Starting phenix.real_space_refine on Fri Dec 8 03:59:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7v_33049/12_2023/7x7v_33049.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7v_33049/12_2023/7x7v_33049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7v_33049/12_2023/7x7v_33049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7v_33049/12_2023/7x7v_33049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7v_33049/12_2023/7x7v_33049.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7v_33049/12_2023/7x7v_33049.pdb" } resolution = 3.83 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= 0.010 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 26 5.16 5 C 4365 2.51 5 N 1124 2.21 5 O 1361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 85": "OE1" <-> "OE2" Residue "L GLU 109": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "F GLU 105": "OE1" <-> "OE2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "E GLU 341": "OE1" <-> "OE2" Residue "E PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 6876 Number of models: 1 Model: "" Number of chains: 9 Chain: "L" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "F" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Chain: "A" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 929 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "C" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 921 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "E" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1513 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 175} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.09, per 1000 atoms: 0.59 Number of scatterers: 6876 At special positions: 0 Unit cell: (98.028, 118.256, 80.134, 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 26 16.00 O 1361 8.00 N 1124 7.00 C 4365 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 323 " - pdb=" SG CYS E 348 " distance=2.03 Simple disulfide: pdb=" SG CYS E 366 " - pdb=" SG CYS E 419 " distance=1.98 Simple disulfide: pdb=" SG CYS E 467 " - pdb=" SG CYS E 474 " distance=2.04 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG B 1 " - " ASN E 330 " " NAG G 1 " - " ASN E 357 " Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.4 seconds 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1586 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 20 sheets defined 4.5% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'H' and resid 61 through 65 removed outlier: 3.623A pdb=" N GLU H 65 " --> pdb=" O LEU H 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.758A pdb=" N ASP A 90 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 91' Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.888A pdb=" N GLY A 105 " --> pdb=" O ASP A 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 removed outlier: 4.086A pdb=" N LYS C 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'E' and resid 324 through 329 removed outlier: 4.005A pdb=" N VAL E 328 " --> pdb=" O PRO E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 340 removed outlier: 4.190A pdb=" N TRP E 340 " --> pdb=" O VAL E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 394 No H-bonds generated for 'chain 'E' and resid 392 through 394' Processing helix chain 'E' and resid 425 through 430 removed outlier: 3.899A pdb=" N ALA E 430 " --> pdb=" O ARG E 426 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.604A pdb=" N THR L 76 " --> pdb=" O SER L 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.220A pdb=" N LEU L 11 " --> pdb=" O GLU L 109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.511A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 46 through 47 removed outlier: 4.670A pdb=" N THR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN H 39 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.609A pdb=" N ARG F 24 " --> pdb=" O THR F 5 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.657A pdb=" N GLU F 105 " --> pdb=" O LEU F 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 44 through 48 removed outlier: 6.824A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.544A pdb=" N VAL A 18 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.657A pdb=" N THR A 78 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.868A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.868A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.779A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE D 75 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER D 74 " --> pdb=" O SER D 63 