Starting phenix.real_space_refine on Fri Jul 19 03:55:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to2_26027/07_2024/7to2_26027_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to2_26027/07_2024/7to2_26027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to2_26027/07_2024/7to2_26027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to2_26027/07_2024/7to2_26027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to2_26027/07_2024/7to2_26027_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to2_26027/07_2024/7to2_26027_neut.cif" } resolution = 3.2 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= 0.004 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 32 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 3733 2.51 5 N 1039 2.21 5 O 1213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 249": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 372": "OD1" <-> "OD2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A ASP 425": "OD1" <-> "OD2" Residue "A TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 481": "OD1" <-> "OD2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A ASP 569": "OD1" <-> "OD2" Residue "A PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 585": "OD1" <-> "OD2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "A GLU 598": "OE1" <-> "OE2" Residue "A ASP 603": "OD1" <-> "OD2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A ASP 705": "OD1" <-> "OD2" Residue "A TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 749": "OE1" <-> "OE2" Residue "A ASP 792": "OD1" <-> "OD2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A GLU 804": "OE1" <-> "OE2" Residue "A ARG 811": "NH1" <-> "NH2" Residue "A ASP 822": "OD1" <-> "OD2" Residue "A GLU 827": "OE1" <-> "OE2" Residue "A GLU 828": "OE1" <-> "OE2" Residue "A ASP 836": "OD1" <-> "OD2" Residue "A PHE 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 872": "OD1" <-> "OD2" Residue "A GLU 883": "OE1" <-> "OE2" Residue "A GLU 895": "OE1" <-> "OE2" Residue "A GLU 914": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6052 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5384 Classifications: {'peptide': 670} Link IDs: {'PTRANS': 25, 'TRANS': 644} Chain breaks: 1 Chain: "B" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 639 Classifications: {'RNA': 30} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 15} Link IDs: {'rna3p': 29} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4570 SG CYS A 810 40.487 21.767 28.769 1.00 38.49 S ATOM 4596 SG CYS A 813 39.020 18.506 27.949 1.00 48.41 S ATOM 4908 SG CYS A 864 40.109 19.526 24.622 1.00 65.65 S ATOM 4947 SG CYS A 869 37.263 21.217 26.585 1.00 66.55 S Time building chain proxies: 4.07, per 1000 atoms: 0.67 Number of scatterers: 6052 At special positions: 0 Unit cell: (87.15, 97.65, 72.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 33 16.00 P 32 15.00 Mg 1 11.99 O 1213 8.00 N 1039 7.00 C 3733 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: 2.65 Conformation dependent library (CDL) restraints added in 978.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 813 " Number of angles added : 6 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1276 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 6 sheets defined 48.8% alpha, 8.8% beta 15 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.621A pdb=" N ALA A 251 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 269 through 283 removed outlier: 3.572A pdb=" N VAL A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.656A pdb=" N GLU A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 removed outlier: 3.567A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.833A pdb=" N ILE A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 366 " --> pdb=" O LEU A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 366' Processing helix chain 'A' and resid 374 through 377 Processing helix chain 'A' and resid 381 through 395 Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.851A pdb=" N LEU A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 491 Processing helix chain 'A' and resid 492 through 496 removed outlier: 3.609A pdb=" N LEU A 496 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 521 removed outlier: 3.519A pdb=" N MET A 521 " --> pdb=" O GLN A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 556 Processing helix chain 'A' and resid 559 through 576 removed outlier: 3.609A pdb=" N ALA A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 593 removed outlier: 3.935A pdb=" N LYS A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 602 Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 636 through 649 Processing helix