Starting phenix.real_space_refine on Fri Jul 19 09:49:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzb_41753/07_2024/8tzb_41753.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzb_41753/07_2024/8tzb_41753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzb_41753/07_2024/8tzb_41753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzb_41753/07_2024/8tzb_41753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzb_41753/07_2024/8tzb_41753.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzb_41753/07_2024/8tzb_41753.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.026 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 S 39 5.16 5 C 4632 2.51 5 N 1274 2.21 5 O 1335 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1745": "OE1" <-> "OE2" Residue "A GLU 1821": "OE1" <-> "OE2" Residue "A TYR 1894": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1984": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2277": "OD1" <-> "OD2" Residue "A GLU 2337": "OE1" <-> "OE2" Residue "A ASP 2377": "OD1" <-> "OD2" Residue "A GLU 2381": "OE1" <-> "OE2" Residue "A ASP 2438": "OD1" <-> "OD2" Residue "B TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 7283 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 920, 6752 Classifications: {'peptide': 920} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PTRANS': 42, 'TRANS': 877} Chain breaks: 33 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 637 Unresolved non-hydrogen angles: 813 Unresolved non-hydrogen dihedrals: 533 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 8, 'TRP:plan': 3, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 346 Chain: "B" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 492 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 231 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 6, 'PHE:plan': 2, 'GLU:plan': 5, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 127 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'T3X': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.31, per 1000 atoms: 0.73 Number of scatterers: 7283 At special positions: 0 Unit cell: (74.8, 94.435, 145.86, 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) S 39 16.00 F 3 9.00 O 1335 8.00 N 1274 7.00 C 4632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A2452 " - pdb=" SG CYS A2492 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.3 seconds 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1920 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 13 sheets defined 32.5% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 1347 through 1352 removed outlier: 3.790A pdb=" N GLN A1352 " --> pdb=" O THR A1348 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1435 removed outlier: 3.685A pdb=" N TRP A1434 " --> pdb=" O ALA A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1460 through 1471 removed outlier: 3.940A pdb=" N ILE A1469 " --> pdb=" O CYS A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1496 through 1510 Processing helix chain 'A' and resid 1529 through 1539 removed outlier: 4.125A pdb=" N SER A1536 " --> pdb=" O LYS A1532 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU A1537 " --> pdb=" O ILE A1533 " (cutoff:3.500A) Processing helix chain 'A' and resid 1550 through 1558 removed outlier: 3.673A pdb=" N ARG A1558 " --> pdb=" O LEU A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1560 through 1565 Processing helix chain 'A' and resid 1606 through 1607 No H-bonds generated for 'chain 'A' and resid 1606 through 1607' Processing helix chain 'A' and resid 1609 through 1612 Processing helix chain 'A' and resid 1643 through 1656 Processing helix chain 'A' and resid 1703 through 1712 Processing helix chain 'A' and resid 1772 through 1790 removed outlier: 3.575A pdb=" N LEU A1776 " --> pdb=" O LYS A1772 " (cutoff:3.500A) Processing helix chain 'A' and resid 1827 through 1837 Processing helix chain 'A' and resid 1851 through 1855 Processing helix chain 'A' and resid 1885 through 1889 removed outlier: 3.655A pdb=" N GLY A1888 " --> pdb=" O LEU A1885 " (cutoff:3.500A) Processing helix chain 'A' and resid 1914 through 1925 Processing helix chain 'A' and resid 1954 through 1961 Processing helix chain 'A' and resid 1967 through 1988 Processing helix chain 'A' and resid 1996 through 1998 No H-bonds generated for 'chain 'A' and resid 1996 through 1998' Processing helix chain 'A' and resid 2051 through 2068 Processing helix chain 'A' and resid 2070 through 2074 removed outlier: 