Starting phenix.real_space_refine on Sat Aug 3 16:33:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw4_30226/08_2024/7bw4_30226.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw4_30226/08_2024/7bw4_30226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw4_30226/08_2024/7bw4_30226.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw4_30226/08_2024/7bw4_30226.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw4_30226/08_2024/7bw4_30226.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bw4_30226/08_2024/7bw4_30226.cif" } resolution = 3.7 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 63 5.16 5 C 5503 2.51 5 N 1430 2.21 5 O 1607 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 218": "OD1" <-> "OD2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A ASP 260": "OD1" <-> "OD2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 481": "OD1" <-> "OD2" Residue "A TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 517": "OD1" <-> "OD2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A ASP 523": "OD1" <-> "OD2" Residue "A ASP 618": "OD1" <-> "OD2" Residue "A ASP 623": "OD1" <-> "OD2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A ASP 684": "OD1" <-> "OD2" Residue "A TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 760": "OD1" <-> "OD2" Residue "A TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A ASP 804": "OD1" <-> "OD2" Residue "A GLU 811": "OE1" <-> "OE2" Residue "A ASP 824": "OD1" <-> "OD2" Residue "A ASP 825": "OD1" <-> "OD2" Residue "A TYR 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A ASP 846": "OD1" <-> "OD2" Residue "A ASP 893": "OD1" <-> "OD2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "C ASP 44": "OD1" <-> "OD2" Residue "D ASP 101": "OD1" <-> "OD2" Residue "D ASP 112": "OD1" <-> "OD2" Residue "D ASP 143": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8605 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6541 Classifications: {'peptide': 811} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 783} Chain breaks: 2 Chain: "B" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 890 Classifications: {'peptide': 115} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 109} Chain: "C" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 496 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "D" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 676 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 82} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1681 SG CYS A 301 37.606 64.202 36.311 1.00 60.22 S ATOM 1722 SG CYS A 306 37.746 61.966 32.323 1.00 54.47 S ATOM 1754 SG CYS A 310 40.444 62.538 35.190 1.00 51.56 S ATOM 3162 SG CYS A 487 18.959 60.096 44.561 1.00 74.40 S ATOM 4415 SG CYS A 645 18.857 59.240 41.138 1.00 73.86 S ATOM 4421 SG CYS A 646 21.336 61.568 42.144 1.00 71.79 S Time building chain proxies: 5.33, per 1000 atoms: 0.62 Number of scatterers: 8605 At special positions: 0 Unit cell: (80.8, 95.2, 124, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 63 16.00 O 1607 8.00 N 1430 7.00 C 5503 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: 3.44 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 6 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2066 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 10 sheets defined 51.5% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 removed outlier: 4.058A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.611A pdb=" N PHE A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 187 removed outlier: 3.590A pdb=" N TYR A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 197 removed outlier: 3.628A pdb=" N CYS A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA A 195 " --> pdb=" O GLN A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.781A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.615A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 246 removed outlier: 4.200A pdb=" N THR A 246 " --> pdb=" O PRO A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.710A pdb=" N ASN A 300 