chain 'A' and resid 674 through 683 Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 746 through 769 Processing helix chain 'A' and resid 772 through 792 Processing helix chain 'A' and resid 835 through 840 removed outlier: 3.524A pdb=" N LYS A 839 " --> pdb=" O GLY A 835 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 835 through 840' Processing sheet with id=AA1, first strand: chain 'A' and resid 321 through 323 removed outlier: 6.958A pdb=" N THR A 322 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL A 293 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU A 346 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N PHE A 295 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N MET A 369 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU A 408 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N PHE A 371 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 462 removed outlier: 6.372A pdb=" N GLN A 457 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU A 740 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHE A 459 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N THR A 742 " --> pdb=" O PHE A 459 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ARG A 461 " --> pdb=" O THR A 742 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 658 through 661 removed outlier: 6.336A pdb=" N GLY A 659 " --> pdb=" O ILE A 695 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 819 removed outlier: 7.226A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 832 through 833 removed outlier: 4.455A pdb=" N ILE A 916 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 842 through 844 removed outlier: 3.968A pdb=" N GLY A 874 " --> pdb=" O ILE A 862 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N CYS A 864 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASP A 872 " --> pdb=" O CYS A 864 " (cutoff:3.500A) 236 hydrogen bonds defined for protein. 690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1473 1.33 - 1.45: 1254 1.45 - 1.57: 3397 1.57 - 1.70: 61 1.70 - 1.82: 46 Bond restraints: 6231 Sorted by residual: bond pdb=" C4 ADP A1003 " pdb=" C5 ADP A1003 " ideal model delta sigma weight residual 1.490 1.394 0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" N ILE A 337 " pdb=" CA ILE A 337 " ideal model delta sigma weight residual 1.458 1.490 -0.032 9.00e-03 1.23e+04 1.25e+01 bond pdb=" N ILE A 467 " pdb=" CA ILE A 467 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.19e-02 7.06e+03 9.61e+00 bond pdb=" N VAL A 800 " pdb=" CA VAL A 800 " ideal model delta sigma weight residual 1.457 1.485 -0.028 9.00e-03 1.23e+04 9.47e+00 bond pdb=" N VAL A 699 " pdb=" CA VAL A 699 " ideal model delta sigma weight residual 1.452 1.488 -0.036 1.18e-02 7.18e+03 9.11e+00 ... (remaining 6226 not shown) Histogram of bond angle deviations from ideal: 99.88 - 106.74: 316 106.74 - 113.60: 3493 113.60 - 120.46: 2586 120.46 - 127.32: 2061 127.32 - 134.18: 94 Bond angle restraints: 8550 Sorted by residual: angle pdb=" C PRO A 658 " pdb=" N GLY A 659 " pdb=" CA GLY A 659 " ideal model delta sigma weight residual 121.65 124.64 -2.99 6.80e-01 2.16e+00 1.93e+01 angle pdb=" C2' U B 8 " pdb=" C1' U B 8 " pdb=" N1 U B 8 " ideal model delta sigma weight residual 112.00 116.55 -4.55 1.50e+00 4.44e-01 9.20e+00 angle pdb=" N1 ADP A1003 " pdb=" C2 ADP A1003 " pdb=" N3 ADP A1003 " ideal model delta sigma weight residual 120.00 129.09 -9.09 3.00e+00 1.11e-01 9.19e+00 angle pdb=" N ILE A 467 " pdb=" CA ILE A 467 " pdb=" C ILE A 467 " ideal model delta sigma weight residual 111.90 109.57 2.33 8.10e-01 1.52e+00 8.27e+00 angle pdb=" CA LYS A 528 " pdb=" C LYS A 528 " pdb=" O LYS A 528 " ideal model delta sigma weight residual 120.70 117.78 2.92 1.03e+00 9.43e-01 8.03e+00 ... (remaining 8545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 3421 16.18 - 32.37: 275 32.37 - 48.55: 77 48.55 - 64.73: 51 64.73 - 80.91: 19 Dihedral angle restraints: 3843 sinusoidal: 1878 harmonic: 1965 Sorted by residual: dihedral pdb=" O2A ADP A1003 " pdb=" O3A ADP A1003 " pdb=" PA ADP A1003 " pdb=" PB ADP A1003 " ideal model delta sinusoidal sigma weight residual -60.00 -7.40 -52.60 1 2.00e+01 2.50e-03 9.42e+00 dihedral pdb=" CA LEU A 430 " pdb=" CB LEU A 430 " pdb=" CG LEU A 430 " pdb=" CD1 LEU A 430 " ideal model delta sinusoidal sigma weight residual 180.00 124.30 55.70 3 1.50e+01 4.44e-03 9.36e+00 dihedral pdb=" CA ASP A 562 " pdb=" CB ASP A 562 " pdb=" CG ASP A 562 " pdb=" OD1 ASP A 562 " ideal model delta sinusoidal sigma weight residual -30.00 -81.64 51.64 1 2.00e+01 2.50e-03 9.11e+00 ... (remaining 3840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 427 0.043 - 0.085: 294 