3.630A pdb=" N ILE A2073 " --> pdb=" O GLY A2070 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A2074 " --> pdb=" O GLY A2071 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2070 through 2074' Processing helix chain 'A' and resid 2094 through 2099 removed outlier: 3.527A pdb=" N TYR A2099 " --> pdb=" O PRO A2095 " (cutoff:3.500A) Processing helix chain 'A' and resid 2107 through 2115 Processing helix chain 'A' and resid 2124 through 2133 Processing helix chain 'A' and resid 2134 through 2139 removed outlier: 4.256A pdb=" N VAL A2138 " --> pdb=" O SER A2134 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N CYS A2139 " --> pdb=" O ALA A2135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2134 through 2139' Processing helix chain 'A' and resid 2276 through 2280 removed outlier: 3.527A pdb=" N VAL A2280 " --> pdb=" O ASP A2277 " (cutoff:3.500A) Processing helix chain 'A' and resid 2339 through 2341 No H-bonds generated for 'chain 'A' and resid 2339 through 2341' Processing helix chain 'A' and resid 2346 through 2351 removed outlier: 3.516A pdb=" N SER A2350 " --> pdb=" O TYR A2346 " (cutoff:3.500A) Processing helix chain 'A' and resid 2389 through 2396 Processing helix chain 'A' and resid 2499 through 2522 removed outlier: 3.856A pdb=" N GLN A2505 " --> pdb=" O PRO A2501 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU A2512 " --> pdb=" O GLU A2508 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 59 Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 117 through 125 removed outlier: 3.677A pdb=" N TYR B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 136 Processing sheet with id=AA1, first strand: chain 'A' and resid 1373 through 1376 removed outlier: 4.813A pdb=" N GLY A1341 " --> pdb=" O PHE A1395 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N HIS A1486 " --> pdb=" O VAL A1447 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU A1449 " --> pdb=" O HIS A1486 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1751 through 1753 removed outlier: 4.436A pdb=" N ILE A1692 " --> pdb=" O LEU A1813 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1730 through 1732 removed outlier: 4.077A pdb=" N ASN A1741 " --> pdb=" O ASN A1730 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASN A1741 " --> pdb=" O CYS A1748 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N CYS A1748 " --> pdb=" O ASN A1741 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1840 through 1841 Processing sheet with id=AA5, first strand: chain 'A' and resid 1893 through 1897 removed outlier: 6.752A pdb=" N GLU A1948 " --> pdb=" O LEU A1935 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N LEU A1935 " --> pdb=" O GLU A1948 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2000 through 2002 Processing sheet with id=AA7, first strand: chain 'A' and resid 2140 through 2148 removed outlier: 6.532A pdb=" N LEU A2140 " --> pdb=" O ASP A2497 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASP A2497 " --> pdb=" O LEU A2140 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER A2491 " --> pdb=" O LEU A2146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2152 through 2157 removed outlier: 6.708A pdb=" N GLY A2170 " --> pdb=" O GLU A2153 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N MET A2155 " --> pdb=" O TRP A2168 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP A2168 " --> pdb=" O MET A2155 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ALA A2157 " --> pdb=" O SER A2166 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N SER A2166 " --> pdb=" O ALA A2157 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN A2178 " --> pdb=" O CYS A2171 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLY A2177 " --> pdb=" O VAL A2194 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2199 through 2207 removed outlier: 6.557A pdb=" N GLY A2218 " --> pdb=" O LEU A2200 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A2202 " --> pdb=" O VAL A2216 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A2216 " --> pdb=" O LEU A2202 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU A2204 " --> pdb=" O TRP A2214 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TRP A2214 " --> pdb=" O LEU A2204 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N HIS A2206 " --> pdb=" O GLU A2212 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLU A2212 " --> pdb=" O HIS A2206 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2245 through 2249 removed outlier: 