: A 198 PHE cc_start: 0.7637 (t80) cc_final: 0.7419 (t80) REVERT: A 545 TYR cc_start: 0.8422 (p90) cc_final: 0.8016 (p90) REVERT: B 198 PHE cc_start: 0.6976 (t80) cc_final: 0.6541 (t80) outliers start: 13 outliers final: 10 residues processed: 132 average time/residue: 0.2032 time to fit residues: 39.7008 Evaluate side-chains 116 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 424 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 99 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: ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10770 Z= 0.207 Angle : 0.532 9.857 14654 Z= 0.262 Chirality : 0.043 0.127 1744 Planarity : 0.004 0.054 1812 Dihedral : 4.323 38.200 1588 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.20 % Allowed : 9.17 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.24), residues: 1352 helix: 1.77 (0.18), residues: 888 sheet: 2.07 (0.70), residues: 52 loop : -0.86 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 70 HIS 0.004 0.001 HIS A 704 PHE 0.015 0.001 PHE A 198 TYR 0.014 0.001 TYR A 578 ARG 0.005 0.000 ARG B 572 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 1.192 Fit side-chains revert: symmetry clash REVERT: A 575 MET cc_start: 0.6883 (tmm) cc_final: 0.6662 (ppp) REVERT: B 198 PHE cc_start: 0.6948 (t80) cc_final: 0.6479 (t80) REVERT: B 694 GLU cc_start: 0.6691 (mm-30) cc_final: 0.6456 (mp0) outliers start: 25 outliers final: 16 residues processed: 137 average time/residue: 0.1821 time to fit residues: 38.0051 Evaluate side-chains 123 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 453 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 124 optimal weight: 40.0000 chunk 131 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10770 Z= 0.259 Angle : 0.542 8.096 14654 Z= 0.271 Chirality : 0.043 0.128 1744 Planarity : 0.004 0.054 1812 Dihedral : 4.217 33.634 1588 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.59 % Allowed : 13.05 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.24), residues: 1352 helix: 1.76 (0.18), residues: 886 sheet: 1.93 (0.69), residues: 52 loop : -0.85 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 70 HIS 0.004 0.001 HIS A 704 PHE 0.015 0.001 PHE A 198 TYR 0.017 0.001 TYR B 578 ARG 0.006 0.001 ARG B 572 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 227 LYS cc_start: 0.7707 (ptmt) cc_final: 0.7380 (ptpt) REVERT: A 694 GLU cc_start: 0.6680 (mm-30) cc_final: 0.6431 (mp0) REVERT: B 198 PHE cc_start: 0.7037 (t80) cc_final: 0.6526 (t80) REVERT: B 227 LYS cc_start: 0.7691 (ptmt) cc_final: 0.7371 (ptpt) outliers start: 18 outliers final: 15 residues processed: 130 average time/residue: 0.2010 time to fit residues: 38.9154 Evaluate side-chains 123 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 452 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10770 Z= 0.152 Angle : 0.506 9.437 14654 Z= 0.249 Chirality : 0.042 0.126 1744 Planarity : 0.004 0.053 1812 Dihedral : 4.039 31.887 1588 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.59 % Allowed : 13.14 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.24), residues: 1352 helix: 1.94 (0.18), residues: 884 sheet: 1.98 (0.69), residues: 52 loop : -0.73 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 70 HIS 0.003 0.001 HIS A 704 PHE 0.018 0.001 PHE A 198 TYR 0.010 0.001 TYR B 578 ARG 0.005 0.000 ARG A 572 