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.367A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N SER D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU D 33 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN D 38 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR D 85 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.657A pdb=" N THR C 71 " --> pdb=" O TYR C 80 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.500A pdb=" N THR C 59 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N CYS C 96 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TRP C 112 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LYS C 98 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.500A pdb=" N THR C 59 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR C 94 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR C 116 " --> pdb=" O TYR C 94 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 341 through 345 removed outlier: 3.804A pdb=" N GLU E 341 " --> pdb=" O SER E 386 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER E 386 " --> pdb=" O GLU E 341 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS E 343 " --> pdb=" O ALA E 384 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA E 384 " --> pdb=" O LYS E 343 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 439 through 441 190 hydrogen bonds defined for protein. 465 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: 2.18 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1592 1.33 - 1.45: 1828 1.45 - 1.58: 3604 1.58 - 1.70: 0 1.70 - 1.82: 32 Bond restraints: 7056 Sorted by residual: bond pdb=" CA CYS E 366 " pdb=" C CYS E 366 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.22e-02 6.72e+03 2.30e+01 bond pdb=" N PRO E 507 " pdb=" CD PRO E 507 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.65e+01 bond pdb=" CA CYS E 366 " pdb=" CB CYS E 366 " ideal model delta sigma weight residual 1.533 1.455 0.078 2.29e-02 1.91e+03 1.16e+01 bond pdb=" C LYS E 365 " pdb=" O LYS E 365 " ideal model delta sigma weight residual 1.236 1.204 0.032 1.22e-02 6.72e+03 6.70e+00 bond pdb=" N CYS E 366 " pdb=" CA CYS E 366 " ideal model delta sigma weight residual 1.455 1.424 0.031 1.23e-02 6.61e+03 6.46e+00 ... (remaining 7051 not shown) Histogram of bond angle deviations from ideal: 98.99 - 106.06: 153 106.06 - 113.13: 3678 113.13 - 120.20: 2531 120.20 - 127.27: 3148 127.27 - 134.33: 87 Bond angle restraints: 9597 Sorted by residual: angle pdb=" CA PRO E 507 " pdb=" N PRO E 507 " pdb=" CD PRO E 507 " ideal model delta sigma weight residual 112.00 98.99 13.01 1.40e+00 5.10e-01 8.63e+01 angle pdb=" N GLY E 418 " pdb=" CA GLY E 418 " pdb=" C GLY E 418 " ideal model delta sigma weight residual 112.54 122.66 -10.12 1.28e+00 6.10e-01 6.25e+01 angle pdb=" N MET E 417 " pdb=" CA MET E 417 " pdb=" C MET E 417 " ideal model delta sigma weight residual 112.92 104.95 7.97 1.23e+00 6.61e-01 4.20e+01 angle pdb=" C ILE L 98 " pdb=" N PRO L 99 " pdb=" CA PRO L 99 " ideal model delta sigma weight residual 119.90 113.52 6.38 1.05e+00 9.07e-01 3.69e+01 angle pdb=" N ASP C 90 " pdb=" CA ASP C 90 " pdb=" C ASP C 90 " ideal model delta sigma weight residual 113.30 105.24 8.06 1.34e+00 5.57e-01 3.62e+01 ... (remaining 9592 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 3661 16.99 - 33.98: 404 33.98 - 50.97: 76 50.97 - 67.96: 11 67.96 - 84.94: 3 Dihedral angle restraints: 4155 sinusoidal: 1639 harmonic: 2516 Sorted by residual: dihedral pdb=" CB CYS E 366 " pdb=" SG CYS E 366 " pdb=" SG CYS E 419 " pdb=" CB CYS E 419 " ideal model delta sinusoidal sigma weight residual 93.00 137.56 -44.56 1 1.00e+01 1.00e-02 2.76e+01 dihedral pdb=" CA CYS E 467 " pdb=" C CYS E 467 " pdb=" N THR E 468 " pdb=" CA THR E 468 " ideal model delta harmonic sigma weight residual 180.00 154.30 25.70 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" N CYS E 366 " pdb=" C CYS E 366 " pdb=" CA CYS E 366 " pdb=" CB CYS E 366 " ideal model delta harmonic sigma weight residual 122.80 135.63 -12.83 0 2.50e+00 1.60e-01 2.63e+01 ... (remaining 4152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 1010 0.151 - 0.301: 25 0.301 - 0.452: 1 0.452 - 0.602: 0 0.602 - 0.753: 1 Chirality restraints: 1037 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.17e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 3.95e+01 chirality pdb=" CA CYS E 366 " pdb=" N CYS E 366 " pdb=" C CYS E 366 " pdb=" CB CYS E 366 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.42e+01 ... (remaining 1034 not shown) Planarity restraints: 1226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " -0.193 2.00e-02 2.50e+03 