4.128A pdb=" N LYS A2289 " --> pdb=" O ILE A2274 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2300 through 2304 removed outlier: 6.559A pdb=" N ILE A2323 " --> pdb=" O LEU A2335 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU A2335 " --> pdb=" O ILE A2323 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER A2325 " --> pdb=" O GLN A2333 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2354 through 2359 removed outlier: 4.731A pdb=" N LYS A2367 " --> pdb=" O VAL A2372 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL A2372 " --> pdb=" O LYS A2367 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2414 through 2418 307 hydrogen bonds defined for protein. 843 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: 2.90 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1235 1.30 - 1.43: 1730 1.43 - 1.56: 4352 1.56 - 1.68: 1 1.68 - 1.81: 59 Bond restraints: 7377 Sorted by residual: bond pdb=" C22 T3X A2601 " pdb=" N21 T3X A2601 " ideal model delta sigma weight residual 1.467 1.313 0.154 2.00e-02 2.50e+03 5.92e+01 bond pdb=" C19 T3X A2601 " pdb=" N18 T3X A2601 " ideal model delta sigma weight residual 1.466 1.314 0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" C24 T3X A2601 " pdb=" N21 T3X A2601 " ideal model delta sigma weight residual 1.451 1.300 0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" C23 T3X A2601 " pdb=" N18 T3X A2601 " ideal model delta sigma weight residual 1.456 1.305 0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" C20 T3X A2601 " pdb=" N21 T3X A2601 " ideal model delta sigma weight residual 1.456 1.320 0.136 2.00e-02 2.50e+03 4.59e+01 ... (remaining 7372 not shown) Histogram of bond angle deviations from ideal: 96.05 - 112.73: 4236 112.73 - 129.41: 5721 129.41 - 146.08: 53 146.08 - 162.76: 0 162.76 - 179.44: 2 Bond angle restraints: 10012 Sorted by residual: angle pdb=" C33 T3X A2601 " pdb=" C37 T3X A2601 " pdb=" N36 T3X A2601 " ideal model delta sigma weight residual 110.71 122.27 -11.56 3.00e+00 1.11e-01 1.49e+01 angle pdb=" C37 T3X A2601 " pdb=" N36 T3X A2601 " pdb=" N35 T3X A2601 " ideal model delta sigma weight residual 106.89 96.05 10.84 3.00e+00 1.11e-01 1.30e+01 angle pdb=" C34 T3X A2601 " pdb=" N35 T3X A2601 " pdb=" N36 T3X A2601 " ideal model delta sigma weight residual 111.78 121.84 -10.06 3.00e+00 1.11e-01 1.13e+01 angle pdb=" N35 T3X A2601 " pdb=" C34 T3X A2601 " pdb=" N38 T3X A2601 " ideal model delta sigma weight residual 127.52 137.47 -9.95 3.00e+00 1.11e-01 1.10e+01 angle pdb=" N VAL A2194 " pdb=" CA VAL A2194 " pdb=" C VAL A2194 " ideal model delta sigma weight residual 113.71 110.63 3.08 9.50e-01 1.11e+00 1.05e+01 ... (remaining 10007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 4003 17.61 - 35.22: 330 35.22 - 52.83: 70 52.83 - 70.44: 18 70.44 - 88.05: 7 Dihedral angle restraints: 4428 sinusoidal: 1509 harmonic: 2919 Sorted by residual: dihedral pdb=" CA VAL A2359 " pdb=" C VAL A2359 " pdb=" N ASP A2360 " pdb=" CA ASP A2360 " ideal model delta harmonic sigma weight residual 180.00 157.00 23.00 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CB CYS A2452 " pdb=" SG CYS A2452 " pdb=" SG CYS A2492 " pdb=" CB CYS A2492 " ideal model delta sinusoidal sigma weight residual -86.00 -55.70 -30.30 1 1.00e+01 1.00e-02 1.31e+01 dihedral pdb=" CB GLU A1789 " pdb=" CG GLU A1789 " pdb=" CD GLU A1789 " pdb=" OE1 GLU A1789 " ideal model delta sinusoidal sigma weight residual 0.00 -88.05 88.05 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 4425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 867 0.042 - 0.083: 262 0.083 - 0.124: 79 0.124 - 0.166: 9 0.166 - 0.207: 1 Chirality restraints: 1218 Sorted by residual: chirality pdb=" CB ILE A2365 " pdb=" CA ILE A2365 " pdb=" CG1 ILE A2365 " pdb=" CG2 ILE A2365 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA LEU B 86 " pdb=" N LEU B 86 " pdb=" C LEU B 86 " pdb=" CB LEU B 86 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA ILE A2336 " pdb=" N ILE A2336 " pdb=" C ILE A2336 " pdb=" CB ILE A2336 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 1215 not shown) Planarity restraints: 1263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A1880 " 0.062 5.00e-02 4.00e+02 9.21e-02 1.36e+01 pdb=" N PRO A1881 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO A1881 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A1881 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A2207 " -0.052 5.00e-02 4.00e+02 7.90e-02 1.00e+01 pdb=" N PRO A2208 