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 1.365 Fit side-chains REVERT: A 227 LYS cc_start: 0.7670 (ptmt) cc_final: 0.7295 (ptpp) REVERT: B 198 PHE cc_start: 0.6981 (t80) cc_final: 0.6453 (t80) REVERT: B 227 LYS cc_start: 0.7650 (ptmt) cc_final: 0.7283 (ptpp) REVERT: B 694 GLU cc_start: 0.6661 (mm-30) cc_final: 0.6411 (mp0) outliers start: 18 outliers final: 16 residues processed: 127 average time/residue: 0.2250 time to fit residues: 41.9915 Evaluate side-chains 125 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 452 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 126 optimal weight: 0.0060 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10770 Z= 0.158 Angle : 0.509 8.671 14654 Z= 0.248 Chirality : 0.041 0.126 1744 Planarity : 0.004 0.054 1812 Dihedral : 4.049 39.760 1588 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.76 % Allowed : 13.67 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.24), residues: 1352 helix: 2.01 (0.18), residues: 888 sheet: 2.04 (0.69), residues: 52 loop : -0.78 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 70 HIS 0.002 0.001 HIS A 704 PHE 0.009 0.001 PHE B 391 TYR 0.010 0.001 TYR A 545 ARG 0.006 0.000 ARG A 572 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 1.166 Fit side-chains REVERT: A 70 TRP cc_start: 0.7917 (p-90) cc_final: 0.7639 (p-90) REVERT: A 227 LYS cc_start: 0.7693 (ptmt) cc_final: 0.7317 (ptpp) REVERT: A 694 GLU cc_start: 0.6618 (mm-30) cc_final: 0.6328 (mp0) REVERT: B 198 PHE cc_start: 0.7008 (t80) cc_final: 0.6466 (t80) REVERT: B 227 LYS cc_start: 0.7651 (ptmt) cc_final: 0.7293 (ptpp) REVERT: B 694 GLU cc_start: 0.6669 (mm-30) cc_final: 0.6440 (mp0) outliers start: 20 outliers final: 17 residues processed: 129 average time/residue: 0.1941 time to fit residues: 37.6020 Evaluate side-chains 125 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 452 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 131 optimal weight: 7.9990 chunk 82 optimal weight: 0.0670 chunk 79 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10770 Z= 0.260 Angle : 0.562 8.543 14654 Z= 0.277 Chirality : 0.043 0.130 1744 Planarity : 0.004 0.055 1812 Dihedral : 4.291 46.925 1588 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.68 % Allowed : 14.29 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.24), residues: 1352 helix: 1.94 (0.18), residues: 888 sheet: 1.82 (0.69), residues: 52 loop : -0.88 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 70 HIS 0.003 0.001 HIS A 704 PHE 0.014 0.001 PHE A 111 TYR 0.015 0.001 TYR A 237 ARG 0.008 0.001 ARG A 572 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.214 Fit side-chains REVERT: A 227 LYS cc_start: 0.7703 (ptmt) cc_final: 0.7376 (ptpt) REVERT: B 198 PHE cc_start: 0.7044 (t80) cc_final: 0.6475 (t80) REVERT: B 227 LYS cc_start: 0.7671 (ptmt) cc_final: 0.7353 (ptpt) outliers start: 19 outliers final: 17 residues processed: 128 average time/residue: 0.2009 time to fit residues: 38.2428 Evaluate side-chains 125 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 452 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 89 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 119 optimal weight: 8.9990 chunk 125 optimal weight: 0.0070 chunk 114 optimal weight: 8.9990 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10770 Z= 0.226 Angle : 0.538 8.018 14654 