Starting phenix.real_space_refine on Thu Jan 18 11:04:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjx_22901/01_2024/7kjx_22901_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjx_22901/01_2024/7kjx_22901.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjx_22901/01_2024/7kjx_22901_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjx_22901/01_2024/7kjx_22901_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjx_22901/01_2024/7kjx_22901_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjx_22901/01_2024/7kjx_22901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjx_22901/01_2024/7kjx_22901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjx_22901/01_2024/7kjx_22901_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjx_22901/01_2024/7kjx_22901_updated.pdb" } resolution = 3.1 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= 0.080 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: 6 Type Number sf(0) Gaussians P 44 5.49 5 Mg 1 5.21 5 S 14 5.16 5 C 5398 2.51 5 N 1453 2.21 5 O 1679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 17": "OD1" <-> "OD2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 113": "OD1" <-> "OD2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "A PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 511": "OD1" <-> "OD2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "B GLU 40": "OE1" <-> "OE2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 302": "OE1" <-> "OE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 344": "OE1" <-> "OE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 396": "OE1" <-> "OE2" Residue "B TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8589 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4359 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 508} Chain breaks: 2 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 3269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3269 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 29, 'TRANS': 373} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 474 Classifications: {'RNA': 22} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 9} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 466 Classifications: {'DNA': 1, 'RNA': 21} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 13} Link IDs: {'rna3p': 21} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {' MG': 1, 'NVP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.19, per 1000 atoms: 0.60 Number of scatterers: 8589 At special positions: 0 Unit cell: (77.9, 106.6, 118.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 14 16.00 P 44 15.00 Mg 1 11.99 O 1679 8.00 N 1453 7.00 C 5398 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.4 seconds 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1784 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 11 sheets defined 34.9% alpha, 13.4% beta 20 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 3.98 Creating SS restraints... Processing helix chain 'A' and resid 28 through 44 Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 78 through 81 No H-bonds generated for 'chain 'A' and resid 78 through 81' Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 125 through 127 No H-bonds generated for 'chain 'A' and resid 125 through 127' Processing helix chain 'A' and resid 154 through 174 removed outlier: 4.792A pdb=" N ALA A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 195 through 212 removed outlier: 3.724A pdb=" N THR A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 254 through 269 removed outlier: 3.921A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.664A pdb=" N LEU A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 310 removed outlier: 3.974A pdb=" N LEU A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 382 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 516 through 527 removed outlier: 3.642A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 552 removed outlier: 3.833A pdb=" N