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO A2208 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A2208 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A1941 " -0.050 5.00e-02 4.00e+02 7.62e-02 9.29e+00 pdb=" N PRO A1942 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A1942 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A1942 " -0.042 5.00e-02 4.00e+02 ... (remaining 1260 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 290 2.72 - 3.27: 7042 3.27 - 3.81: 11427 3.81 - 4.36: 13606 4.36 - 4.90: 23376 Nonbonded interactions: 55741 Sorted by model distance: nonbonded pdb=" O VAL A2152 " pdb=" OH TYR A2475 " model vdw 2.177 2.440 nonbonded pdb=" OH TYR A1992 " pdb=" ND2 ASN A1999 " model vdw 2.185 2.520 nonbonded pdb=" OH TYR A2249 " pdb=" OE1 GLU A2305 " model vdw 2.252 2.440 nonbonded pdb=" NE1 TRP A2104 " pdb=" O LEU A2137 " model vdw 2.256 2.520 nonbonded pdb=" N ARG A2456 " pdb=" O LEU A2473 " model vdw 2.272 2.520 ... (remaining 55736 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.580 Find NCS groups from input model: 0.090 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.154 7377 Z= 0.451 Angle : 0.648 11.564 10012 Z= 0.327 Chirality : 0.043 0.207 1218 Planarity : 0.005 0.092 1263 Dihedral : 14.682 88.051 2505 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.74 % Favored : 94.15 % Rotamer: Outliers : 0.30 % Allowed : 17.72 % Favored : 81.98 % 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: -0.33 (0.28), residues: 940 helix: 0.92 (0.33), residues: 279 sheet: -0.64 (0.34), residues: 213 loop : -0.65 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2496 HIS 0.009 0.001 HIS A2391 PHE 0.014 0.001 PHE A2059 TYR 0.019 0.001 TYR A1739 ARG 0.006 0.001 ARG A2446 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.858 Fit side-chains REVERT: A 2018 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.7828 (m-80) REVERT: A 2274 ILE cc_start: 0.8204 (mp) cc_final: 0.7838 (mt) outliers start: 2 outliers final: 1 residues processed: 85 average time/residue: 0.2119 time to fit residues: 24.3037 Evaluate side-chains 84 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2018 TYR Chi-restraints excluded: chain A residue 2359 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.0484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7377 Z= 0.208 Angle : 0.527 8.352 10012 Z= 0.265 Chirality : 0.042 0.140 1218 Planarity : 0.004 0.068 1263 Dihedral : 4.331 30.948 1060 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.21 % Favored : 94.68 % Rotamer: Outliers : 1.95 % Allowed : 17.42 % Favored : 80.63 % 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: -0.19 (0.28), residues: 940 helix: 1.10 (0.32), residues: 296 sheet: -0.64 (0.35), residues: 208 loop : -0.63 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A2496 HIS 0.007 0.001 HIS A2391 PHE 0.014 0.001 PHE A2059 TYR 0.012 0.001 TYR A1739 ARG 0.005 0.000 ARG A2446 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.947 Fit side-chains REVERT: A 1788 MET cc_start: 0.8138 (mtp) cc_final: 0.7828 (mtp) REVERT: A 1944 MET cc_start: 0.6728 (OUTLIER) cc_final: 0.4595 (ppp) REVERT: A 2018 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.7922 (m-80) REVERT: A 2274 ILE cc_start: 0.8179 (mp) cc_final: 0.7844 (mt) outliers start: 13 outliers final: 4 residues processed: 96 average time/residue: 0.2207 time to fit residues: 29.1557 Evaluate side-chains 90 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1872 ASN Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 2018 TYR Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2375 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 25 optimal weight: 0.0570 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.0600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7377 Z= 0.202 Angle : 0.516 6.687 10012 Z= 0.262 Chirality : 0.042 0.141 1218 Planarity : 0.004 0.060 1263 Dihedral : 4.306 30.354 1060 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.89 % Favored : 95.00 % Rotamer: Outliers : 1.95 % Allowed : 19.37 % Favored : 78.68 % 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: -0.15 (0.28), residues: 940 helix: 1.16 (0.32), residues: 297 sheet: -0.66 (0.35), residues: 208 loop : -0.62 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A2496 HIS 0.007 0.001 HIS A2391 PHE 0.014 0.001 PHE A2059 TYR 0.012 0.001 TYR A1739 ARG 0.005 0.000 ARG A2339 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.851 Fit side-chains REVERT: A 1788 MET