Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 08:34:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw2_27749/04_2023/8dw2_27749.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw2_27749/04_2023/8dw2_27749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw2_27749/04_2023/8dw2_27749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw2_27749/04_2023/8dw2_27749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw2_27749/04_2023/8dw2_27749.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dw2_27749/04_2023/8dw2_27749.pdb" } resolution = 4.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 5906 2.51 5 N 1565 2.21 5 O 1858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 163": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 162": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9364 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1153 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "B" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1521 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 10, 'TRANS': 181} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1624 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Chain: "D" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1715 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215} Chain: "H" Number of atoms: 1609 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 216, 1607 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 216, 1607 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 bond proxies already assigned to first conformer: 1646 Chain: "L" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1703 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.14, per 1000 atoms: 0.66 Number of scatterers: 9364 At special positions: 0 Unit cell: (79.443, 129.204, 173.727, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1858 8.00 N 1565 7.00 C 5906 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 89 " distance=2.04 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 210 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 140 " - pdb=" SG CYS L 200 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG E 1 " - " ASN B 343 " Time building additional restraints: 3.80 Conformation dependent library (CDL) restraints added in 1.9 seconds 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2236 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 22 sheets defined 14.2% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 16 through 25 removed outlier: 3.917A pdb=" N GLU A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 49 through 58 Processing helix chain 'A' and resid 59 through 69 removed outlier: 3.658A pdb=" N TYR A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 91 Processing helix chain 'A' and resid 92 through 103 removed outlier: 4.045A pdb=" N VAL A 96 " --> pdb=" O HIS A 92 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 126 through 135 removed outlier: 3.608A pdb=" N GLU A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.972A pdb=" N ILE A 152 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 168 removed outlier: 3.520A pdb=" N LEU A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.978A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.605A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.585A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.695A pdb=" N LEU C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 187 removed outlier: 3.746A pdb=" N GLU C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 187' Processing helix chain 'D' and resid 87 through 91 removed outlier: 4.081A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 203 No H-bonds generated for 'chain 'D' and resid 201 through 203' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'L' and resid 85 through 89 removed outlier: 4.127A pdb=" N VAL L 89 " --> pdb=" O ALA L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 134 removed outlier: 3.550A pdb=" N GLY L 134 " --> pdb=" O GLN L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 194 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.544A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.876A pdb=" N ARG C 24 " --> pdb=" O THR C 5 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.711A pdb=" N TYR C 50 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.711A pdb=" N TYR C 50 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 114 through 118 removed outlier: 6.373A pdb=" N TYR C 173 