LEU A 551 " --> pdb=" O GLN A 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 44 removed outlier: 3.708A pdb=" N GLU B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 85 through 89 Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.670A pdb=" N PHE B 116 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 128 removed outlier: 4.529A pdb=" N LYS B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N TYR B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 122 through 128' Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 154 through 174 removed outlier: 3.855A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 195 through 212 removed outlier: 3.846A pdb=" N TRP B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 254 through 270 removed outlier: 4.068A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE B 270 " --> pdb=" O TRP B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 283 removed outlier: 3.673A pdb=" N LEU B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 365 through 382 Processing helix chain 'B' and resid 395 through 401 Processing sheet with id= A, first strand: chain 'A' and resid 47 through 49 removed outlier: 3.597A pdb=" N SER A 48 " --> pdb=" O GLN A 145 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 60 through 63 Processing sheet with id= C, first strand: chain 'A' and resid 179 through 182 Processing sheet with id= D, first strand: chain 'A' and resid 227 through 229 Processing sheet with id= E, first strand: chain 'A' and resid 326 through 331 Processing sheet with id= F, first strand: chain 'A' and resid 389 through 391 Processing sheet with id= G, first strand: chain 'A' and resid 464 through 470 removed outlier: 3.842A pdb=" N LYS A 465 " --> pdb=" O TYR A 457 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 457 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 455 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP A 443 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A 438 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LYS A 530 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE A 495 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N TYR A 532 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR A 497 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ALA A 534 " --> pdb=" O THR A 497 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 49 Processing sheet with id= I, first strand: chain 'B' and resid 60 through 64 Processing sheet with id= J, first strand: chain 'B' and resid 105 through 110 Processing sheet with id= K, first strand: chain 'B' and resid 414 through 416 removed outlier: 5.857A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLN B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) 262 hydrogen bonds defined for protein. 741 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 2.82 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2443 1.34 - 1.46: 1780 1.46 - 1.58: 4573 1.58 - 1.69: 86 1.69 - 1.81: 24 Bond restraints: 8906 Sorted by residual: bond pdb=" C4' G47 D 71 " pdb=" C3' G47 D 71 " ideal model delta sigma weight residual 1.303 1.513 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C4' G47 D 71 " pdb=" O4' G47 D 71 " ideal model delta sigma weight residual 1.623 1.450 0.173 2.00e-02 2.50e+03 7.46e+01 bond pdb=" N3 G47 D 71 " pdb=" C4 G47 D 71 " ideal model delta sigma weight residual 1.492 1.347 0.145 2.00e-02 2.50e+03 5.22e+01 bond pdb=" C2 G47 D 71 " pdb=" N3 G47 D 71 " ideal model delta sigma weight residual 1.462 1.320 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C2 G47 D 71 " pdb=" N2 G47 D 71 " ideal model delta sigma weight residual 1.454 1.340 0.114 2.00e-02 2.50e+03 3.23e+01 ... (remaining 8901 not shown) Histogram of bond angle deviations from ideal: 59.75 - 74.63: 3 74.63 - 89.51: 0 89.51 - 104.39: 326 104.39 - 119.28: 7506 119.28 - 134.16: 4484 Bond angle restraints: 12319 Sorted by residual: angle pdb=" C1' G47 D 71 " pdb=" N9 G47 D 71 " pdb=" C8 G47 D 71 " ideal model delta sigma weight residual 104.99 129.57 -24.58 3.00e+00 1.11e-01 6.71e+01 angle pdb=" O1P G47 D 71 " pdb=" P G47 D 71 " pdb=" O2P G47 D 71 " ideal model delta sigma weight residual 109.47 119.01 -9.54 3.00e+00 1.11e-01 1.01e+01 angle pdb=" C ASP A 256 " pdb=" N ILE A 257 " pdb=" CA ILE A 257 " ideal model delta sigma weight residual 120.30 115.22 5.08 1.64e+00 3.72e-01 9.58e+00 angle pdb=" C5 G47 D 71 " pdb=" C4 G47 D 71 " pdb=" N3 G47 D 71 " ideal model delta sigma weight residual 120.01 129.07 -9.06 3.00e+00 1.11e-01 9.13e+00 angle pdb=" C5 G47 D 71 " pdb=" C6 G47 D 71 " pdb=" O6 G47 D 71 " ideal model delta sigma weight residual 120.00 128.65 -8.65 3.00e+00 1.11e-01 8.32e+00 ... (remaining 12314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.55: 4769 18.55 - 37.10: 421 37.10 - 55.65: 96 55.65 - 74.21: 70 74.21 - 92.76: 13 Dihedral angle restraints: 5369 sinusoidal: 2605 harmonic: 2764 Sorted by residual: dihedral pdb=" C2 NVP A 602 " pdb=" C7 NVP A 602 " pdb=" N8 NVP A 602 " pdb=" C9 NVP A 602 " ideal model delta sinusoidal sigma weight residual 49.71 -43.05 92.76 1 3.00e+01 1.11e-03 1.12e+01 dihedral pdb=" CB GLU A 224 " pdb=" CG GLU A 224 " pdb=" CD GLU A 224 " pdb=" OE1 GLU A 224 " ideal model delta sinusoidal sigma weight residual 0.00 89.71 -89.71 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" C15 NVP A 602 " pdb=" CA NVP A 602 " pdb=" N1 NVP A 602 " pdb=" CC NVP A 602 " ideal model delta sinusoidal sigma weight residual -22.83 65.83 -88.66 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 5366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1257 0.073 - 0.147: 127 0.147 - 0.220: 4 0.220 - 0.293: 1 0.293 - 0.367: 1 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CA NVP A 602 " pdb=" CB NVP A 602 " pdb=" CC NVP A 602 " pdb=" N1 NVP A 602 " both_signs ideal model delta sigma weight residual True 2.04 -2.41 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA TRP B 401 " pdb=" N TRP B 401 " pdb=" C TRP B 401 " pdb=" CB TRP B 401 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C4' G47 D 71 " pdb=" C5' G47 D 71 " pdb=" O4' G47 D 71 " pdb=" C3' G47 D 71 " both_signs ideal model delta sigma weight residual False -2.53 -2.32 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1387 not shown) Planarity restraints: 1383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G47 D 71 " -0.050 2.00e-02 2.50e+03 9.30e-02 2.81e+02 pdb=" N9 G47 D 71 " -0.005 2.00e-02 2.50e+03 pdb=" C8 G47 D 71 " 0.046 2.00e-02 2.50e+03 pdb=" N7 G47 D 71 " 0.063 2.00e-02 2.50e+03 pdb=" C5 G47 D 71 " 0.017 2.00e-02 2.50e+03 pdb=" C6 G47 D 71 " 0.010 2.00e-02 2.50e+03 pdb=" O6 G47 D 71 " 0.045 2.00e-02 2.50e+03 pdb=" N1 G47 D 71 " -0.045 2.00e-02 2.50e+03 pdb=" C2 G47 D 71 " -0.088 2.00e-02 2.50e+03 pdb=" N2 G47 D 71 " -0.138 2.00e-02 2.50e+03 pdb=" N3 G47 D 71 " -0.080 2.00e-02 2.50e+03 pdb=" C4 G47 D 71 " -0.029 2.00e-02 2.50e+03 pdb=" C6A G47 D 71 " 0.256 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" OE NVP A 602 " -0.024 2.00e-02 2.50e+03 4.65e-02 2.70e+01 pdb=" C10 NVP A 602 " 0.021 2.00e-02 2.50e+03 pdb=" C7 NVP A 602 " -0.048 2.00e-02 2.50e+03 pdb=" C9 NVP A 602 " -0.030 2.00e-02 2.50e+03 pdb=" N8 NVP A 602 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 195 " 0.023 2.00e-02 2.50e+03 2.47e-02 1.82e+01 pdb=" N9 G C 195 " -0.067 2.00e-02 2.50e+03 pdb=" C8 G C 195 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G C 195 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G C 195 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G C 195 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G C 195 " -0.000 2.00e-02 2.50e+03 pdb=" N1 G C 195 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G C 195 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G C 195 " -0.006 2.00e-02 2.50e+03 pdb=" N3 G C 195 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G C 195 " 0.047 2.00e-02 2.50e+03 ... (remaining 1380 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 