1.60e-01 3.18e+02 pdb=" C7 NAG G 1 " 0.052 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " -0.139 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " 0.260 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.173 2.00e-02 2.50e+03 1.47e-01 2.70e+02 pdb=" C7 NAG B 1 " 0.046 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.125 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.245 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " 0.092 2.00e-02 2.50e+03 7.60e-02 7.23e+01 pdb=" C7 NAG G 2 " -0.026 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " 0.070 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " -0.121 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " -0.016 2.00e-02 2.50e+03 ... (remaining 1223 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1968 2.80 - 3.32: 5448 3.32 - 3.85: 11089 3.85 - 4.37: 11905 4.37 - 4.90: 21706 Nonbonded interactions: 52116 Sorted by model distance: nonbonded pdb=" OG SER E 336 " pdb=" O LYS E 439 " model vdw 2.274 2.440 nonbonded pdb=" O ILE F 29 " pdb=" OG1 THR F 92 " model vdw 2.276 2.440 nonbonded pdb=" OG SER E 380 " pdb=" O LEU E 503 " model vdw 2.291 2.440 nonbonded pdb=" OG SER E 346 " pdb=" ND2 ASN E 381 " model vdw 2.302 2.520 nonbonded pdb=" OH TYR L 36 " pdb=" O TYR E 436 " model vdw 2.311 2.440 ... (remaining 52111 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 'B' selection = chain 'G' } 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=0.67 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: 24.020 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: 43.070 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 22.490 Find NCS groups from input model: 0.260 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 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 : 0.006 0.078 7056 Z= 0.432 Angle : 0.975 13.009 9597 Z= 0.562 Chirality : 0.064 0.753 1037 Planarity : 0.011 0.160 1224 Dihedral : 13.942 84.945 2542 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.10 % Favored : 92.78 % Rotamer: Outliers : 0.41 % Allowed : 9.09 % Favored : 90.50 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 8.33 % 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: -3.88 (0.25), residues: 859 helix: -5.12 (0.37), residues: 8 sheet: -2.34 (0.25), residues: 363 loop : -2.76 (0.23), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 423 HIS 0.006 0.001 HIS E 445 PHE 0.018 0.002 PHE E 334 TYR 0.021 0.002 TYR D 91 ARG 0.005 0.001 ARG F 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 247 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 250 average time/residue: 0.2299 time to fit residues: 72.3115 Evaluate side-chains 197 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 195 time to evaluate : 0.718 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0669 time to fit residues: 1.1912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN A 5 GLN A 39 GLN C 33 ASN E 457 ASN E 473 ASN E 479 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7056 Z= 0.286 Angle : 0.679 9.199 9597 Z= 0.351 Chirality : 0.045 0.242 1037 Planarity : 0.006 0.061 1224 Dihedral : 6.471 63.495 1046 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.93 % Allowed : 18.45 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -3.28 (0.26), residues: 859 helix: -5.16 (0.31), residues: 14 sheet: -1.82 (0.26), residues: 342 loop : -2.40 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 423 HIS 0.003 0.001 HIS C 82 PHE 0.016 0.002 PHE D 94 TYR 0.016 0.001 TYR F 49 ARG 0.007 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 203 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 212 average time/residue: 0.2327 time to fit residues: 62.5094 Evaluate side-chains 201 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 183 time to evaluate : 0.778 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0938 time to fit residues: 3.7000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 90 GLN D 30 ASN ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 445 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7056 Z= 0.300 Angle : 0.653 10.224 9597 Z= 0.336 Chirality : 0.044 0.230 1037 Planarity : 0.005 0.057 1224 Dihedral : 6.175 58.022 1046 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.53 % Allowed : 19.95 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.93 (0.27), residues: 859 helix: -5.10 (0.34), residues: 14 sheet: -1.53 (0.26), residues: 358 loop : -2.21 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 109 HIS 0.007 0.001 HIS E 445 PHE 0.018 0.001 PHE D 94 TYR 0.018 0.001 TYR F 49 ARG 