Starting phenix.real_space_refine on Sat Apr 6 14:10:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fqd_29384/04_2024/8fqd_29384_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fqd_29384/04_2024/8fqd_29384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fqd_29384/04_2024/8fqd_29384.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fqd_29384/04_2024/8fqd_29384.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fqd_29384/04_2024/8fqd_29384_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fqd_29384/04_2024/8fqd_29384_updated.pdb" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 64 5.16 5 Cl 4 4.86 5 C 5332 2.51 5 N 1384 2.21 5 O 1600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 419": "OE1" <-> "OE2" Residue "A GLU 644": "OE1" <-> "OE2" Residue "A ASP 668": "OD1" <-> "OD2" Residue "B ASP 456": "OD1" <-> "OD2" Residue "B GLU 644": "OE1" <-> "OE2" Residue "B ASP 668": "OD1" <-> "OD2" Residue "B ASP 728": "OD1" <-> "OD2" Residue "C GLU 419": "OE1" <-> "OE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 447": "OD1" <-> "OD2" Residue "C TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 486": "OE1" <-> "OE2" Residue "C ASP 638": "OD1" <-> "OD2" Residue "C ASP 651": "OD1" <-> "OD2" Residue "C ASP 668": "OD1" <-> "OD2" Residue "C ASP 719": "OD1" <-> "OD2" Residue "C ASP 728": "OD1" <-> "OD2" Residue "C TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 634": "OE1" <-> "OE2" Residue "D GLU 637": "OE1" <-> "OE2" Residue "D TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 713": "OE1" <-> "OE2" Residue "B GLU 1301": "OE1" <-> "OE2" Residue "D GLU 1301": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8384 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "B" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "D" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.83, per 1000 atoms: 0.58 Number of scatterers: 8384 At special positions: 0 Unit cell: (121.212, 92.547, 83.538, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 64 16.00 O 1600 8.00 N 1384 7.00 C 5332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 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: 3.29 Conformation dependent library (CDL) restraints added in 1.6 seconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 16 sheets defined 35.4% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 417 through 420 removed outlier: 3.653A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 420' Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 636 through 641 Processing helix chain 'A' and resid 655 through 660 Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 743 through 756 Processing helix chain 'A' and resid 758 through 767 Processing helix chain 'B' and resid 417 through 420 Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 636 through 641 Processing helix chain 'B' and resid 654 through 660 Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 686 through 695 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 758 through 767 Processing helix chain 'C' and resid 417 through 420 removed outlier: 3.829A pdb=" N ARG C 420 " --> pdb=" O GLY C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 483 through 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' Processing helix chain 'C' and resid 636 through 641 Processing helix chain 'C' and resid 655 through 660 Processing helix chain 'C' and resid 665 through 675 Processing helix chain 'C' and resid 686 through 694 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 742 through 755 Processing helix chain 'C' and resid 758 through 767 Processing helix chain 'D' and resid 417 through 420 Processing helix chain 'D' and resid 424 through 435 Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 637 through 641 Processing helix chain 'D' and resid 654 through 661 Processing helix chain 'D' and resid 665 through 675 Processing helix chain 'D' and resid 686 through 695 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 758 through 767 Processing sheet with id= A, first strand: chain 'A' and resid 395 through 399 Processing sheet with id= B, first strand: chain 'A' and resid 489 through 491 Processing sheet with id= C, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.122A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 720 through 723 removed outlier: 4.164A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 395 through 399 Processing sheet with id= F, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= G, first strand: chain 'B' and resid 496 through 498 removed outlier: 4.209A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 720 through 723 removed outlier: 4.138A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= J, first strand: chain 'C' and resid 489 through 491 Processing sheet with id= K, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.208A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 702 through 705 removed outlier: 4.409A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 395 through 399 Processing sheet with id= N, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= O, first strand: chain 'D' and resid 496 through 498 removed outlier: 4.141A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 720 through 723 removed outlier: 4.134A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) 264 hydrogen bonds defined for protein. 