Starting phenix.real_space_refine on Wed Mar 12 05:00:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xw2_33489/03_2025/7xw2_33489.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xw2_33489/03_2025/7xw2_33489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xw2_33489/03_2025/7xw2_33489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xw2_33489/03_2025/7xw2_33489.map" model { file = "/net/cci-nas-00/data/ceres_data/7xw2_33489/03_2025/7xw2_33489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xw2_33489/03_2025/7xw2_33489.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 52 5.49 5 S 29 5.16 5 C 4279 2.51 5 N 1182 2.21 5 O 1448 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6992 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5854 Classifications: {'peptide': 725} Link IDs: {'PTRANS': 50, 'TRANS': 674} Chain breaks: 4 Chain: "C" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1136 Inner-chain residues flagged as termini: ['pdbres=" A C 46 "'] Classifications: {'RNA': 54} Modifications used: {'5*END': 2, 'rna2p_pyr': 2, 'rna3p_pur': 25, 'rna3p_pyr': 27} Link IDs: {'rna2p': 2, 'rna3p': 51} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.82, per 1000 atoms: 0.69 Number of scatterers: 6992 At special positions: 0 Unit cell: (78.108, 83.202, 139.236, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 29 16.00 P 52 15.00 O 1448 8.00 N 1182 7.00 C 4279 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.82 Conformation dependent library (CDL) restraints added in 794.3 milliseconds 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1392 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 8 sheets defined 44.0% alpha, 6.8% beta 10 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'A' and resid 754 through 758 Processing helix chain 'A' and resid 839 through 855 Processing helix chain 'A' and resid 968 through 976 removed outlier: 3.657A pdb=" N TYR A 972 " --> pdb=" O PHE A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1028 removed outlier: 4.079A pdb=" N ALA A1022 " --> pdb=" O GLU A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1053 removed outlier: 4.103A pdb=" N LYS A1050 " --> pdb=" O SER A1046 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N CYS A1053 " --> pdb=" O ARG A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1061 Processing helix chain 'A' and resid 1068 through 1074 Processing helix chain 'A' and resid 1293 through 1298 Processing helix chain 'A' and resid 1315 through 1335 removed outlier: 3.508A pdb=" N GLY A1319 " --> pdb=" O LEU A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1351 Processing helix chain 'A' and resid 1352 through 1364 removed outlier: 3.781A pdb=" N LYS A1362 " --> pdb=" O ARG A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1369 removed outlier: 4.017A pdb=" N ARG A1368 " --> pdb=" O GLY A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1375 through 1380 Processing helix chain 'A' and resid 1555 through 1575 removed outlier: 3.975A pdb=" N ILE A1559 " --> pdb=" O ALA A1555 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A1560 " --> pdb=" O ASP A1556 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU A1564 " --> pdb=" O ALA A1560 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A1567 " --> pdb=" O VAL A1563 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1587 Processing helix chain 'A' and resid 1665 through 1674 removed outlier: 3.944A pdb=" N PHE A1669 " --> pdb=" O GLY A1665 " (cutoff:3.500A) Processing helix chain 'A' and resid 1680 through 1686 Processing helix chain 'A' and resid 1701 through 1722 removed outlier: 3.597A pdb=" N GLU A1705 " --> pdb=" O TYR A1701 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A1706 " --> pdb=" O GLN A1702 " (cutoff:3.500A) Processing helix chain 'A' and resid 1728 through 1741 Processing helix chain 'A' and resid 1741 through 1752 removed outlier: 3.629A pdb=" N TYR A1752 " --> pdb=" O LEU A1748 " (cutoff:3.500A) Processing helix chain 'A' and resid 1754 through 1758 removed outlier: 3.594A pdb=" N TYR A1757 " --> pdb=" O TYR A1754 " (cutoff:3.500A) Processing helix chain 'A' and resid 1764 through 1777 removed outlier: 3.866A pdb=" N VAL A1768 " --> pdb=" O GLU A1764 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE A1769 " --> pdb=" O LEU A1765 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1812 removed outlier: 3.608A pdb=" N GLY A1809 " --> pdb=" O PRO A1805 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A1812 " --> pdb=" O