0.011 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 196 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 17 residues processed: 204 average time/residue: 0.2315 time to fit residues: 59.7420 Evaluate side-chains 201 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 184 time to evaluate : 0.733 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0872 time to fit residues: 3.4474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.2980 chunk 56 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 5 GLN C 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7056 Z= 0.216 Angle : 0.615 8.703 9597 Z= 0.313 Chirality : 0.043 0.208 1037 Planarity : 0.005 0.055 1224 Dihedral : 5.928 55.243 1046 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.80 % Allowed : 21.57 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.70 (0.27), residues: 859 helix: -5.09 (0.33), residues: 14 sheet: -1.43 (0.26), residues: 369 loop : -1.97 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 423 HIS 0.003 0.001 HIS L 94 PHE 0.013 0.001 PHE F 87 TYR 0.015 0.001 TYR F 49 ARG 0.010 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 188 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 200 average time/residue: 0.2399 time to fit residues: 60.4774 Evaluate side-chains 197 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 180 time to evaluate : 0.723 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0689 time to fit residues: 3.0990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 0.0970 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN D 30 ASN C 82 HIS ** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 445 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7056 Z= 0.236 Angle : 0.620 8.825 9597 Z= 0.316 Chirality : 0.044 0.298 1037 Planarity : 0.005 0.051 1224 Dihedral : 5.773 51.674 1046 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.90 % Allowed : 25.10 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.50 (0.28), residues: 859 helix: -5.06 (0.34), residues: 14 sheet: -1.23 (0.27), residues: 365 loop : -1.90 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 109 HIS 0.006 0.001 HIS E 445 PHE 0.014 0.001 PHE A 64 TYR 0.015 0.001 TYR F 49 ARG 0.013 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 185 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 190 average time/residue: 0.2418 time to fit residues: 57.5201 Evaluate side-chains 181 residues out of total 737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 173 time to evaluate : 0.708 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1075 time to fit residues: 2.2942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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: 57.77 > 50: distance: 24 - 31: 12.171 distance: 31 - 32: 23.429 distance: 32 - 33: 8.254 distance: 32 - 35: 15.100 distance: 33 - 34: 12.694 distance: 33 - 37: 47.933 distance: 35 - 36: 41.484 distance: 37 - 38: 11.245 distance: 38 - 39: 38.138 distance: 39 - 40: 24.765 distance: 39 - 41: 28.950 distance: 41 - 42: 24.409 distance: 42 - 43: 15.318 distance: 42 - 45: 26.497 distance: 43 - 44: 16.629 distance: 43 - 48: 17.185 distance: 45 - 46: 18.619 distance: 45 - 47: 32.200 distance: 48 - 49: 22.981 distance: 48 - 54: 16.533 distance: 49 - 50: 10.891 distance: 49 - 52: 22.213 distance: 50 - 51: 17.465 distance: 50 - 55: 25.581 distance: 52 - 53: 11.617 distance: 53 - 54: 28.914 distance: 56 - 57: 19.630 distance: 56 - 59: 14.259 distance: 57 - 58: 13.517 distance: 57 - 60: 31.131 distance: 60 - 61: 31.488 distance: 61 - 62: 5.441 distance: 61 - 64: 12.464 distance: 62 - 63: 22.970 distance: 62 - 71: 16.836 distance: 64 - 65: 20.682 distance: 65 - 66: 21.973 distance: 66 - 67: 19.882 distance: 67 - 68: 8.071 distance: 68 - 69: 24.400 distance: 68 - 70: 7.820 distance: 71 - 72: 14.800 distance: 72 - 73: 16.419 distance: 72 - 75: 31.324 distance: 73 - 74: 25.724 distance: 73 - 82: 8.343 distance: 75 - 76: 12.865 distance: 76 - 77: 6.535 distance: 76 - 78: 8.954 distance: 77 - 79: 18.917 distance: 78 - 80: 26.696 distance: 79 - 81: 15.411 distance: 80 - 81: 26.281 distance: 82 - 83: 19.031 distance: 82 - 127: 20.205 distance: 83 - 84: 27.980 distance: 83 - 86: 29.893 distance: 84 - 85: 19.123 distance: 84 - 88: 24.361 distance: 85 - 124: 29.946 distance: 86 - 87: 34.690 distance: 88 - 89: 28.772 distance: 89 - 90: 14.738 distance: 90 - 91: 29.756 distance: 90 - 92: 30.101 distance: 92 - 93: 14.185 distance: 92 - 114: 30.368 distance: 93 - 96: 26.514 distance: 94 - 95: 15.181 distance: 94 - 98: 28.549 distance: 96 - 97: 6.631