128 2.66 - 3.22: 7870 3.22 - 3.78: 13947 3.78 - 4.34: 19287 4.34 - 4.90: 31048 Nonbonded interactions: 72280 Sorted by model distance: nonbonded pdb=" OD2 ASP A 443 " pdb="MG MG A 601 " model vdw 2.100 2.170 nonbonded pdb=" O ASN A 474 " pdb=" OG1 THR A 477 " model vdw 2.206 2.440 nonbonded pdb=" NZ LYS B 323 " pdb=" OE2 GLU B 344 " model vdw 2.213 2.520 nonbonded pdb=" OE2 GLU A 79 " pdb=" NH2 ARG A 83 " model vdw 2.268 2.520 nonbonded pdb=" OG SER B 134 " pdb=" O THR B 139 " model vdw 2.282 2.440 ... (remaining 72275 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.160 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: 0.010 Extract box with map and model: 12.610 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 29.310 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 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 : 0.005 0.210 8906 Z= 0.309 Angle : 0.694 24.577 12319 Z= 0.353 Chirality : 0.044 0.367 1390 Planarity : 0.006 0.093 1383 Dihedral : 16.903 92.757 3585 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.12 % Allowed : 0.25 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.94 (0.29), residues: 938 helix: 2.07 (0.32), residues: 317 sheet: -0.79 (0.42), residues: 161 loop : 0.25 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP B 414 HIS 0.006 0.001 HIS B 198 PHE 0.010 0.001 PHE A 130 TYR 0.011 0.001 TYR B 144 ARG 0.002 0.000 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 0.817 Fit side-chains REVERT: A 78 ARG cc_start: 0.6435 (OUTLIER) cc_final: 0.5311 (ttm-80) REVERT: A 186 ASP cc_start: 0.7784 (m-30) cc_final: 0.7516 (m-30) REVERT: A 211 ARG cc_start: 0.8366 (ttm-80) cc_final: 0.8038 (mtm110) REVERT: A 452 LEU cc_start: 0.8174 (mp) cc_final: 0.7930 (mp) REVERT: B 28 GLU cc_start: 0.6718 (tt0) cc_final: 0.6478 (tt0) REVERT: B 32 LYS cc_start: 0.7834 (mtpt) cc_final: 0.7577 (mttp) REVERT: B 70 LYS cc_start: 0.8269 (ttpp) cc_final: 0.7549 (pptt) REVERT: B 344 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7409 (mm-30) REVERT: B 401 TRP cc_start: 0.8165 (m-90) cc_final: 0.7628 (m100) outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.2407 time to fit residues: 39.3120 Evaluate side-chains 92 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.0670 chunk 39 optimal weight: 0.0470 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8906 Z= 0.170 Angle : 0.497 7.272 12319 Z= 0.243 Chirality : 0.040 0.166 1390 Planarity : 0.004 0.041 1383 Dihedral : 15.497 88.441 1679 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.12 % Allowed : 5.16 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.93 (0.29), residues: 938 helix: 1.88 (0.31), residues: 319 sheet: -0.51 (0.41), residues: 170 loop : 0.27 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 414 HIS 0.004 0.001 HIS B 198 PHE 0.010 0.001 PHE A 130 TYR 0.009 0.001 TYR A 146 ARG 0.003 0.000 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 1.050 Fit side-chains REVERT: A 142 ILE cc_start: 0.7594 (mp) cc_final: 0.7356 (mt) REVERT: A 186 ASP cc_start: 0.7828 (m-30) cc_final: 0.7565 (m-30) REVERT: A 483 TYR cc_start: 0.7947 (t80) cc_final: 0.7717 (t80) REVERT: B 28 GLU cc_start: 0.6863 (tt0) cc_final: 0.6658 (tt0) REVERT: B 154 LYS cc_start: 0.8386 (mttt) cc_final: 0.7560 (mmmt) REVERT: B 401 TRP cc_start: 0.8210 (m-90) cc_final: 0.7857 (m100) outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.2164 time to fit residues: 29.8850 Evaluate side-chains 86 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 96 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN B 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8906 Z= 0.361 Angle : 0.560 7.179 12319 Z= 0.277 Chirality : 0.042 0.139 1390 Planarity : 0.004 0.038 1383 Dihedral : 15.449 88.861 1675 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.23 % Allowed : 6.51 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.59 (0.28), residues: 938 helix: 1.40 (0.30), residues: 318 sheet: -0.67 (0.42), residues: 