MET A1808 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1823 removed outlier: 3.753A pdb=" N GLY A1817 " --> pdb=" O GLU A1813 " (cutoff:3.500A) Processing helix chain 'A' and resid 1826 through 1849 removed outlier: 3.661A pdb=" N VAL A1830 " --> pdb=" O SER A1826 " (cutoff:3.500A) Proline residue: A1836 - end of helix Proline residue: A1840 - end of helix removed outlier: 4.615A pdb=" N ALA A1847 " --> pdb=" O GLU A1843 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1861 Processing helix chain 'A' and resid 1896 through 1912 removed outlier: 3.817A pdb=" N SER A1911 " --> pdb=" O ARG A1907 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A1912 " --> pdb=" O ALA A1908 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 747 through 750 Processing sheet with id=AA2, first strand: chain 'A' and resid 769 through 770 Processing sheet with id=AA3, first strand: chain 'A' and resid 801 through 804 Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 820 removed outlier: 3.762A pdb=" N THR A 820 " --> pdb=" O GLY A 823 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A 823 " --> pdb=" O THR A 820 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 866 through 867 removed outlier: 4.742A pdb=" N GLU A 866 " --> pdb=" O VAL A1386 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A1386 " --> pdb=" O GLU A 866 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1032 through 1033 removed outlier: 3.506A pdb=" N LEU A1033 " --> pdb=" O LEU A 988 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA A 930 " --> pdb=" O VAL A 947 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL A 931 " --> pdb=" O HIS A1041 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1871 through 1872 removed outlier: 3.638A pdb=" N GLU A1871 " --> pdb=" O ARG A1879 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1881 through 1883 210 hydrogen bonds defined for protein. 600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 2.88 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1028 1.31 - 1.44: 2237 1.44 - 1.56: 3854 1.56 - 1.69: 104 1.69 - 1.81: 42 Bond restraints: 7265 Sorted by residual: bond pdb=" N THR A 955 " pdb=" CA THR A 955 " ideal model delta sigma weight residual 1.455 1.489 -0.034 7.00e-03 2.04e+04 2.30e+01 bond pdb=" N ILE A 933 " pdb=" CA ILE A 933 " ideal model delta sigma weight residual 1.460 1.502 -0.042 9.30e-03 1.16e+04 2.00e+01 bond pdb=" N VAL A1804 " pdb=" CA VAL A1804 " ideal model delta sigma weight residual 1.461 1.499 -0.038 9.10e-03 1.21e+04 1.76e+01 bond pdb=" N LYS A 862 " pdb=" CA LYS A 862 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.54e+01 bond pdb=" N ILE A1802 " pdb=" CA ILE A1802 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.11e-02 8.12e+03 1.45e+01 ... (remaining 7260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 9604 2.34 - 4.68: 445 4.68 - 7.02: 40 7.02 - 9.35: 8 9.35 - 11.69: 3 Bond angle restraints: 10100 Sorted by residual: angle pdb=" N GLU A1068 " pdb=" CA GLU A1068 " pdb=" C GLU A1068 " ideal model delta sigma weight residual 112.93 101.24 11.69 1.12e+00 7.97e-01 1.09e+02 angle pdb=" N LEU A1065 " pdb=" CA LEU A1065 " pdb=" C LEU A1065 " ideal model delta sigma weight residual 111.28 101.22 10.06 1.09e+00 8.42e-01 8.51e+01 angle pdb=" N GLU A1069 " pdb=" CA GLU A1069 " pdb=" C GLU A1069 " ideal model delta sigma weight residual 112.38 105.22 7.16 1.22e+00 6.72e-01 3.44e+01 angle pdb=" N LEU A1315 " pdb=" CA LEU A1315 " pdb=" C LEU A1315 " ideal model delta sigma weight residual 114.56 107.21 7.35 1.27e+00 6.20e-01 3.35e+01 angle pdb=" N LEU A1061 " pdb=" CA LEU A1061 " pdb=" C LEU A1061 " ideal model delta sigma weight residual 111.71 105.23 6.48 1.15e+00 7.56e-01 3.18e+01 ... (remaining 10095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 4310 35.64 - 71.27: 161 71.27 - 106.91: 20 106.91 - 142.55: 0 142.55 - 178.18: 1 Dihedral angle restraints: 4492 sinusoidal: 2340 harmonic: 2152 Sorted by residual: dihedral pdb=" O4' U C 1 " pdb=" C1' U C 1 " pdb=" N1 U C 1 " pdb=" C2 U C 1 " ideal model delta sinusoidal sigma weight residual -128.00 50.18 -178.18 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA GLU A1883 " pdb=" C GLU A1883 " pdb=" N VAL A1884 " pdb=" CA VAL A1884 " ideal model delta harmonic sigma weight residual 180.00 151.52 28.48 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA GLN A1389 " pdb=" C GLN A1389 " pdb=" N ASP A1390 " pdb=" CA ASP A1390 " ideal model delta harmonic sigma weight residual 180.00 