Starting phenix.real_space_refine on Sun Dec 10 09:47:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/12_2023/6bze_7314.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/12_2023/6bze_7314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/12_2023/6bze_7314.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/12_2023/6bze_7314.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/12_2023/6bze_7314.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/12_2023/6bze_7314.pdb" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 0.006 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7072 atoms to isotropic. 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 16 5.16 5 C 4408 2.51 5 N 1296 2.21 5 O 1352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 11": "OE1" <-> "OE2" Residue "A GLU 22": "OE1" <-> "OE2" Residue "A GLU 30": "OE1" <-> "OE2" Residue "B GLU 11": "OE1" <-> "OE2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "C GLU 11": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "D GLU 11": "OE1" <-> "OE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "E GLU 11": "OE1" <-> "OE2" Residue "E GLU 22": "OE1" <-> "OE2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "F GLU 11": "OE1" <-> "OE2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "G GLU 11": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 30": "OE1" <-> "OE2" Residue "H GLU 11": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 30": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7072 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "B" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "C" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "D" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "E" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "F" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "G" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "H" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Time building chain proxies: 4.00, per 1000 atoms: 0.57 Number of scatterers: 7072 At special positions: 0 Unit cell: (105.7, 105.7, 87.58, 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 16 16.00 O 1352 8.00 N 1296 7.00 C 4408 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: 2.94 Conformation dependent library (CDL) restraints added in 1.3 seconds 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 74.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 12 through 25 removed outlier: 3.778A pdb=" N VAL A 16 " --> pdb=" O ASP A 12 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS A 18 " --> pdb=" O THR A 14 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 38 through 44 removed outlier: 4.213A pdb=" N ARG A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 44 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 58 removed outlier: 3.834A pdb=" N GLU A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 73 removed outlier: 3.709A pdb=" N LEU A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 removed outlier: 3.521A pdb=" N VAL A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 115 removed outlier: 3.568A pdb=" N LEU A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 25 removed outlier: 3.691A pdb=" N VAL B 16 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS B 18 " --> pdb=" O THR B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 38 through 44 removed outlier: 4.184A pdb=" N ARG B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 44 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 58 removed outlier: 3.922A pdb=" N GLU B 53 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 73 removed outlier: 3.927A pdb=" N LEU B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 87 Processing helix chain 'B' and resid 95 through 115 removed outlier: 3.808A pdb=" N LEU B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 25 removed outlier: 3.634A pdb=" N VAL C 16 " --> pdb=" O ASP C 12 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS C 18 " --> pdb=" O THR C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 38 Processing helix chain 'C' and resid 38 through 44 removed outlier: 4.216A pdb=" N ARG C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS C 44 " --> pdb=" O HIS C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 58 removed outlier: 3.844A pdb=" N GLU C 53 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 73 removed outlier: 3.891A pdb=" N LEU C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 removed outlier: 3.502A