cc_start: 0.8093 (mtp) cc_final: 0.7869 (mtp) REVERT: A 1944 MET cc_start: 0.6686 (OUTLIER) cc_final: 0.4561 (ppp) REVERT: A 2018 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: A 2274 ILE cc_start: 0.8193 (mp) cc_final: 0.7865 (mt) outliers start: 13 outliers final: 6 residues processed: 94 average time/residue: 0.1856 time to fit residues: 24.1579 Evaluate side-chains 89 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1872 ASN Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 2018 TYR Chi-restraints excluded: chain A residue 2156 VAL Chi-restraints excluded: chain A residue 2293 ILE Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2375 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.0070 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.0625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7377 Z= 0.205 Angle : 0.517 6.687 10012 Z= 0.262 Chirality : 0.042 0.141 1218 Planarity : 0.004 0.060 1263 Dihedral : 4.307 30.354 1060 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.89 % Favored : 95.00 % Rotamer: Outliers : 1.20 % Allowed : 20.42 % Favored : 78.38 % 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: -0.15 (0.28), residues: 940 helix: 1.16 (0.32), residues: 297 sheet: -0.66 (0.35), residues: 208 loop : -0.62 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A2496 HIS 0.007 0.001 HIS A2391 PHE 0.014 0.001 PHE A2059 TYR 0.012 0.001 TYR A1739 ARG 0.005 0.000 ARG A2339 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 1.015 Fit side-chains REVERT: A 1944 MET cc_start: 0.6689 (OUTLIER) cc_final: 0.4563 (ppp) REVERT: A 2018 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: A 2274 ILE cc_start: 0.8194 (mp) cc_final: 0.7865 (mt) outliers start: 8 outliers final: 6 residues processed: 87 average time/residue: 0.1939 time to fit residues: 23.1972 Evaluate side-chains 88 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1872 ASN Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 2018 TYR Chi-restraints excluded: chain A residue 2156 VAL Chi-restraints excluded: chain A residue 2293 ILE Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2375 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 72 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.0625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7377 Z= 0.207 Angle : 0.516 6.692 10012 Z= 0.262 Chirality : 0.042 0.141 1218 Planarity : 0.004 0.060 1263 Dihedral : 4.354 30.358 1060 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.89 % Favored : 95.00 % Rotamer: Outliers : 1.20 % Allowed : 20.42 % Favored : 78.38 % 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: -0.15 (0.28), residues: 940 helix: 1.17 (0.32), residues: 297 sheet: -0.66 (0.35), residues: 208 loop : -0.62 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A2496 HIS 0.007 0.001 HIS A2391 PHE 0.014 0.001 PHE A2059 TYR 0.012 0.001 TYR A1739 ARG 0.005 0.000 ARG A2339 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.844 Fit side-chains REVERT: A 1944 MET cc_start: 0.6691 (OUTLIER) cc_final: 0.4566 (ppp) REVERT: A 2018 TYR cc_start: 0.8274 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: A 2274 ILE cc_start: 0.8195 (mp) cc_final: 0.7865 (mt) outliers start: 8 outliers final: 6 residues processed: 86 average time/residue: 0.1922 time to fit residues: 22.9632 Evaluate side-chains 88 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1872 ASN Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 2018 TYR Chi-restraints excluded: chain A residue 2156 VAL Chi-restraints excluded: chain A residue 2293 ILE Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2375 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 57 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 81 optimal weight: 0.0980 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 20.0000 chunk 32 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.0625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7377 Z= 0.206 Angle : 0.516 6.689 10012 Z= 0.262 Chirality : 0.042 0.142 1218 Planarity : 0.004 0.060 1263 Dihedral : 4.535 46.359 1060 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.89 % Favored : 95.00 % Rotamer: Outliers : 1.20 % Allowed : 20.42 % Favored : 78.38 % 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: -0.15 (0.28), residues: 940 helix: 1.17 (0.32), residues: 297 sheet: -0.66 (0.35), residues: 208 loop : -0.62 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A2496 HIS 0.006 0.001 HIS A2391 PHE 0.013 0.001 PHE