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 145 through 150 Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.346A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 134 through 138 Processing sheet with id=AB3, first strand: chain 'D' and resid 165 through 168 Processing sheet with id=AB4, first strand: chain 'H' and resid 2 through 6 Processing sheet with id=AB5, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.623A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL H 108 " --> pdb=" O GLY H 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.623A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 124 through 128 removed outlier: 6.227A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 124 through 128 removed outlier: 6.227A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER H 181 " --> pdb=" O VAL H 173 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 154 through 158 removed outlier: 3.847A pdb=" N TYR H 198 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'L' and resid 59 through 60 removed outlier: 6.617A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 120 through 124 removed outlier: 5.447A pdb=" N TYR L 179 " --> pdb=" O ASN L 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 150 through 156 366 hydrogen bonds defined for protein. 948 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: 2.67 Time building geometry restraints manager: 4.16 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: 3009 1.34 - 1.46: 2391 1.46 - 1.59: 4134 1.59 - 1.71: 1 1.71 - 1.83: 44 Bond restraints: 9579 Sorted by residual: bond pdb=" CA ASN D 211 " pdb=" CB ASN D 211 " ideal model delta sigma weight residual 1.530 1.565 -0.035 1.55e-02 4.16e+03 5.10e+00 bond pdb=" CB PRO C 81 " pdb=" CG PRO C 81 " ideal model delta sigma weight residual 1.492 1.604 -0.112 5.00e-02 4.00e+02 4.99e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" CA ARG L 67 " pdb=" C ARG L 67 " ideal model delta sigma weight residual 1.523 1.542 -0.018 1.34e-02 5.57e+03 1.90e+00 bond pdb=" CB PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 1.492 1.559 -0.067 5.00e-02 4.00e+02 1.81e+00 ... (remaining 9574 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.71: 192 105.71 - 112.85: 5058 112.85 - 119.98: 3224 119.98 - 127.12: 4447 127.12 - 134.25: 107 Bond angle restraints: 13028 Sorted by residual: angle pdb=" CA PRO C 81 " pdb=" N PRO C 81 " pdb=" CD PRO C 81 " ideal model delta sigma weight residual 112.00 104.54 7.46 1.40e+00 5.10e-01 2.84e+01 angle pdb=" C SER C 95 " pdb=" CA SER C 95 " pdb=" CB SER C 95 " ideal model delta sigma weight residual 116.54 111.33 5.21 1.15e+00 7.56e-01 2.05e+01 angle pdb=" CB MET H 40 " pdb=" CG MET H 40 " pdb=" SD MET H 40 " ideal model delta sigma weight residual 112.70 125.79 -13.09 3.00e+00 1.11e-01 1.90e+01 angle pdb=" N ALA D 92 " pdb=" CA ALA D 92 " pdb=" C ALA D 92 " ideal model delta sigma weight residual 108.24 113.74 -5.50 1.32e+00 5.74e-01 1.74e+01 angle pdb=" CA LYS B 444 " pdb=" CB LYS B 444 " pdb=" CG LYS B 444 " ideal model delta sigma weight residual 114.10 122.22 -8.12 2.00e+00 2.50e-01 1.65e+01 ... (remaining 13023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 4782 17.63 - 35.25: 710 35.25 - 52.88: 152 52.88 - 70.50: 26 70.50 - 88.12: 7 Dihedral angle restraints: 5677 sinusoidal: 2165 harmonic: 3512 Sorted by residual: dihedral pdb=" CB CYS C 134 " pdb=" SG CYS C 134 " pdb=" SG CYS C 194 " pdb=" CB CYS C 194 " ideal model delta sinusoidal sigma weight residual 93.00 151.64 -58.64 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CA CYS B 361 " pdb=" C CYS B 361 " pdb=" N VAL B 362 " pdb=" CA VAL B 362 " ideal model delta harmonic sigma weight residual 180.00 148.89 31.11 0 5.00e+00 4.00e-02 3.87e+01 dihedral pdb=" CA ASP B 420 " pdb=" C ASP B 420 " pdb=" N TYR B 421 " pdb=" CA TYR B 421 " ideal model delta harmonic sigma weight residual -180.00 -151.38 -28.62 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 5674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1168 0.055 - 0.109: 251 0.109 - 0.164: 42 0.164 - 0.218: 4 0.218 - 0.273: 1 Chirality restraints: 1466 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA ASN L 144 " pdb=" N ASN L 144 " pdb=" C ASN L 144 " pdb=" CB ASN L 144 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.46e-01 chirality pdb=" CA VAL H 117 " pdb=" N VAL H 117 " pdb=" C VAL H 117 " pdb=" CB VAL H 117 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.76e-01 ... (remaining 1463 not shown) Planarity