pdb=" N VAL C 83 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 115 removed outlier: 3.649A pdb=" N LEU C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 25 removed outlier: 3.810A pdb=" N VAL D 16 " --> pdb=" O ASP D 12 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS D 18 " --> pdb=" O THR D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 38 Processing helix chain 'D' and resid 38 through 44 removed outlier: 4.478A pdb=" N ARG D 42 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS D 44 " --> pdb=" O HIS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 58 removed outlier: 3.530A pdb=" N GLU D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG D 58 " --> pdb=" O GLU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 75 removed outlier: 4.003A pdb=" N LEU D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU D 74 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN D 75 " --> pdb=" O TYR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 Processing helix chain 'D' and resid 95 through 115 removed outlier: 3.684A pdb=" N LEU D 114 " --> pdb=" O LYS D 110 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 25 removed outlier: 3.736A pdb=" N VAL E 16 " --> pdb=" O ASP E 12 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS E 18 " --> pdb=" O THR E 14 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP E 19 " --> pdb=" O GLU E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 38 Processing helix chain 'E' and resid 38 through 44 removed outlier: 4.343A pdb=" N ARG E 42 " --> pdb=" O PHE E 38 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS E 44 " --> pdb=" O HIS E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 58 removed outlier: 3.862A pdb=" N GLU E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG E 58 " --> pdb=" O GLU E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 72 removed outlier: 4.102A pdb=" N LEU E 72 " --> pdb=" O LEU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 87 Processing helix chain 'E' and resid 95 through 115 removed outlier: 3.658A pdb=" N LEU E 114 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 25 removed outlier: 3.650A pdb=" N VAL F 16 " --> pdb=" O ASP F 12 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS F 18 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP F 19 " --> pdb=" O GLU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 38 Processing helix chain 'F' and resid 38 through 44 removed outlier: 4.390A pdb=" N ARG F 42 " --> pdb=" O PHE F 38 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS F 44 " --> pdb=" O HIS F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 58 removed outlier: 3.881A pdb=" N GLU F 53 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG F 58 " --> pdb=" O GLU F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 72 removed outlier: 4.089A pdb=" N LEU F 72 " --> pdb=" O LEU F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 87 Processing helix chain 'F' and resid 95 through 115 removed outlier: 3.702A pdb=" N LEU F 114 " --> pdb=" O LYS F 110 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 25 removed outlier: 3.914A pdb=" N VAL G 16 " --> pdb=" O ASP G 12 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS G 18 " --> pdb=" O THR G 14 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP G 19 " --> pdb=" O GLU G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 38 Processing helix chain 'G' and resid 38 through 44 removed outlier: 4.369A pdb=" N ARG G 42 " --> pdb=" O PHE G 38 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS G 44 " --> pdb=" O HIS G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 58 removed outlier: 3.820A pdb=" N GLU G 53 " --> pdb=" O ARG G 49 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG G 58 " --> pdb=" O GLU G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 72 removed outlier: 4.103A pdb=" N LEU G 72 " --> pdb=" O LEU G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 87 Processing helix chain 'G' and resid 95 through 115 removed outlier: 3.580A pdb=" N LEU G 114 " --> pdb=" O LYS G 110 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS G 115 " --> pdb=" O LEU G 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 25 removed outlier: 3.699A pdb=" N VAL H 16 " --> pdb=" O ASP H 12 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS H 18 " --> pdb=" O THR H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 36 Processing helix chain 'H' and resid 38 through 44 removed outlier: 4.412A