153.17 26.83 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 4489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 971 0.076 - 0.151: 148 0.151 - 0.226: 33 0.226 - 0.302: 16 0.302 - 0.377: 3 Chirality restraints: 1171 Sorted by residual: chirality pdb=" CA THR A1066 " pdb=" N THR A1066 " pdb=" C THR A1066 " pdb=" CB THR A1066 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CA LEU A 890 " pdb=" N LEU A 890 " pdb=" C LEU A 890 " pdb=" CB LEU A 890 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA ASN A 938 " pdb=" N ASN A 938 " pdb=" C ASN A 938 " pdb=" CB ASN A 938 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 1168 not shown) Planarity restraints: 1092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1332 " -0.018 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C PHE A1332 " 0.060 2.00e-02 2.50e+03 pdb=" O PHE A1332 " -0.022 2.00e-02 2.50e+03 pdb=" N CYS A1333 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A1063 " -0.016 2.00e-02 2.50e+03 3.38e-02 1.15e+01 pdb=" C CYS A1063 " 0.058 2.00e-02 2.50e+03 pdb=" O CYS A1063 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU A1064 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A1314 " 0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ARG A1314 " -0.057 2.00e-02 2.50e+03 pdb=" O ARG A1314 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU A1315 " 0.019 2.00e-02 2.50e+03 ... (remaining 1089 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 18 2.49 - 3.09: 4796 3.09 - 3.70: 10579 3.70 - 4.30: 15726 4.30 - 4.90: 24783 Nonbonded interactions: 55902 Sorted by model distance: nonbonded pdb=" OE2 GLU A1705 " pdb="CA CA A2002 " model vdw 1.891 2.510 nonbonded pdb=" OP1 C C 52 " pdb="CA CA A2001 " model vdw 1.983 2.510 nonbonded pdb=" OP1 U C 23 " pdb="CA CA A2002 " model vdw 2.043 2.510 nonbonded pdb=" O2' U C 24 " pdb=" OP2 A C 25 " model vdw 2.385 3.040 nonbonded pdb=" O SER A 760 " pdb=" OG SER A 760 " model vdw 2.385 3.040 ... (remaining 55897 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.540 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.010 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.010 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:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 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 : 0.007 0.049 7265 Z= 0.465 Angle : 1.051 11.692 10100 Z= 0.714 Chirality : 0.068 0.377 1171 Planarity : 0.007 0.054 1092 Dihedral : 17.355 178.182 3100 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.92 % Allowed : 6.91 % Favored : 92.17 % Cbeta Deviations : 0.29 % 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: -3.30 (0.26), residues: 715 helix: -1.82 (0.27), residues: 284 sheet: -3.43 (0.51), residues: 49 loop : -2.32 (0.27), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP A1048 HIS 0.010 0.002 HIS A1062 PHE 0.017 0.003 PHE A1745 TYR 0.025 0.003 TYR A1754 ARG 0.005 0.001 ARG A 906 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.716 Fit side-chains REVERT: A 895 LYS cc_start: 0.8157 (mppt) cc_final: 0.7644 (ttpp) outliers start: 6 outliers final: 2 residues processed: 104 average time/residue: 0.2613 time to fit residues: 34.2714 Evaluate side-chains 65 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1063 CYS Chi-restraints excluded: chain A residue 1705 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 928 GLN A 938 ASN A 985 GLN A1006 ASN A1029 ASN A1062 HIS A1073 GLN A1293 ASN A1379 ASN A1389 GLN A1689 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.202812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.162434 restraints weight = 8387.835| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 2.37 r_work: 0.3994 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7265 Z= 0.188 Angle : 0.617 7.167 10100 Z= 0.320 Chirality : 0.039 0.146 1171 Planarity : 0.005 0.048 1092 Dihedral : 16.695 179.442 1633 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.38 % Allowed : 11.67 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.28), residues: 715 helix: -0.55 (0.30), residues: 290 sheet: -2.97 (0.52), residues: 51 loop : -1.83 (0.28), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1048 HIS 0.019 0.001 HIS A1062 PHE 0.026 0.002 PHE A 960 TYR 0.035 0.002 TYR A 946 ARG 0.007 0.001 ARG A1855 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: A 1705 GLU cc_start: 0.6033 (OUTLIER) cc_final: 0.5720 (pp20) REVERT: A 1808 MET cc_start: 0.6358 (mmp) cc_final: 0.6115 (mmp) REVERT: A 1859 