A2059 TYR 0.012 0.001 TYR A1739 ARG 0.004 0.000 ARG A2339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 1.074 Fit side-chains REVERT: A 1944 MET cc_start: 0.6691 (OUTLIER) cc_final: 0.4564 (ppp) REVERT: A 2018 TYR cc_start: 0.8274 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: A 2274 ILE cc_start: 0.8195 (mp) cc_final: 0.7865 (mt) outliers start: 8 outliers final: 6 residues processed: 86 average time/residue: 0.1939 time to fit residues: 23.0815 Evaluate side-chains 88 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1872 ASN Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 2018 TYR Chi-restraints excluded: chain A residue 2156 VAL Chi-restraints excluded: chain A residue 2293 ILE Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2375 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.0010 chunk 55 optimal weight: 0.1980 chunk 71 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 38 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 overall best weight: 0.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7377 Z= 0.144 Angle : 0.483 7.417 10012 Z= 0.248 Chirality : 0.041 0.133 1218 Planarity : 0.004 0.060 1263 Dihedral : 4.045 28.288 1060 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.36 % Favored : 95.53 % Rotamer: Outliers : 1.65 % Allowed : 19.82 % Favored : 78.53 % 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 (0.28), residues: 940 helix: 1.45 (0.32), residues: 296 sheet: -0.49 (0.35), residues: 220 loop : -0.57 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2316 HIS 0.008 0.001 HIS A2391 PHE 0.012 0.001 PHE A2059 TYR 0.010 0.001 TYR A1739 ARG 0.003 0.000 ARG A1711 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.894 Fit side-chains REVERT: A 1340 VAL cc_start: 0.6528 (m) cc_final: 0.6252 (m) REVERT: A 1944 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.4627 (ppp) REVERT: A 2274 ILE cc_start: 0.8172 (mp) cc_final: 0.7839 (mt) REVERT: A 2470 MET cc_start: 0.7593 (ttm) cc_final: 0.7335 (tpt) outliers start: 11 outliers final: 9 residues processed: 97 average time/residue: 0.2009 time to fit residues: 26.4906 Evaluate side-chains 98 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1872 ASN Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1989 MET Chi-restraints excluded: chain A residue 2004 THR Chi-restraints excluded: chain A residue 2156 VAL Chi-restraints excluded: chain A residue 2293 ILE Chi-restraints excluded: chain A residue 2316 TRP Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2375 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 61 optimal weight: 0.0970 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7377 Z= 0.229 Angle : 0.538 10.446 10012 Z= 0.270 Chirality : 0.042 0.139 1218 Planarity : 0.004 0.059 1263 Dihedral : 4.066 21.796 1058 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.21 % Favored : 94.68 % Rotamer: Outliers : 1.95 % Allowed : 19.97 % Favored : 78.08 % 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: 0.07 (0.28), residues: 940 helix: 1.41 (0.32), residues: 296 sheet: -0.48 (0.35), residues: 219 loop : -0.56 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2316 HIS 0.008 0.001 HIS A2391 PHE 0.013 0.001 PHE A2059 TYR 0.015 0.001 TYR A1739 ARG 0.006 0.001 ARG A2339 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.905 Fit side-chains REVERT: A 1944 MET cc_start: 0.6713 (OUTLIER) cc_final: 0.4684 (ppp) REVERT: A 2274 ILE cc_start: 0.8183 (mp) cc_final: 0.7857 (mt) outliers start: 13 outliers final: 10 residues processed: 93 average time/residue: 0.1845 time to fit residues: 24.3319 Evaluate side-chains 89 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1872 ASN Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1989 MET Chi-restraints excluded: chain A residue 2004 THR Chi-restraints excluded: chain A residue 2134 SER Chi-restraints excluded: chain A residue 2156 VAL Chi-restraints excluded: chain A residue 2215 ILE Chi-restraints excluded: chain A residue 2293 ILE Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2375 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.7980 chunk 93 optimal weight: 0.0070 chunk 54 optimal weight: 0.0470 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 0.0040 chunk 85 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.2908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7377 Z= 0.141 Angle : 0.490 8.291 10012 Z= 0.250 Chirality : 0.041 0.132 1218 Planarity : 0.004 0.058 1263 Dihedral : 3.855 22.295 1058 