pdb=" N ARG H 42 " --> pdb=" O PHE H 38 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS H 44 " --> pdb=" O HIS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 58 removed outlier: 3.790A pdb=" N GLU H 53 " --> pdb=" O ARG H 49 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG H 58 " --> pdb=" O GLU H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 72 removed outlier: 3.856A pdb=" N LEU H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 87 Processing helix chain 'H' and resid 95 through 115 removed outlier: 3.778A pdb=" N LEU H 114 " --> pdb=" O LYS H 110 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 963 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: 1.61 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1247 1.28 - 1.41: 1457 1.41 - 1.54: 4361 1.54 - 1.68: 47 1.68 - 1.81: 16 Bond restraints: 7128 Sorted by residual: bond pdb=" C GLU B 74 " pdb=" O GLU B 74 " ideal model delta sigma weight residual 1.235 1.145 0.091 1.26e-02 6.30e+03 5.18e+01 bond pdb=" C GLU D 74 " pdb=" O GLU D 74 " ideal model delta sigma weight residual 1.235 1.151 0.084 1.26e-02 6.30e+03 4.49e+01 bond pdb=" C GLU A 74 " pdb=" O GLU A 74 " ideal model delta sigma weight residual 1.235 1.161 0.074 1.26e-02 6.30e+03 3.46e+01 bond pdb=" C GLU C 74 " pdb=" O GLU C 74 " ideal model delta sigma weight residual 1.235 1.164 0.071 1.26e-02 6.30e+03 3.19e+01 bond pdb=" ND1 HIS G 40 " pdb=" CE1 HIS G 40 " ideal model delta sigma weight residual 1.321 1.359 -0.038 1.00e-02 1.00e+04 1.46e+01 ... (remaining 7123 not shown) Histogram of bond angle deviations from ideal: 101.89 - 108.29: 242 108.29 - 114.69: 4360 114.69 - 121.09: 2852 121.09 - 127.49: 2040 127.49 - 133.89: 26 Bond angle restraints: 9520 Sorted by residual: angle pdb=" N THR F 100 " pdb=" CA THR F 100 " pdb=" C THR F 100 " ideal model delta sigma weight residual 111.36 101.89 9.47 1.09e+00 8.42e-01 7.55e+01 angle pdb=" N THR H 100 " pdb=" CA THR H 100 " pdb=" C THR H 100 " ideal model delta sigma weight residual 111.82 101.98 9.84 1.16e+00 7.43e-01 7.20e+01 angle pdb=" N THR G 100 " pdb=" CA THR G 100 " pdb=" C THR G 100 " ideal model delta sigma weight residual 111.36 102.22 9.14 1.09e+00 8.42e-01 7.03e+01 angle pdb=" N THR A 100 " pdb=" CA THR A 100 " pdb=" C THR A 100 " ideal model delta sigma weight residual 111.36 102.30 9.06 1.09e+00 8.42e-01 6.91e+01 angle pdb=" N THR C 100 " pdb=" CA THR C 100 " pdb=" C THR C 100 " ideal model delta sigma weight residual 111.36 102.68 8.68 1.09e+00 8.42e-01 6.35e+01 ... (remaining 9515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 3971 17.56 - 35.13: 430 35.13 - 52.69: 124 52.69 - 70.25: 42 70.25 - 87.81: 17 Dihedral angle restraints: 4584 sinusoidal: 2064 harmonic: 2520 Sorted by residual: dihedral pdb=" CA SER A 56 " pdb=" C SER A 56 " pdb=" N CYS A 57 " pdb=" CA CYS A 57 " ideal model delta harmonic sigma weight residual -180.00 -162.05 -17.95 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" C PHE B 38 " pdb=" N PHE B 38 " pdb=" CA PHE B 38 " pdb=" CB PHE B 38 " ideal model delta harmonic sigma weight residual -122.60 -131.30 8.70 0 2.50e+00 1.60e-01 1.21e+01 dihedral pdb=" CG ARG D 49 " pdb=" CD ARG D 49 " pdb=" NE ARG D 49 " pdb=" CZ ARG D 49 " ideal model delta sinusoidal sigma weight residual 90.00 41.95 48.05 2 1.50e+01 4.44e-03 1.18e+01 ... (remaining 4581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 756 0.079 - 0.157: 286 0.157 - 0.236: 54 0.236 - 0.315: 5 0.315 - 0.394: 3 Chirality restraints: 1104 Sorted by residual: chirality pdb=" CA PHE B 38 " pdb=" N PHE B 38 " pdb=" C PHE B 38 " pdb=" CB PHE B 38 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CA PHE D 38 " pdb=" N PHE D 38 " pdb=" C PHE D 38 " pdb=" CB PHE D 38 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA PHE A 38 " pdb=" N PHE A 38 " pdb=" C PHE A 38 " pdb=" CB PHE A 38 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 1101 not shown) Planarity restraints: 1216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 94 " 0.036 2.00e-02 2.50e+03 2.58e-02 1.17e+01 pdb=" CG PHE F 94 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE F 94 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE F 94 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE F 94 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE F 94 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 94 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 92 " 0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C GLN B 92 " -0.058 2.00e-02 