0.085 - 0.128: 224 0.128 - 0.171: 32 0.171 - 0.213: 2 Chirality restraints: 979 Sorted by residual: chirality pdb=" CB VAL A 332 " pdb=" CA VAL A 332 " pdb=" CG1 VAL A 332 " pdb=" CG2 VAL A 332 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB ILE A 631 " pdb=" CA ILE A 631 " pdb=" CG1 ILE A 631 " pdb=" CG2 ILE A 631 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" P G B 45 " pdb=" OP1 G B 45 " pdb=" OP2 G B 45 " pdb=" O5' G B 45 " both_signs ideal model delta sigma weight residual True 2.41 -2.25 0.16 2.00e-01 2.50e+01 6.41e-01 ... (remaining 976 not shown) Planarity restraints: 979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 10 " -0.026 2.00e-02 2.50e+03 9.93e-03 2.96e+00 pdb=" N9 G B 10 " 0.015 2.00e-02 2.50e+03 pdb=" C8 G B 10 " 0.009 2.00e-02 2.50e+03 pdb=" N7 G B 10 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G B 10 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 10 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G B 10 " -0.012 2.00e-02 2.50e+03 pdb=" N1 G B 10 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G B 10 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G B 10 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G B 10 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G B 10 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 490 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.64e+00 pdb=" C CYS A 490 " -0.028 2.00e-02 2.50e+03 pdb=" O CYS A 490 " 0.010 2.00e-02 2.50e+03 pdb=" N LYS A 491 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP A1003 " 0.011 2.00e-02 2.50e+03 9.35e-03 2.40e+00 pdb=" C2 ADP A1003 " 0.012 2.00e-02 2.50e+03 pdb=" C4 ADP A1003 " -0.002 2.00e-02 2.50e+03 pdb=" C5 ADP A1003 " -0.008 2.00e-02 2.50e+03 pdb=" C6 ADP A1003 " -0.003 2.00e-02 2.50e+03 pdb=" C8 ADP A1003 " 0.015 2.00e-02 2.50e+03 pdb=" N1 ADP A1003 " 0.003 2.00e-02 2.50e+03 pdb=" N3 ADP A1003 " -0.013 2.00e-02 2.50e+03 pdb=" N6 ADP A1003 " 0.006 2.00e-02 2.50e+03 pdb=" N7 ADP A1003 " -0.008 2.00e-02 2.50e+03 pdb=" N9 ADP A1003 " -0.013 2.00e-02 2.50e+03 ... (remaining 976 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1185 2.81 - 3.33: 5962 3.33 - 3.85: 10226 3.85 - 4.38: 11711 4.38 - 4.90: 19769 Nonbonded interactions: 48853 Sorted by model distance: nonbonded pdb=" O SER A 378 " pdb=" ND2 ASN A 384 " model vdw 2.284 2.520 nonbonded pdb=" O HIS A 557 " pdb=" OH TYR A 715 " model vdw 2.296 2.440 nonbonded pdb=" O THR A 662 " pdb=" NE2 GLN A 678 " model vdw 2.334 2.520 nonbonded pdb=" O ASP A 690 " pdb=" ND1 HIS A 691 " model vdw 2.348 2.520 nonbonded pdb=" O SER A 698 " pdb=" OG SER A 698 " model vdw 2.353 2.440 ... (remaining 48848 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: 0.600 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 23.960 Find NCS groups from input model: 0.110 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 : 0.011 0.096 6231 Z= 0.693 Angle : 1.131 9.092 8550 Z= 0.827 Chirality : 0.069 0.213 979 Planarity : 0.004 0.016 979 Dihedral : 15.499 80.913 2567 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.84 % Allowed : 6.86 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.30), residues: 666 helix: 0.75 (0.28), residues: 298 sheet: -3.26 (0.49), residues: 75 loop : -3.04 (0.29), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 771 HIS 0.005 0.001 HIS A 782 PHE 0.011 0.003 PHE A 460 TYR 0.012 0.003 TYR A 548 ARG 0.008 0.001 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.693 Fit side-chains REVERT: A 457 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7624 (tp-100) outliers start: 5 outliers final: 3 residues processed: 94 average time/residue: 0.2029 time to fit residues: 24.7530 Evaluate side-chains 60 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 691 HIS Chi-restraints excluded: chain A residue 775 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN A 375 HIS ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN A 477 GLN A 500 GLN A 769 GLN A 830 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6231 Z= 0.173 Angle : 0.480 6.636 8550 Z= 0.234 Chirality : 0.038 0.138 979 Planarity : 0.003 0.026 979 Dihedral : 14.967 81.027 1203 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.84 % Allowed : 13.04 % Favored : 85.12 % 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: -0.82 (0.32), residues: 666 helix: 1.89 (0.30), residues: 305 sheet: -3.02 (0.52), residues: 76 loop : -2.69 (0.30), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 512 HIS 0.002 0.000 HIS A 876 PHE 0.006 0.001 PHE A 295 TYR 0.006 0.001 TYR A 246 ARG 0.004 0.000 ARG A 602 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.647 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 