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.36 % Favored : 95.53 % Rotamer: Outliers : 1.80 % Allowed : 19.97 % Favored : 78.23 % 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: 0.24 (0.28), residues: 940 helix: 1.65 (0.32), residues: 296 sheet: -0.41 (0.35), residues: 215 loop : -0.53 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A2316 HIS 0.008 0.001 HIS A2391 PHE 0.011 0.001 PHE A2059 TYR 0.008 0.001 TYR A1739 ARG 0.006 0.000 ARG A2339 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.854 Fit side-chains REVERT: A 1340 VAL cc_start: 0.6344 (m) cc_final: 0.6071 (m) REVERT: A 1944 MET cc_start: 0.6575 (OUTLIER) cc_final: 0.4749 (ppp) REVERT: A 2274 ILE cc_start: 0.8166 (mp) cc_final: 0.7839 (mt) outliers start: 12 outliers final: 9 residues processed: 98 average time/residue: 0.2088 time to fit residues: 27.8549 Evaluate side-chains 96 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1872 ASN Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 2004 THR Chi-restraints excluded: chain A residue 2134 SER Chi-restraints excluded: chain A residue 2156 VAL Chi-restraints excluded: chain A residue 2215 ILE Chi-restraints excluded: chain A residue 2293 ILE Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2375 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 0.0470 chunk 100 optimal weight: 0.0570 chunk 92 optimal weight: 7.9990 chunk 80 optimal weight: 0.0570 chunk 8 optimal weight: 30.0000 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 0.0870 chunk 63 optimal weight: 5.9990 chunk 85 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 overall best weight: 0.1092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7377 Z= 0.123 Angle : 0.476 8.785 10012 Z= 0.242 Chirality : 0.041 0.134 1218 Planarity : 0.004 0.059 1263 Dihedral : 3.687 22.136 1058 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.00 % Favored : 94.89 % Rotamer: Outliers : 1.05 % Allowed : 20.42 % Favored : 78.53 % 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: 0.47 (0.29), residues: 940 helix: 1.91 (0.32), residues: 296 sheet: -0.19 (0.35), residues: 214 loop : -0.50 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1742 HIS 0.008 0.001 HIS A2391 PHE 0.007 0.001 PHE A2059 TYR 0.008 0.001 TYR A2064 ARG 0.007 0.000 ARG A2339 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 1340 VAL cc_start: 0.6132 (m) cc_final: 0.5831 (m) REVERT: A 1788 MET cc_start: 0.7876 (mtp) cc_final: 0.7564 (mtp) REVERT: A 1944 MET cc_start: 0.6490 (OUTLIER) cc_final: 0.4518 (ppp) REVERT: A 2274 ILE cc_start: 0.8190 (mp) cc_final: 0.7877 (mt) outliers start: 7 outliers final: 6 residues processed: 96 average time/residue: 0.1760 time to fit residues: 23.7511 Evaluate side-chains 92 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1673 LEU Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 2156 VAL Chi-restraints excluded: chain A residue 2215 ILE Chi-restraints excluded: chain A residue 2293 ILE Chi-restraints excluded: chain A residue 2359 VAL Chi-restraints excluded: chain A residue 2375 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 71.7579 > 50: distance: 39 - 89: 34.105 distance: 63 - 66: 35.054 distance: 66 - 67: 57.737 distance: 67 - 68: 56.300 distance: 68 - 69: 69.071 distance: 71 - 77: 41.122 distance: 73 - 78: 38.811 distance: 75 - 76: 40.385 distance: 78 - 79: 41.398 distance: 79 - 80: 41.169 distance: 80 - 81: 42.215 distance: 80 - 86: 52.926 distance: 82 - 83: 40.917 distance: 83 - 84: 39.877 distance: 83 - 85: 40.738 distance: 86 - 87: 37.469 distance: 87 - 88: 39.358 distance: 87 - 90: 40.507 distance: 88 - 89: 56.180 distance: 88 - 91: 70.523 distance: 91 - 92: 57.586 distance: 92 - 93: 58.441 distance: 92 - 95: 57.601 distance: 93 - 94: 55.625 distance: 93 - 99: 40.986 distance: 95 - 96: 39.989 distance: 95 - 97: 56.806 distance: 96 - 98: 40.604 distance: 100 - 101: 39.752 distance: 100 - 103: 18.247 distance: 101 - 102: 55.762 distance: 101 - 107: 57.906 distance: 103 - 104: 28.363 distance: 104 - 105: 44.076 distance: 104 - 106: 21.967 distance: 108 - 109: 39.850 distance: 108 - 111: 48.506 distance: 109 - 115: 56.887 distance: 111 - 112: 44.298 distance: 112 - 113: 12.647 distance: 112 - 114: 28.316 distance: 116 - 117: 41.072 distance: 117 - 118: 56.282 distance: 117 - 123: 40.271 distance: 119 - 121: 56.339 distance: 123 - 124: 8.229 distance: 124 - 125: 51.440 distance: 125 - 127: 40.181 distance: 127 - 128: 57.117 distance: 129 - 135: 34.350 distance: 131 - 132: 39.481