restraints: 1672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " -0.062 5.00e-02 4.00e+02 9.55e-02 1.46e+01 pdb=" N PRO B 521 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 158 " -0.021 2.00e-02 2.50e+03 2.02e-02 1.02e+01 pdb=" CG TRP H 158 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP H 158 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP H 158 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP H 158 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP H 158 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP H 158 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 158 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 158 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 158 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE H 150 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.05e+00 pdb=" N PRO H 151 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO H 151 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO H 151 " -0.035 5.00e-02 4.00e+02 ... (remaining 1669 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 338 2.68 - 3.24: 9285 3.24 - 3.79: 14814 3.79 - 4.35: 18704 4.35 - 4.90: 29833 Nonbonded interactions: 72974 Sorted by model distance: nonbonded pdb=" O TYR C 186 " pdb=" OH TYR C 192 " model vdw 2.127 2.440 nonbonded pdb=" OG SER B 514 " pdb=" OE2 GLU B 516 " model vdw 2.174 2.440 nonbonded pdb=" O SER H 192 " pdb=" OG SER H 192 " model vdw 2.199 2.440 nonbonded pdb=" OD2 ASP A 110 " pdb=" OH TYR B 489 " model vdw 2.201 2.440 nonbonded pdb=" OD1 ASP L 176 " pdb=" OG1 THR L 178 " model vdw 2.205 2.440 ... (remaining 72969 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2 or resid 4 through 8 or resid 11 or resid 14 or resid 16 \ through 20 or resid 23 or resid 26 through 27 or resid 29 through 31 or resid 3 \ 4 through 43 or resid 45 or resid 47 through 50 or resid 52 through 53 or resid \ 55 or resid 58 or resid 60 through 77 or resid 79 or resid 82 through 83 or resi \ d 85 through 91 or resid 94 or resid 97 through 99 or resid 101 through 213)) selection = (chain 'L' and (resid 2 or resid 4 through 8 or resid 11 or resid 14 or resid 16 \ through 20 or resid 23 or resid 26 through 27 or resid 29 or resid 32 through 3 \ 3 or resid 39 through 48 or resid 50 or resid 52 through 55 or resid 57 through \ 58 or resid 60 or resid 63 or resid 65 through 82 or resid 84 or resid 87 throug \ h 88 or resid 90 through 96 or resid 100 or resid 103 through 105 or resid 107 t \ hrough 219)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.480 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: 4.460 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.870 Find NCS groups from input model: 0.430 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 : 0.003 0.112 9579 Z= 0.235 Angle : 0.812 13.087 13028 Z= 0.408 Chirality : 0.047 0.273 1466 Planarity : 0.006 0.095 1671 Dihedral : 17.020 88.125 3405 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.20 % Favored : 93.71 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.24), residues: 1209 helix: -0.95 (0.39), residues: 146 sheet: 0.33 (0.26), residues: 427 loop : -1.22 (0.25), residues: 636 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 146 average time/residue: 0.2092 time to fit residues: 43.1722 Evaluate side-chains 133 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 1.106 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0903 time to fit residues: 1.8922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 48 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 chunk 36 optimal weight: 0.4980 chunk 56 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN D 65 GLN L 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 9579 Z= 0.273 Angle : 0.688 7.535 13028 Z= 0.354 Chirality : 0.045 0.210 1466 Planarity : 0.006 0.075 1671 Dihedral : 5.070 28.480 1313 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.44 % Favored : 91.48 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % 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: -0.92 (0.24), residues: 1209 helix: -0.71 (0.41), residues: 148 sheet: 0.45 (0.26), residues: 408 loop : -1.30 (0.24), residues: 653 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 185 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 186 average time/residue: 0.2232 time to fit residues: 57.0651 Evaluate side-chains 127 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0847 time to fit residues: 1.7443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 89 optimal weight: 40.0000 chunk 73 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 138 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 82 GLN ** H 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 9579 Z= 0.349 Angle : 0.717 8.614 13028 Z= 0.371 Chirality : 0.045 0.193 1466 Planarity : 0.006 0.070 1671 Dihedral : 5.460 31.950 1313 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.52 % Favored : 91.