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.6159 (mp0) outliers start: 9 outliers final: 5 residues processed: 74 average time/residue: 0.1766 time to fit residues: 18.4014 Evaluate side-chains 61 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 1063 CYS Chi-restraints excluded: chain A residue 1697 ILE Chi-restraints excluded: chain A residue 1705 GLU Chi-restraints excluded: chain A residue 1859 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 62 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 0.0070 chunk 59 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 850 HIS A 992 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.189941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.148617 restraints weight = 8681.987| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.41 r_work: 0.3825 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 7265 Z= 0.467 Angle : 0.806 11.244 10100 Z= 0.412 Chirality : 0.048 0.169 1171 Planarity : 0.007 0.065 1092 Dihedral : 16.937 176.215 1633 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.23 % Allowed : 11.52 % Favored : 85.25 % 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: -2.49 (0.29), residues: 715 helix: -0.89 (0.29), residues: 282 sheet: -2.80 (0.49), residues: 80 loop : -1.96 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A1048 HIS 0.009 0.002 HIS A 850 PHE 0.022 0.003 PHE A 896 TYR 0.027 0.003 TYR A 946 ARG 0.009 0.001 ARG A1003 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.906 Fit side-chains REVERT: A 844 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8064 (mt-10) REVERT: A 895 LYS cc_start: 0.8483 (mppt) cc_final: 0.7635 (ttpp) REVERT: A 1357 TYR cc_start: 0.7164 (OUTLIER) cc_final: 0.6660 (t80) REVERT: A 1736 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.6647 (ttm170) REVERT: A 1859 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.6109 (mp0) outliers start: 21 outliers final: 10 residues processed: 69 average time/residue: 0.3105 time to fit residues: 28.4034 Evaluate side-chains 65 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 1063 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1705 GLU Chi-restraints excluded: chain A residue 1736 ARG Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1859 GLU Chi-restraints excluded: chain A residue 1881 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 21 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.194577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.153672 restraints weight = 8643.381| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 2.39 r_work: 0.3883 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7265 Z= 0.237 Angle : 0.620 7.567 10100 Z= 0.315 Chirality : 0.041 0.277 1171 Planarity : 0.006 0.054 1092 Dihedral : 16.695 177.571 1633 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.53 % Allowed : 12.29 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.29), residues: 715 helix: -0.31 (0.30), residues: 288 sheet: -1.86 (0.65), residues: 56 loop : -1.89 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1048 HIS 0.004 0.001 HIS A 992 PHE 0.021 0.002 PHE A 960 TYR 0.027 0.002 TYR A 946 ARG 0.007 0.001 ARG A1855 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.926 Fit side-chains REVERT: A 844 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.8006 (mt-10) REVERT: A 895 LYS cc_start: 0.8356 (mppt) cc_final: 0.7589 (ttpp) REVERT: A 1357 TYR cc_start: 0.7027 (OUTLIER) cc_final: 0.6606 (t80) REVERT: A 1808 MET cc_start: 0.6407 (mmp) cc_final: 0.6136 (mmp) REVERT: A 1859 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.6060 (mp0) outliers start: 23 outliers final: 11 residues processed: 70 average time/residue: 0.2952 time to fit residues: 27.6380 Evaluate side-chains 66 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 923 LYS Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1041 HIS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1554 ILE Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1697 ILE Chi-restraints excluded: chain A residue 1705 GLU Chi-restraints excluded: chain A residue 1802 ILE Chi-restraints excluded: chain A residue 1859 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 55 optimal weight: 0.0670 chunk 54 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.196841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.156489 restraints weight = 8497.874| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.37 r_work: 0.3922 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7265 