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS A 301 " --> pdb=" O CYS A 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 301' Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 378 through 384 Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.938A pdb=" N TYR A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 458 Processing helix chain 'A' and resid 466 through 480 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.735A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.649A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 641 removed outlier: 3.728A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 684 through 709 removed outlier: 4.208A pdb=" N ALA A 688 " --> pdb=" O ASP A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.952A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 removed outlier: 3.571A pdb=" N CYS A 799 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.648A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 866 removed outlier: 4.046A pdb=" N MET A 855 " --> pdb=" O ASP A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 874 through 895 removed outlier: 4.166A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 79 through 97 removed outlier: 3.648A pdb=" N LYS B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 109 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.608A pdb=" N TYR B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.601A pdb=" N ILE B 172 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 removed outlier: 4.020A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 24 removed outlier: 3.563A pdb=" N SER C 24 " --> pdb=" O ARG C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 25 through 40 Processing helix chain 'C' and resid 46 through 62 removed outlier: 3.649A pdb=" N GLU C 50 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 99 removed outlier: 3.775A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 removed outlier: 3.576A pdb=" N ASN D 104 " --> pdb=" O ASN D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 141 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 removed outlier: 4.178A pdb=" N ILE A 37 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY A 44 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 224 removed outlier: 5.836A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.320A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 390 removed outlier: 3.567A pdb=" N VAL B 131 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR B 187 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN B 158 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA B 191 " --> pdb=" O TRP B 154 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TRP B 154 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.427A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA8, first strand: chain 'A' and resid 816 through 821 Processing sheet with id=AA9, first strand: chain 'D' and resid 115 through 116 removed outlier: 4.120A pdb=" N VAL D 115 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 188 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL D 130 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL D 186 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU D 189 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU D 155 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 142 through 143 396 hydrogen bonds defined for protein. 1131 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: 2.78 Time building geometry restraints manager: 3.79 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: 2411 1.33 - 1.45: 1541 1.45 - 1.57: 4746 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 8794 Sorted by residual: bond pdb=" N LEU A 401 " pdb=" CA LEU A 401 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.37e-02 5.33e+03 8.89e+00 bond pdb=" N THR A 248 " pdb=" CA THR A 248 " ideal model delta sigma weight residual 1.455 1.495 -0.041 1.37e-02 5.33e+03 8.86e+00 bond pdb=" N ARG A 249 " pdb=" CA ARG A 249 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.36e+00 