2.50e+03 pdb=" O GLN B 92 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN B 93 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS F 37 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.49e+00 pdb=" C HIS F 37 " -0.053 2.00e-02 2.50e+03 pdb=" O HIS F 37 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE F 38 " 0.018 2.00e-02 2.50e+03 ... (remaining 1213 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 87 2.30 - 2.95: 4208 2.95 - 3.60: 11653 3.60 - 4.25: 17484 4.25 - 4.90: 26284 Nonbonded interactions: 59716 Sorted by model distance: nonbonded pdb=" OG SER D 48 " pdb=" NE2 HIS H 37 " model vdw 1.648 2.520 nonbonded pdb=" OD2 ASP A 70 " pdb=" NH2 ARG D 49 " model vdw 1.789 2.520 nonbonded pdb=" OG SER A 48 " pdb=" NE2 HIS E 37 " model vdw 1.793 2.520 nonbonded pdb=" O ARG F 49 " pdb=" NH1 ARG F 49 " model vdw 1.879 2.520 nonbonded pdb=" O ARG C 49 " pdb=" NH1 ARG C 49 " model vdw 1.883 2.520 ... (remaining 59711 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.000 Extract box with map and model: 0.680 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.410 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 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:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4815 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 : 0.009 0.091 7128 Z= 0.563 Angle : 1.421 10.371 9520 Z= 1.027 Chirality : 0.082 0.394 1104 Planarity : 0.005 0.033 1216 Dihedral : 17.335 87.814 2920 Min Nonbonded Distance : 1.648 Molprobity Statistics. All-atom Clashscore : 79.81 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.22 % Favored : 86.42 % Rotamer: Outliers : 9.00 % Allowed : 19.62 % Favored : 71.38 % 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: -5.34 (0.22), residues: 832 helix: -4.12 (0.14), residues: 528 sheet: None (None), residues: 0 loop : -1.99 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS H 37 PHE 0.055 0.006 PHE F 94 TYR 0.006 0.001 TYR H 71 ARG 0.005 0.001 ARG G 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 426 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 18 residues processed: 470 average time/residue: 0.2748 time to fit residues: 156.1926 Evaluate side-chains 298 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 280 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2111 time to fit residues: 6.0760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 97 GLN B 37 HIS B 92 GLN B 97 GLN B 113 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN C 97 GLN D 37 HIS ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS E 92 GLN E 97 GLN E 113 HIS F 23 ASN ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN F 113 HIS ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN G 113 HIS ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 HIS ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4916 moved from start: 0.7013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7128 Z= 0.301 Angle : 0.963 8.538 9520 Z= 0.516 Chirality : 0.053 0.413 1104 Planarity : 0.006 0.050 1216 Dihedral : 6.172 18.357 944 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 33.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 7.50 % Allowed : 26.12 % Favored : 66.38 % 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: -3.73 (0.26), residues: 832 helix: -2.17 (0.19), residues: 584 sheet: None (None), residues: 0 loop : -2.81 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS G 37 PHE 0.027 0.004 PHE H 94 TYR 0.012 0.002 TYR B 71 ARG 0.010 0.001 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 366 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 30 residues processed: 396 average time/residue: 0.2876 time to fit residues: 137.9815 Evaluate side-chains 296 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 266 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.0802 time to fit residues: 5.4636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 50.0000 chunk 22 optimal weight: 10.0000 chunk 60 optimal weight: 40.0000 chunk 49 optimal weight: 9.9990 chunk 20 optimal weight: 40.0000 chunk 72 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS D 92 GLN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 ASN ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 GLN G 113 HIS ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4999 moved from start: 0.8928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7128 Z= 0.280 Angle : 0.880 11.367 9520 Z= 0.465 Chirality : 0.049 0.304 1104 Planarity : 0.006 0.079 1216 Dihedral : 6.571 59.563 944 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 33.