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.00 (0.24), residues: 1209 helix: -0.63 (0.42), residues: 148 sheet: 0.30 (0.26), residues: 419 loop : -1.35 (0.24), residues: 642 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2179 time to fit residues: 43.2227 Evaluate side-chains 114 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.183 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 30 optimal weight: 0.2980 chunk 95 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN D 214 HIS H 3 GLN ** H 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 9579 Z= 0.182 Angle : 0.639 7.135 13028 Z= 0.325 Chirality : 0.045 0.164 1466 Planarity : 0.005 0.064 1671 Dihedral : 4.987 36.064 1313 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.03 % Favored : 92.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.69 (0.24), residues: 1209 helix: -0.54 (0.42), residues: 141 sheet: 0.52 (0.26), residues: 419 loop : -1.11 (0.25), residues: 649 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2115 time to fit residues: 49.7201 Evaluate side-chains 131 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 58 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN ** H 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 9579 Z= 0.328 Angle : 0.704 8.636 13028 Z= 0.362 Chirality : 0.045 0.190 1466 Planarity : 0.006 0.061 1671 Dihedral : 5.302 32.038 1313 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.18 % Favored : 90.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.96 (0.24), residues: 1209 helix: -0.62 (0.42), residues: 148 sheet: 0.20 (0.26), residues: 430 loop : -1.24 (0.25), residues: 631 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1939 time to fit residues: 40.4646 Evaluate side-chains 113 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.156 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/iotbx/cli_parser.py", line 870, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.3383 > 50: distance: 14 - 139: 33.928 distance: 17 - 136: 21.962 distance: 24 - 125: 21.754 distance: 27 - 122: 10.060 distance: 34 - 112: 9.251 distance: 37 - 109: 31.788 distance: 70 - 118: 7.726 distance: 73 - 115: 14.952 distance: 97 - 103: 22.640 distance: 103 - 104: 7.771 distance: 104 - 105: 14.749 distance: 104 - 107: 38.342 distance: 105 - 106: 14.747 distance: 105 - 109: 4.559 distance: 107 - 108: 40.837 distance: 109 - 110: 3.425 distance: 110 - 111: 16.521 distance: 110 - 113: 25.031 distance: 111 - 112: 19.638 distance: 111 - 115: 8.230 distance: 113 - 114: 17.788 distance: 115 - 116: 8.980 distance: 116 - 117: 21.167 distance: 116 - 119: 21.676 distance: 117 - 118: 12.900 distance: 117 - 122: 7.130 distance: 119 - 120: 15.819 distance: 122 - 123: 18.133 distance: 123 - 124: 9.554 distance: 123 - 126: 28.865 distance: 124 - 125: 18.836 distance: 124 - 129: 21.120 distance: 126 - 127: 12.489 distance: 126 - 128: 29.699 distance: 129 - 130: 6.841 distance: 130 - 131: 22.506 distance: 130 - 133: 11.864 distance: 131 - 132: 4.023 distance: 131 - 136: 35.707 distance: 133 - 134: 11.159 distance: 133 - 135: 20.090 distance: 136 - 137: 22.831 distance: 137 - 138: 17.387 distance: 137 - 140: 24.920 distance: 138 - 139: 24.123 distance: 138 - 143: 11.243 distance: 140 - 141: 31.268 distance: 140 - 142: 55.268 distance: 143 - 144: 23.585 distance: 143 - 149: 16.067 distance: 144 - 145: 22.615 distance: 144 - 147: 21.681 distance: 145 - 146: 17.154 distance: 145 - 150: 32.053 distance: 147 - 148: 29.869 distance: 148 - 149: 19.999 distance: 150 - 151: 11.500 distance: 151 - 152: 37.528 distance: 151 - 154: 28.114 distance: 152 - 153: 18.149 distance: 152 - 156: 29.821 distance: 154 - 155: 14.326 distance: 156 - 157: 17.427 distance: 157 - 158: 15.726 distance: 157 - 160: 35.018 distance: 158 - 159: 54.261 distance: 158 - 162: 22.601 distance: 160 - 161: 4.568 distance: 162 - 163: 16.038 distance: 163 - 164: 10.015 distance: 163 - 166: 30.474 distance: 164 - 165: 27.721 distance: 164 - 168: 23.257 distance: 166 - 167: 13.592