bond pdb=" N VAL A 166 " pdb=" CA VAL A 166 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.18e+00 bond pdb=" N VAL A 174 " pdb=" CA VAL A 174 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.84e+00 ... (remaining 8789 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.57: 209 106.57 - 113.42: 4782 113.42 - 120.27: 3305 120.27 - 127.13: 3563 127.13 - 133.98: 79 Bond angle restraints: 11938 Sorted by residual: angle pdb=" C THR A 248 " pdb=" CA THR A 248 " pdb=" CB THR A 248 " ideal model delta sigma weight residual 109.55 116.90 -7.35 1.68e+00 3.54e-01 1.91e+01 angle pdb=" C VAL A 166 " pdb=" CA VAL A 166 " pdb=" CB VAL A 166 " ideal model delta sigma weight residual 111.29 104.38 6.91 1.64e+00 3.72e-01 1.78e+01 angle pdb=" N VAL A 166 " pdb=" CA VAL A 166 " pdb=" C VAL A 166 " ideal model delta sigma weight residual 109.34 117.99 -8.65 2.08e+00 2.31e-01 1.73e+01 angle pdb=" N ASN A 447 " pdb=" CA ASN A 447 " pdb=" C ASN A 447 " ideal model delta sigma weight residual 111.71 106.96 4.75 1.15e+00 7.56e-01 1.71e+01 angle pdb=" N LEU A 247 " pdb=" CA LEU A 247 " pdb=" C LEU A 247 " ideal model delta sigma weight residual 111.82 107.38 4.44 1.16e+00 7.43e-01 1.47e+01 ... (remaining 11933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4637 17.99 - 35.98: 495 35.98 - 53.97: 78 53.97 - 71.95: 12 71.95 - 89.94: 8 Dihedral angle restraints: 5230 sinusoidal: 2035 harmonic: 3195 Sorted by residual: dihedral pdb=" CA ASP D 161 " pdb=" C ASP D 161 " pdb=" N ALA D 162 " pdb=" CA ALA D 162 " ideal model delta harmonic sigma weight residual 180.00 150.73 29.27 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA THR A 462 " pdb=" C THR A 462 " pdb=" N MET A 463 " pdb=" CA MET A 463 " ideal model delta harmonic sigma weight residual 180.00 152.65 27.35 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA TRP A 617 " pdb=" C TRP A 617 " pdb=" N ASP A 618 " pdb=" CA ASP A 618 " ideal model delta harmonic sigma weight residual 180.00 153.05 26.95 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 5227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 988 0.055 - 0.111: 295 0.111 - 0.166: 53 0.166 - 0.221: 11 0.221 - 0.276: 3 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CA LEU A 251 " pdb=" N LEU A 251 " pdb=" C LEU A 251 " pdb=" CB LEU A 251 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA THR A 248 " pdb=" N THR A 248 " pdb=" C THR A 248 " pdb=" CB THR A 248 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA SER B 177 " pdb=" N SER B 177 " pdb=" C SER B 177 " pdb=" CB SER B 177 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 1347 not shown) Planarity restraints: 1517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 686 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C THR A 686 " 0.063 2.00e-02 2.50e+03 pdb=" O THR A 686 " -0.024 2.00e-02 2.50e+03 pdb=" N THR A 687 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 572 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C HIS A 572 " 0.057 2.00e-02 2.50e+03 pdb=" O HIS A 572 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN A 573 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 570 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C GLN A 570 " 0.056 2.00e-02 2.50e+03 pdb=" O GLN A 570 " -0.021 2.00e-02 2.50e+03 pdb=" N PHE A 571 " -0.019 2.00e-02 2.50e+03 ... (remaining 1514 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 148 2.64 - 3.21: 8024 3.21 - 3.77: 13095 3.77 - 4.34: 17510 4.34 - 4.90: 28137 Nonbonded interactions: 66914 Sorted by model distance: nonbonded pdb=" O ASN A 168 " pdb=" ND2 ASN A 168 " model vdw 2.078 3.120 nonbonded pdb=" N LYS D 127 " pdb=" O ALA D 188 " model vdw 2.159 3.120 nonbonded pdb=" OG1 THR A 120 " pdb=" O TYR A 122 " model vdw 2.180 3.040 nonbonded pdb=" OH TYR A 122 " pdb=" OE1 GLU A 144 " model vdw 2.185 3.040 nonbonded pdb=" O VAL A 174 " pdb=" N ASN A 177 " model vdw 2.193 3.120 ... (remaining 66909 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 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: 