771 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: 1.98 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2630 1.35 - 1.48: 2040 1.48 - 1.60: 3724 1.60 - 1.73: 40 1.73 - 1.85: 104 Bond restraints: 8538 Sorted by residual: bond pdb=" C3 CYZ A1302 " pdb=" C4 CYZ A1302 " ideal model delta sigma weight residual 1.334 1.578 -0.244 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ B1302 " pdb=" C4 CYZ B1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ C1302 " pdb=" C4 CYZ C1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ D1302 " pdb=" C4 CYZ D1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C5 CYZ C1302 " pdb=" C6 CYZ C1302 " ideal model delta sigma weight residual 1.553 1.331 0.222 2.00e-02 2.50e+03 1.23e+02 ... (remaining 8533 not shown) Histogram of bond angle deviations from ideal: 91.80 - 100.24: 21 100.24 - 108.68: 392 108.68 - 117.11: 5719 117.11 - 125.55: 5277 125.55 - 133.98: 111 Bond angle restraints: 11520 Sorted by residual: angle pdb=" CB MET C 408 " pdb=" CG MET C 408 " pdb=" SD MET C 408 " ideal model delta sigma weight residual 112.70 123.70 -11.00 3.00e+00 1.11e-01 1.35e+01 angle pdb=" N LYS A 410 " pdb=" CA LYS A 410 " pdb=" C LYS A 410 " ideal model delta sigma weight residual 114.75 110.36 4.39 1.26e+00 6.30e-01 1.22e+01 angle pdb=" C9 CYZ B1302 " pdb=" S1 CYZ B1302 " pdb=" N1 CYZ B1302 " ideal model delta sigma weight residual 101.75 111.45 -9.70 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C9 CYZ D1302 " pdb=" S1 CYZ D1302 " pdb=" N1 CYZ D1302 " ideal model delta sigma weight residual 101.75 111.42 -9.67 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C9 CYZ C1302 " pdb=" S1 CYZ C1302 " pdb=" N1 CYZ C1302 " ideal model delta sigma weight residual 101.75 111.40 -9.65 3.00e+00 1.11e-01 1.04e+01 ... (remaining 11515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.84: 4719 22.84 - 45.68: 453 45.68 - 68.52: 52 68.52 - 91.36: 13 91.36 - 114.20: 11 Dihedral angle restraints: 5248 sinusoidal: 2196 harmonic: 3052 Sorted by residual: dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 166.55 -73.55 1 1.00e+01 1.00e-02 6.88e+01 dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual 93.00 158.00 -65.00 1 1.00e+01 1.00e-02 5.54e+01 dihedral pdb=" N2 CYZ C1302 " pdb=" C8 CYZ C1302 " pdb=" N1 CYZ C1302 " pdb=" S1 CYZ C1302 " ideal model delta sinusoidal sigma weight residual 55.73 -58.47 114.20 1 3.00e+01 1.11e-03 1.50e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1171 0.085 - 0.170: 97 0.170 - 0.255: 0 0.255 - 0.340: 0 0.340 - 0.425: 16 Chirality restraints: 1284 Sorted by residual: chirality pdb=" C2 CYZ A1302 " pdb=" C1 CYZ A1302 " pdb=" C3 CYZ A1302 " pdb=" C7 CYZ A1302 " both_signs ideal model delta sigma weight residual False 3.31 2.88 0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" C2 CYZ B1302 " pdb=" C1 CYZ B1302 " pdb=" C3 CYZ B1302 " pdb=" C7 CYZ B1302 " both_signs ideal model delta sigma weight residual False 3.31 2.89 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" C8 CYZ A1302 " pdb=" C1 CYZ A1302 " pdb=" N1 CYZ A1302 " pdb=" N2 CYZ A1302 " both_signs ideal model delta sigma weight residual False 2.20 2.63 -0.42 2.00e-01 2.50e+01 4.46e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 736 " 0.022 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO C 737 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 737 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 737 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 766 " 0.010 2.00e-02 2.50e+03 7.83e-03 1.53e+00 pdb=" CG TRP B 766 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP B 766 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 766 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 766 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 766 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 766 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 766 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 766 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 766 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 493 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO C 494 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO C 494 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 494 " -0.016 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2026 2.79 - 3.32: 7687 3.32 - 3.85: 14022 3.85 - 4.37: 16634 4.37 - 4.90: 28574 Nonbonded interactions: 68943 Sorted by model distance: nonbonded pdb=" OE1 GLU D 402 " pdb=" OH TYR D 450 " model vdw 2.264 2.440 nonbonded pdb=" O ARG B 692 " pdb=" OG SER B 696 " model vdw 2.278 2.440 nonbonded pdb=" OH TYR A 424 " pdb=" O HOH A1401 " model vdw 2.327 2.440 nonbonded pdb=" N ASP A 719 " pdb=" OD1 ASP A 719 " model vdw 2.334 2.520 nonbonded pdb=" O LEU D 639 " pdb=" NE2 GLN D 642 " model vdw 2.335 2.520 ... (remaining 68938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'D' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) } 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: 2.290 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: 10.250 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 25.700 Find NCS groups from input model: 0.480 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.015 0.244 8538 Z= 0.931 Angle : 0.732 11.004 11520 Z= 0.325 Chirality : 0.062 0.425 1284 Planarity : 0.003 0.036 1422 Dihedral : 17.597 114.195 3288 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.11 % Allowed : 18.57 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.68 (0.25), residues: 1044 helix: 0.79 (0.25), residues: 430 sheet: -0.75 (0.40), residues: 146 loop : -1.52 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 766 HIS 0.004 0.001 HIS C 412 PHE 0.014 0.001 PHE D 495 TYR 0.010 0.001 TYR A 702 ARG 