Z= 0.267 Chirality : 0.042 0.125 1744 Planarity : 0.004 0.055 1812 Dihedral : 4.377 50.374 1588 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.76 % Allowed : 15.17 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.24), residues: 1352 helix: 2.01 (0.18), residues: 884 sheet: 1.83 (0.69), residues: 52 loop : -0.78 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 70 HIS 0.009 0.001 HIS B 704 PHE 0.011 0.001 PHE B 391 TYR 0.012 0.001 TYR A 237 ARG 0.009 0.000 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.271 Fit side-chains REVERT: A 227 LYS cc_start: 0.7722 (ptmt) cc_final: 0.7372 (ptpt) REVERT: A 694 GLU cc_start: 0.6596 (mm-30) cc_final: 0.6330 (mp0) REVERT: B 198 PHE cc_start: 0.7084 (t80) cc_final: 0.6485 (t80) REVERT: B 227 LYS cc_start: 0.7652 (ptmt) cc_final: 0.7332 (ptpt) REVERT: B 694 GLU cc_start: 0.6661 (mm-30) cc_final: 0.6436 (mp0) outliers start: 20 outliers final: 18 residues processed: 125 average time/residue: 0.2095 time to fit residues: 39.0756 Evaluate side-chains 124 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 452 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.5677 > 50: distance: 8 - 34: 6.081 distance: 28 - 34: 5.614 distance: 34 - 35: 6.688 distance: 35 - 36: 8.390 distance: 35 - 38: 13.895 distance: 36 - 37: 9.630 distance: 36 - 45: 5.892 distance: 38 - 39: 3.484 distance: 39 - 40: 17.395 distance: 39 - 41: 14.353 distance: 40 - 42: 8.309 distance: 41 - 43: 4.600 distance: 42 - 44: 18.693 distance: 43 - 44: 19.591 distance: 45 - 46: 5.571 distance: 46 - 47: 5.606 distance: 47 - 48: 4.119 distance: 47 - 54: 8.010 distance: 49 - 50: 9.034 distance: 50 - 51: 10.720 distance: 51 - 52: 7.743 distance: 52 - 53: 6.346 distance: 54 - 55: 18.152 distance: 55 - 56: 22.686 distance: 55 - 58: 8.970 distance: 56 - 57: 8.630 distance: 56 - 63: 12.674 distance: 58 - 59: 13.093 distance: 59 - 60: 8.446 distance: 60 - 61: 10.196 distance: 60 - 62: 13.546 distance: 63 - 64: 10.271 distance: 64 - 65: 3.553 distance: 64 - 67: 12.363 distance: 65 - 66: 6.890 distance: 65 - 72: 10.820 distance: 67 - 68: 20.986 distance: 68 - 69: 12.602 distance: 69 - 70: 16.573 distance: 70 - 71: 4.399 distance: 72 - 73: 24.763 distance: 73 - 74: 7.935 distance: 73 - 76: 12.201 distance: 74 - 75: 6.057 distance: 74 - 80: 7.436 distance: 76 - 77: 7.597 distance: 77 - 78: 16.057 distance: 77 - 79: 19.346 distance: 80 - 81: 3.390 distance: 80 - 86: 8.614 distance: 81 - 82: 5.360 distance: 81 - 84: 7.940 distance: 82 - 83: 9.408 distance: 82 - 87: 20.193 distance: 84 - 85: 9.296 distance: 85 - 86: 7.424 distance: 87 - 88: 6.285 distance: 88 - 89: 17.831 distance: 88 - 91: 22.221 distance: 89 - 90: 8.269 distance: 89 - 92: 9.363 distance: 92 - 93: 27.257 distance: 92 - 98: 13.323 distance: 93 - 94: 20.293 distance: 93 - 96: 19.198 distance: 94 - 95: 4.355 distance: 94 - 99: 6.091 distance: 96 - 97: 9.716 distance: 97 - 98: 25.617 distance: 99 - 100: 16.084 distance: 100 - 101: 25.369 distance: 100 - 103: 27.129 distance: 101 - 102: 20.793 distance: 101 - 107: 6.293 distance: 103 - 104: 20.944 distance: 103 - 105: 31.361 distance: 104 - 106: 25.355 distance: 107 - 108: 19.339 distance: 107 - 113: 9.036 distance: 108 - 109: 4.585 distance: 108 - 111: 13.130 distance: 109 - 110: 13.235 distance: 109 - 114: 18.977 distance: 111 - 112: 16.856 distance: 112 - 113: 14.479