1.070 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 28.300 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 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 : 0.004 0.041 8794 Z= 0.245 Angle : 0.655 8.651 11938 Z= 0.421 Chirality : 0.055 0.276 1350 Planarity : 0.004 0.042 1517 Dihedral : 15.164 89.943 3164 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.34 % Favored : 95.47 % Rotamer: Outliers : 1.68 % Allowed : 4.73 % Favored : 93.59 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 5.71 % 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 (0.22), residues: 1060 helix: -0.74 (0.21), residues: 493 sheet: -1.63 (0.55), residues: 76 loop : -2.66 (0.22), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 154 HIS 0.004 0.001 HIS A 309 PHE 0.017 0.001 PHE A 571 TYR 0.013 0.001 TYR A 453 ARG 0.002 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 256 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7484 (m-80) cc_final: 0.7121 (m-80) REVERT: A 191 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: A 217 TYR cc_start: 0.6078 (p90) cc_final: 0.5854 (p90) REVERT: A 316 LEU cc_start: 0.7504 (tp) cc_final: 0.7298 (tt) REVERT: A 500 LYS cc_start: 0.6395 (mttp) cc_final: 0.5666 (tttm) REVERT: A 548 ILE cc_start: 0.8426 (mp) cc_final: 0.8121 (mp) REVERT: A 575 LEU cc_start: 0.7481 (tp) cc_final: 0.7233 (tt) REVERT: A 868 PRO cc_start: 0.8302 (Cg_exo) cc_final: 0.8011 (Cg_endo) REVERT: A 882 HIS cc_start: 0.8059 (m-70) cc_final: 0.7858 (m90) REVERT: A 889 ARG cc_start: 0.8152 (mtt90) cc_final: 0.7325 (mmt90) REVERT: B 91 LEU cc_start: 0.9249 (mt) cc_final: 0.8839 (mt) REVERT: C 18 GLN cc_start: 0.7945 (tm-30) cc_final: 0.7730 (tm-30) REVERT: C 31 GLN cc_start: 0.7389 (mt0) cc_final: 0.7078 (mt0) REVERT: C 51 LYS cc_start: 0.8731 (mttm) cc_final: 0.8482 (mmtp) outliers start: 16 outliers final: 7 residues processed: 268 average time/residue: 0.2522 time to fit residues: 87.4419 Evaluate side-chains 192 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 184 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 196 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 96 optimal weight: 0.0970 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 191 GLN A 210 GLN A 213 ASN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN A 439 HIS A 447 ASN A 497 ASN A 568 ASN A 572 HIS A 650 HIS A 703 ASN A 713 ASN A 722 ASN A 789 GLN A 928 HIS B 104 ASN B 118 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8794 Z= 0.201 Angle : 0.643 9.441 11938 Z= 0.345 Chirality : 0.046 0.193 1350 Planarity : 0.004 0.044 1517 Dihedral : 6.782 89.082 1187 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.13 % Rotamer: Outliers : 2.31 % Allowed : 13.46 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.62 (0.24), residues: 1060 helix: -0.01 (0.23), residues: 508 sheet: -1.71 (0.57), residues: 66 loop : -2.16 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 617 HIS 0.005 0.001 HIS A 309 PHE 0.012 0.001 PHE B 147 TYR 0.018 0.001 TYR A 887 ARG 0.006 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 200 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7325 (m-80) cc_final: 0.6739 (m-80) REVERT: A 316 LEU cc_start: 0.7817 (tp) cc_final: 0.7561 (tt) REVERT: A 456 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.7041 (t80) REVERT: A 500 LYS cc_start: 0.6084 (mttp) cc_final: 0.5757 (tttm) REVERT: A 882 HIS cc_start: 0.8088 (m-70) cc_final: 0.7879 (m-70) REVERT: A 889 ARG cc_start: 0.8192 (mtt90) cc_final: 0.7388 (mmt90) REVERT: C 21 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8266 (mtm-85) REVERT: C 31 GLN cc_start: 0.7253 (mt0) cc_final: 0.6998 (mt0) REVERT: D 87 MET cc_start: 0.6480 (tpt) cc_final: 0.6264 (tpt) outliers start: 22 outliers final: 12 residues processed: 212 average time/residue: 0.2021 time to fit residues: 58.7518 Evaluate side-chains 189 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 45 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 96 optimal weight: 0.0570 chunk 104 