0.008 0.001 ARG C 453 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 0.965 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 151 average time/residue: 0.2986 time to fit residues: 56.9974 Evaluate side-chains 142 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8538 Z= 0.215 Angle : 0.515 6.297 11520 Z= 0.254 Chirality : 0.044 0.149 1284 Planarity : 0.004 0.037 1422 Dihedral : 10.502 96.475 1267 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.46 % Allowed : 17.00 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -0.86 (0.25), residues: 1044 helix: 0.57 (0.25), residues: 426 sheet: -1.00 (0.36), residues: 178 loop : -1.46 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 766 HIS 0.003 0.001 HIS C 412 PHE 0.015 0.002 PHE D 495 TYR 0.012 0.001 TYR A 702 ARG 0.005 0.001 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 0.978 Fit side-chains REVERT: A 705 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7362 (mm-30) outliers start: 22 outliers final: 12 residues processed: 151 average time/residue: 0.2835 time to fit residues: 54.4698 Evaluate side-chains 150 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 498 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 8538 Z= 0.541 Angle : 0.730 10.109 11520 Z= 0.359 Chirality : 0.053 0.206 1284 Planarity : 0.005 0.044 1422 Dihedral : 12.079 111.191 1267 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.91 % Allowed : 18.46 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 (0.23), residues: 1044 helix: -0.50 (0.24), residues: 418 sheet: -1.01 (0.35), residues: 184 loop : -1.63 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 767 HIS 0.004 0.001 HIS A 412 PHE 0.023 0.003 PHE D 495 TYR 0.017 0.003 TYR A 702 ARG 0.005 0.001 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 143 time to evaluate : 0.936 Fit side-chains REVERT: A 705 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7456 (mm-30) REVERT: A 715 ARG cc_start: 0.7709 (mmt180) cc_final: 0.7424 (mpt180) outliers start: 35 outliers final: 23 residues processed: 165 average time/residue: 0.2994 time to fit residues: 62.0957 Evaluate side-chains 152 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 498 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8538 Z= 0.183 Angle : 0.518 9.659 11520 Z= 0.256 Chirality : 0.044 0.139 1284 Planarity : 0.004 0.045 1422 Dihedral : 10.782 97.988 1267 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.02 % Allowed : 19.91 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: -1.23 (0.24), residues: 1044 helix: 0.07 (0.25), residues: 424 sheet: -0.89 (0.36), residues: 182 loop : -1.60 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 766 HIS 0.005 0.001 HIS A 412 PHE 0.016 0.001 PHE D 495 TYR 0.009 0.001 TYR D 673 ARG 0.006 0.000 ARG A 453 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 0.977 Fit side-chains REVERT: A 705 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7180 (mm-30) outliers start: 27 outliers final: 15 residues processed: 173 average time/residue: 0.2922 time to fit residues: 63.8616 Evaluate side-chains 160 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 498 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/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-5288/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-5288/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-5288/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-5288/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-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/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-5288/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-5288/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-5288/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: 55.1643 > 50: distance: 39 - 40: 6.684 distance: 40 - 41: 9.701 distance: 40 - 43: 4.692 distance: 41 - 42: 9.246 distance: 41 - 47: 7.676 distance: 43 - 44: 26.104 distance: 44 - 45: 16.681 distance: 44 - 46: 7.823 distance: 47 - 48: 13.589 distance: 48 - 49: 18.649 distance: 48 - 51: 9.506 distance: 49 - 50: 30.131 distance: 49 - 54: 15.967 distance: 51 - 52: 9.453 distance: 51 - 53: 19.626 distance: 54 - 55: 7.446 distance: 55 - 56: 11.421 distance: 56 - 57: 15.740 distance: 56 - 61: 12.476 distance: 58 - 59: 10.400 distance: 58 - 60: 19.582 distance: 61 - 62: 11.615 distance: 62 - 63: 5.951 distance: 62 - 65: 5.697 distance: 63 - 64: 10.967 distance: 63 - 70: 9.564 distance: 65 - 66: 4.867 distance: 67 - 68: 4.651 distance: 67 - 69: 6.274 distance: 70 - 71: 15.977 distance: 71 - 72: 8.887 distance: 71 - 74: 16.574 distance: 72 - 73: 30.265 distance: 72 - 81: 14.679 distance: 74 - 75: 17.487 distance: 75 - 76: 7.076 distance: 76 - 77: 5.969 distance: 77 - 78: 8.168 distance: 78 - 79: 3.183 distance: 81 - 82: 17.548 distance: 82 - 83: 18.233 distance: 82 - 85: 9.145 distance: 83 - 84: 19.407 distance: 83 - 89: 28.243 distance: 85 - 86: 17.581 distance: 86 - 87: 22.489 distance: 87 - 88: 4.474 distance: 89 - 90: 21.824 distance: 90 - 91: 13.957 distance: 90 - 93: 28.798 distance: 91 - 92: 28.470 distance: 91 - 96: 28.546 distance: 93 - 94: 35.555 distance: 93 - 95: 17.260 distance: 96 - 97: 20.227 distance: 97 - 98: 29.296 distance: 97 - 100: 25.033 distance: 98 - 99: 26.096 distance: 98 - 102: 18.064 distance: 100 - 101: 26.986 distance: 102 - 103: 8.812 distance: 102 - 108: 24.396 distance: 103 - 104: 12.150 distance: 103 - 106: 19.908 distance: 104 - 105: 11.922 distance: 104 - 109: 12.818 distance: 106 - 107: 11.358 distance: 107 - 108: 48.816