73 average time/residue: 0.1553 time to fit residues: 15.9322 Evaluate side-chains 63 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 691 HIS Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6231 Z= 0.209 Angle : 0.488 5.739 8550 Z= 0.237 Chirality : 0.038 0.138 979 Planarity : 0.003 0.030 979 Dihedral : 14.922 83.179 1199 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.17 % Allowed : 14.88 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.33), residues: 666 helix: 2.21 (0.30), residues: 305 sheet: -2.61 (0.61), residues: 64 loop : -2.39 (0.31), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 512 HIS 0.002 0.000 HIS A 876 PHE 0.006 0.001 PHE A 295 TYR 0.013 0.001 TYR A 473 ARG 0.003 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.700 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 69 average time/residue: 0.1311 time to fit residues: 13.4687 Evaluate side-chains 64 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6231 Z= 0.230 Angle : 0.493 5.639 8550 Z= 0.243 Chirality : 0.038 0.146 979 Planarity : 0.003 0.031 979 Dihedral : 14.914 84.487 1197 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.01 % Allowed : 15.22 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.33), residues: 666 helix: 2.33 (0.29), residues: 305 sheet: -2.45 (0.62), residues: 64 loop : -2.20 (0.32), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 512 HIS 0.002 0.000 HIS A 280 PHE 0.006 0.001 PHE A 295 TYR 0.013 0.001 TYR A 473 ARG 0.002 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 62 time to evaluate : 0.580 Fit side-chains REVERT: A 878 LYS cc_start: 0.8345 (tmtt) cc_final: 0.7579 (tmtt) outliers start: 18 outliers final: 9 residues processed: 76 average time/residue: 0.1418 time to fit residues: 15.5874 Evaluate side-chains 67 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 0.0570 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6231 Z= 0.222 Angle : 0.498 5.891 8550 Z= 0.244 Chirality : 0.038 0.137 979 Planarity : 0.003 0.032 979 Dihedral : 14.930 85.264 1197 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.17 % Allowed : 17.39 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.33), residues: 666 helix: 2.43 (0.29), residues: 306 sheet: -2.30 (0.63), residues: 64 loop : -2.16 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 512 HIS 0.002 0.000 HIS A 280 PHE 0.005 0.001 PHE A 295 TYR 0.013 0.001 TYR A 473 ARG 0.002 0.000 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 878 LYS cc_start: 0.8339 (tmtt) cc_final: 0.7565 (tmtt) outliers start: 13 outliers final: 8 residues processed: 67 average time/residue: 0.1428 time to fit residues: 14.0907 Evaluate side-chains 65 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.5213 > 50: distance: 145 - 149: 7.164 distance: 149 - 150: 9.226 distance: 150 - 151: 9.438 distance: 150 - 153: 12.040 distance: 151 - 152: 50.605 distance: 151 - 155: 9.225 distance: 153 - 154: 19.129 distance: 155 - 156: 8.570 distance: 156 - 157: 14.338 distance: 157 - 158: 36.857 distance: 157 - 159: 8.988 distance: 159 - 160: 31.087 distance: 159 - 165: 30.169 distance: 160 - 161: 17.410 distance: 160 - 163: 29.685 distance: 161 - 162: 29.523 distance: 161 - 166: 18.017 distance: 163 - 164: 18.102 distance: 164 - 165: 32.021 distance: 166 - 167: 24.118 distance: 167 - 168: 13.534 distance: 167 - 170: 22.467 distance: 168 - 169: 16.154 distance: 168 - 174: 8.743 distance: 170 - 171: 5.924 distance: 171 - 172: 11.730 distance: 171 - 173: 16.866 distance: 174 - 180: 7.967 distance: 175 - 176: 10.674 distance: 175 - 178: 5.481 distance: 176 - 177: 14.738 distance: 176 - 181: 9.166 distance: 178 - 179: 22.788 distance: 179 - 180: 14.172 distance: 181 - 182: 14.162 distance: 182 - 183: 8.137 distance: 183 - 184: 8.472 distance: 183 - 190: 8.553 distance: 185 - 186: 17.136 distance: 186 - 187: 10.818 distance: 187 - 188: 14.518 distance: 187 - 189: 17.315 distance: 190 - 191: 13.288 distance: 191 - 192: 15.284 distance: 191 - 194: 16.197 distance: 192 - 193: 13.795 distance: 192 - 197: 3.636 distance: 194 - 195: 16.057 distance: 194 - 196: 9.710 distance: 197 - 198: 6.055 distance: 198 - 199: 16.473 distance: 198 - 201: 12.201 distance: 199 - 200: 18.351 distance: 199 - 205: 6.778 distance: 201 - 202: 14.912 distance: 201 - 203: 34.219 distance: 202 - 204: 14.744 distance: 205 - 206: 12.228 distance: 206 - 207: 23.911 distance: 207 - 208: 22.123 distance: 207 - 209: 16.077 distance: 209 - 210: 21.340 distance: 210 - 211: 21.977 distance: 210 - 213: 17.353 distance: 211 - 212: 18.021 distance: 211 - 217: 23.241 distance: 213 - 214: 31.696 distance: 214 - 215: 17.161 distance: 214 - 216: 19.782