Z= 0.193 Angle : 0.566 7.178 10100 Z= 0.288 Chirality : 0.039 0.224 1171 Planarity : 0.005 0.054 1092 Dihedral : 16.573 178.012 1632 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.46 % Allowed : 14.13 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.30), residues: 715 helix: 0.20 (0.31), residues: 282 sheet: -1.86 (0.66), residues: 56 loop : -1.68 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1048 HIS 0.003 0.001 HIS A 992 PHE 0.019 0.002 PHE A 960 TYR 0.025 0.001 TYR A 946 ARG 0.006 0.000 ARG A1855 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 844 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: A 1357 TYR cc_start: 0.6992 (OUTLIER) cc_final: 0.6586 (t80) REVERT: A 1808 MET cc_start: 0.6391 (mmp) cc_final: 0.6116 (mmp) REVERT: A 1859 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6106 (mp0) outliers start: 16 outliers final: 10 residues processed: 69 average time/residue: 0.2039 time to fit residues: 18.9506 Evaluate side-chains 66 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 923 LYS Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1041 HIS Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1554 ILE Chi-restraints excluded: chain A residue 1705 GLU Chi-restraints excluded: chain A residue 1802 ILE Chi-restraints excluded: chain A residue 1859 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 50 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 4 optimal weight: 0.0470 chunk 71 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1549 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.199275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.158885 restraints weight = 8584.802| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 2.41 r_work: 0.3943 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7265 Z= 0.162 Angle : 0.535 6.813 10100 Z= 0.273 Chirality : 0.038 0.203 1171 Planarity : 0.005 0.052 1092 Dihedral : 16.492 178.661 1632 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.30 % Allowed : 14.75 % Favored : 82.95 % 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: -0.99 (0.31), residues: 715 helix: 0.55 (0.31), residues: 283 sheet: -1.84 (0.67), residues: 56 loop : -1.43 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1024 HIS 0.003 0.001 HIS A 992 PHE 0.017 0.001 PHE A 960 TYR 0.023 0.001 TYR A 946 ARG 0.005 0.000 ARG A1855 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 844 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: A 1357 TYR cc_start: 0.7034 (OUTLIER) cc_final: 0.6611 (t80) REVERT: A 1808 MET cc_start: 0.6375 (mmp) cc_final: 0.6151 (mmp) REVERT: A 1859 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.6018 (mp0) outliers start: 15 outliers final: 9 residues processed: 67 average time/residue: 0.2552 time to fit residues: 24.1020 Evaluate side-chains 64 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 923 LYS Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1697 ILE Chi-restraints excluded: chain A residue 1802 ILE Chi-restraints excluded: chain A residue 1859 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 21 optimal weight: 8.9990 chunk 20 optimal weight: 0.3980 chunk 13 optimal weight: 0.0010 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 overall best weight: 2.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.191895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.150445 restraints weight = 8533.933| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.39 r_work: 0.3847 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7265 Z= 0.344 Angle : 0.652 7.892 10100 Z= 0.331 Chirality : 0.043 0.218 1171 Planarity : 0.006 0.055 1092 Dihedral : 16.362 175.070 1629 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.23 % Allowed : 15.51 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.31), residues: 715 helix: -0.06 (0.30), residues: 288 sheet: -2.34 (0.64), residues: 64 loop : -1.48 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A1048 HIS 0.004 0.001 HIS A 992 PHE 0.017 0.002 PHE A 896 TYR 0.031 0.002 TYR A 946 ARG 0.007 0.001 ARG A1855 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 49 time to evaluate : 0.595 Fit side-chains REVERT: A 844 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8065 (mt-10) REVERT: A 1357 TYR cc_start: 0.7020 (OUTLIER) cc_final: 0.6529 (t80) REVERT: A 1358 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.7159 (ttm110) REVERT: A 1705 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5908 (pp20) REVERT: A 1808 MET