159 loop : 0.20 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 414 HIS 0.005 0.001 HIS A 315 PHE 0.015 0.002 PHE A 130 TYR 0.012 0.002 TYR A 127 ARG 0.007 0.001 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.902 Fit side-chains REVERT: A 142 ILE cc_start: 0.7550 (mp) cc_final: 0.7337 (mt) REVERT: A 283 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7408 (mp) REVERT: A 452 LEU cc_start: 0.8250 (mp) cc_final: 0.8025 (tt) REVERT: A 478 GLN cc_start: 0.6159 (OUTLIER) cc_final: 0.5904 (mm-40) REVERT: B 401 TRP cc_start: 0.8267 (m-90) cc_final: 0.8003 (m100) outliers start: 10 outliers final: 2 residues processed: 95 average time/residue: 0.2120 time to fit residues: 28.4886 Evaluate side-chains 79 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 296 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 94 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 278 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8906 Z= 0.284 Angle : 0.513 7.113 12319 Z= 0.251 Chirality : 0.040 0.163 1390 Planarity : 0.004 0.035 1383 Dihedral : 15.418 89.067 1675 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.60 % Allowed : 8.23 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.51 (0.28), residues: 938 helix: 1.35 (0.30), residues: 321 sheet: -0.67 (0.41), residues: 159 loop : 0.12 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 406 HIS 0.003 0.001 HIS A 315 PHE 0.012 0.001 PHE A 130 TYR 0.009 0.001 TYR A 339 ARG 0.002 0.000 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 0.934 Fit side-chains REVERT: A 283 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7237 (mp) REVERT: A 452 LEU cc_start: 0.8250 (mp) cc_final: 0.8027 (tt) REVERT: A 483 TYR cc_start: 0.8345 (t80) cc_final: 0.7990 (t80) REVERT: B 401 TRP cc_start: 0.8252 (m-90) cc_final: 0.8017 (m100) outliers start: 13 outliers final: 6 residues processed: 84 average time/residue: 0.2031 time to fit residues: 24.4385 Evaluate side-chains 82 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 308 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 51.1768 > 50: distance: 79 - 81: 6.159 distance: 81 - 82: 3.998 distance: 82 - 85: 3.042 distance: 83 - 84: 21.337 distance: 83 - 89: 7.840 distance: 85 - 86: 16.497 distance: 85 - 87: 26.969 distance: 86 - 88: 12.238 distance: 90 - 91: 14.144 distance: 91 - 92: 19.323 distance: 91 - 93: 17.759 distance: 93 - 94: 6.837 distance: 94 - 95: 20.079 distance: 95 - 96: 25.637 distance: 95 - 97: 12.124 distance: 97 - 98: 6.850 distance: 98 - 99: 18.880 distance: 98 - 101: 22.543 distance: 99 - 100: 9.650 distance: 99 - 105: 12.557 distance: 100 - 130: 13.660 distance: 101 - 102: 4.163 distance: 102 - 103: 5.472 distance: 102 - 104: 3.700 distance: 105 - 106: 7.969 distance: 106 - 107: 11.073 distance: 106 - 109: 4.124 distance: 107 - 108: 5.351 distance: 107 - 114: 3.043 distance: 108 - 138: 14.356 distance: 109 - 110: 14.960 distance: 110 - 111: 10.030 distance: 111 - 112: 5.310 distance: 111 - 113: 11.082 distance: 114 - 115: 7.880 distance: 115 - 116: 9.119 distance: 116 - 117: 25.084 distance: 116 - 123: 29.647 distance: 118 - 119: 16.775 distance: 119 - 120: 23.690 distance: 120 - 121: 16.892 distance: 120 - 122: 4.653 distance: 123 - 124: 12.877 distance: 124 - 125: 12.063 distance: 124 - 127: 5.709 distance: 125 - 126: 10.741 distance: 125 - 130: 13.622 distance: 126 - 155: 15.085 distance: 127 - 128: 22.143 distance: 127 - 129: 9.389 distance: 130 - 131: 6.817 distance: 131 - 132: 6.057 distance: 131 - 134: 4.898 distance: 132 - 138: 4.278 distance: 134 - 135: 9.059 distance: 135 - 136: 5.775 distance: 135 - 137: 8.995 distance: 138 - 139: 3.512 distance: 139 - 140: 3.356 distance: 139 - 142: 5.147 distance: 140 - 147: 3.506 distance: 142 - 143: 10.498 distance: 143 - 144: 11.003 distance: 144 - 145: 8.311 distance: 145 - 146: 26.385 distance: 147 - 148: 7.352 distance: 148 - 149: 4.547 distance: 148 - 151: 5.560 distance: 149 - 150: 9.088 distance: 149 - 155: 5.161