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 5.75 % Allowed : 28.12 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.28), residues: 832 helix: -1.08 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -2.95 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS A 40 PHE 0.018 0.004 PHE G 38 TYR 0.008 0.001 TYR F 27 ARG 0.007 0.001 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 319 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 21 residues processed: 348 average time/residue: 0.2839 time to fit residues: 119.3125 Evaluate side-chains 280 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 259 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.0916 time to fit residues: 4.4292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 8 optimal weight: 0.0040 chunk 34 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 20 optimal weight: 30.0000 chunk 64 optimal weight: 8.9990 overall best weight: 5.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 ASN C 113 HIS D 37 HIS D 73 GLN F 23 ASN ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5008 moved from start: 0.9749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7128 Z= 0.262 Angle : 0.834 10.582 9520 Z= 0.438 Chirality : 0.048 0.293 1104 Planarity : 0.005 0.048 1216 Dihedral : 6.449 58.850 944 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 31.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 4.38 % Allowed : 30.50 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.29), residues: 832 helix: -0.76 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -3.11 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS G 37 PHE 0.015 0.003 PHE E 38 TYR 0.009 0.001 TYR B 27 ARG 0.008 0.001 ARG G 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 308 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 22 residues processed: 321 average time/residue: 0.2757 time to fit residues: 107.5304 Evaluate side-chains 274 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 252 time to evaluate : 0.833 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.0776 time to fit residues: 4.0733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 66.5859 > 50: distance: 7 - 28: 21.758 distance: 13 - 33: 27.767 distance: 16 - 20: 28.114 distance: 17 - 41: 27.500 distance: 20 - 21: 31.577 distance: 21 - 22: 19.441 distance: 21 - 24: 13.275 distance: 22 - 23: 16.697 distance: 22 - 28: 19.613 distance: 23 - 50: 50.399 distance: 24 - 25: 36.589 distance: 25 - 26: 5.971 distance: 25 - 27: 9.315 distance: 28 - 29: 14.597 distance: 29 - 30: 6.887 distance: 29 - 32: 19.436 distance: 30 - 31: 9.924 distance: 30 - 33: 23.592 distance: 31 - 58: 28.358 distance: 33 - 34: 7.706 distance: 34 - 35: 8.803 distance: 35 - 36: 4.878 distance: 35 - 41: 25.750 distance: 36 - 66: 21.299 distance: 37 - 38: 24.423 distance: 38 - 40: 30.597 distance: 41 - 42: 14.655 distance: 42 - 43: 18.384 distance: 42 - 45: 14.331 distance: 43 - 44: 13.230 distance: 43 - 50: 25.696 distance: 45 - 46: 26.255 distance: 46 - 47: 17.832 distance: 47 - 48: 13.088 distance: 47 - 49: 16.689 distance: 50 - 51: 32.046 distance: 51 - 52: 14.916 distance: 51 - 54: 24.469 distance: 52 - 53: 15.041 distance: 52 - 58: 32.845 distance: 54 - 55: 34.333 distance: 55 - 56: 36.701 distance: 58 - 59: 7.121 distance: 59 - 60: 20.995 distance: 59 - 62: 27.523 distance: 60 - 66: 8.051 distance: 62 - 63: 18.862 distance: 63 - 64: 15.017 distance: 63 - 65: 11.025 distance: 66 - 67: 27.766 distance: 67 - 68: 6.937 distance: 67 - 70: 19.807 distance: 68 - 69: 31.097 distance: 68 - 77: 24.472 distance: 70 - 71: 43.199 distance: 71 - 72: 11.747 distance: 72 - 73: 8.217 distance: 73 - 74: 23.927 distance: 74 - 75: 21.673 distance: 74 - 76: 33.575 distance: 77 - 78: 38.204 distance: 78 - 79: 12.682 distance: 78 - 81: 40.294 distance: 79 - 80: 18.535 distance: 79 - 84: 38.385 distance: 84 - 85: 12.073 distance: 85 - 86: 26.079 distance: 85 - 88: 8.659 distance: 86 - 87: 11.553 distance: 86 - 96: 36.689 distance: 88 - 89: 8.479 distance: 89 - 90: 3.208 distance: 89 - 91: 19.091 distance: 90 - 92: 15.414 distance: 91 - 93: 6.123 distance: 92 - 94: 4.229 distance: 93 - 94: 5.680 distance: 94 - 95: 20.157 distance: 96 - 97: 34.023 distance: 97 - 98: 18.869 distance: 97 - 100: 6.898 distance: 98 - 99: 37.793 distance: 98 - 104: 21.160 distance: 100 - 101: 15.752 distance: 101 - 102: 41.820 distance: 101 - 103: 13.638