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN C 19 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8794 Z= 0.171 Angle : 0.596 8.959 11938 Z= 0.320 Chirality : 0.044 0.260 1350 Planarity : 0.004 0.046 1517 Dihedral : 5.371 52.254 1177 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.73 % Allowed : 16.19 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.12 (0.25), residues: 1060 helix: 0.38 (0.23), residues: 510 sheet: -1.65 (0.54), residues: 76 loop : -1.84 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 154 HIS 0.005 0.001 HIS A 309 PHE 0.010 0.001 PHE B 147 TYR 0.016 0.001 TYR A 453 ARG 0.006 0.000 ARG A 836 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 205 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7315 (m-80) cc_final: 0.6702 (m-80) REVERT: A 217 TYR cc_start: 0.5829 (p90) cc_final: 0.5202 (p90) REVERT: A 456 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.7060 (t80) REVERT: A 500 LYS cc_start: 0.6147 (mttp) cc_final: 0.5781 (tttm) REVERT: A 575 LEU cc_start: 0.7150 (tp) cc_final: 0.6267 (tt) REVERT: A 665 GLU cc_start: 0.6889 (pm20) cc_final: 0.6606 (pm20) REVERT: A 811 GLU cc_start: 0.6784 (tp30) cc_final: 0.6523 (tp30) REVERT: A 882 HIS cc_start: 0.8088 (m-70) cc_final: 0.7883 (m-70) REVERT: A 889 ARG cc_start: 0.8122 (mtt90) cc_final: 0.7371 (mmt90) REVERT: C 18 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7704 (tm-30) REVERT: C 19 GLN cc_start: 0.8263 (tp40) cc_final: 0.8018 (mm-40) REVERT: C 31 GLN cc_start: 0.7400 (mt0) cc_final: 0.7103 (mt0) REVERT: D 129 MET cc_start: 0.7202 (tpp) cc_final: 0.6991 (tpt) outliers start: 26 outliers final: 15 residues processed: 219 average time/residue: 0.2072 time to fit residues: 62.3390 Evaluate side-chains 190 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 174 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 184 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 51.5084 > 50: distance: 40 - 59: 28.426 distance: 54 - 59: 24.582 distance: 59 - 60: 15.971 distance: 60 - 61: 40.423 distance: 60 - 63: 8.681 distance: 61 - 62: 27.973 distance: 61 - 67: 30.356 distance: 63 - 64: 24.302 distance: 64 - 65: 29.003 distance: 64 - 66: 27.671 distance: 67 - 68: 15.911 distance: 68 - 69: 8.976 distance: 68 - 71: 9.196 distance: 69 - 70: 21.890 distance: 69 - 75: 29.937 distance: 71 - 72: 17.831 distance: 72 - 73: 12.900 distance: 72 - 74: 8.820 distance: 75 - 76: 22.148 distance: 76 - 77: 25.446 distance: 76 - 79: 22.888 distance: 77 - 78: 6.959 distance: 77 - 80: 12.735 distance: 80 - 81: 18.039 distance: 81 - 82: 23.212 distance: 81 - 84: 22.963 distance: 82 - 83: 10.156 distance: 82 - 89: 15.456 distance: 84 - 85: 17.548 distance: 85 - 86: 8.850 distance: 86 - 87: 28.503 distance: 87 - 88: 9.158 distance: 89 - 90: 16.057 distance: 90 - 91: 25.300 distance: 90 - 93: 5.202 distance: 91 - 97: 18.784 distance: 93 - 94: 6.503 distance: 94 - 95: 15.944 distance: 94 - 96: 12.771 distance: 97 - 98: 22.420 distance: 98 - 99: 5.564 distance: 98 - 101: 20.432 distance: 99 - 100: 7.308 distance: 99 - 104: 33.985 distance: 101 - 102: 7.755 distance: 101 - 103: 12.145 distance: 104 - 105: 12.087 distance: 105 - 106: 26.147 distance: 105 - 108: 21.741 distance: 106 - 107: 22.522 distance: 106 - 111: 28.050 distance: 108 - 109: 20.957 distance: 108 - 110: 15.241 distance: 111 - 112: 12.466 distance: 112 - 113: 16.417 distance: 112 - 115: 15.501 distance: 113 - 114: 5.381 distance: 113 - 120: 14.689 distance: 114 - 145: 17.872 distance: 115 - 116: 29.414 distance: 116 - 117: 27.842 distance: 117 - 118: 14.070 distance: 117 - 119: 15.787 distance: 121 - 122: 25.194 distance: 121 - 124: 9.089 distance: 122 - 123: 15.786 distance: 123 - 154: 28.778 distance: 125 - 126: 5.320 distance: 126 - 127: 9.787 distance: 126 - 129: 12.264 distance: 127 - 128: 12.336 distance: 127 - 136: 16.802 distance: 128 - 160: 9.554 distance: 129 - 130: 7.639 distance: 130 - 131: 9.228 distance: 130 - 132: 13.527 distance: 131 - 133: 16.245 distance: 132 - 134: 14.900 distance: 133 - 135: 17.526 distance: 134 - 135: 13.792