cc_start: 0.6325 (mmp) cc_final: 0.5970 (mmp) REVERT: A 1859 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.6008 (mp0) outliers start: 21 outliers final: 12 residues processed: 64 average time/residue: 0.3215 time to fit residues: 27.5502 Evaluate side-chains 68 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 923 LYS Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1041 HIS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1358 ARG Chi-restraints excluded: chain A residue 1569 CYS Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1697 ILE Chi-restraints excluded: chain A residue 1705 GLU Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1802 ILE Chi-restraints excluded: chain A residue 1859 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 0.2980 chunk 66 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 73 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.195832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.154530 restraints weight = 8556.091| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.41 r_work: 0.3894 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7265 Z= 0.204 Angle : 0.562 7.647 10100 Z= 0.287 Chirality : 0.039 0.201 1171 Planarity : 0.006 0.054 1092 Dihedral : 16.257 176.670 1629 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.61 % Allowed : 16.44 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.31), residues: 715 helix: 0.28 (0.31), residues: 282 sheet: -1.76 (0.70), residues: 56 loop : -1.42 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1048 HIS 0.004 0.001 HIS A 992 PHE 0.016 0.002 PHE A 960 TYR 0.027 0.001 TYR A 946 ARG 0.006 0.000 ARG A1855 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.724 Fit side-chains REVERT: A 844 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: A 1357 TYR cc_start: 0.6994 (OUTLIER) cc_final: 0.6535 (t80) REVERT: A 1361 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6641 (ttpt) REVERT: A 1705 GLU cc_start: 0.6242 (OUTLIER) cc_final: 0.5790 (pp20) REVERT: A 1808 MET cc_start: 0.6256 (mmp) cc_final: 0.5909 (mmp) REVERT: A 1859 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.5975 (mp0) outliers start: 17 outliers final: 9 residues processed: 65 average time/residue: 0.2151 time to fit residues: 19.4285 Evaluate side-chains 66 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 923 LYS Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1063 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1361 LYS Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1705 GLU Chi-restraints excluded: chain A residue 1802 ILE Chi-restraints excluded: chain A residue 1859 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.0040 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.196352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.155389 restraints weight = 8611.973| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 2.39 r_work: 0.3908 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7265 Z= 0.196 Angle : 0.558 7.533 10100 Z= 0.282 Chirality : 0.039 0.202 1171 Planarity : 0.006 0.054 1092 Dihedral : 16.222 176.989 1629 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.76 % Allowed : 16.28 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.31), residues: 715 helix: 0.43 (0.32), residues: 278 sheet: -1.68 (0.72), residues: 56 loop : -1.40 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1048 HIS 0.004 0.001 HIS A 992 PHE 0.016 0.002 PHE A 960 TYR 0.026 0.001 TYR A 946 ARG 0.006 0.000 ARG A1855 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1430 Ramachandran restraints generated. 715 Oldfield, 0 Emsley, 715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.712 Fit side-chains REVERT: A 844 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: A 1357 TYR cc_start: 0.6995 (OUTLIER) cc_final: 0.6472 (t80) REVERT: A 1361 LYS cc_start: 0.6937 (OUTLIER) cc_final: 0.6637 (ttpt) REVERT: A 1705 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.5785 (pp20) REVERT: A 1808 MET cc_start: 0.6332 (mmp) cc_final: 0.6002 (mmp) REVERT: A 1859 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.6006 (mp0) outliers start: 18 outliers final: 9 residues processed: 65 average time/residue: 0.2071 time to fit residues: 18.3256 Evaluate side-chains 65 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 923 LYS Chi-restraints excluded: chain A residue 946 TYR Chi-restraints excluded: chain A residue 1063 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain A residue 1357 TYR Chi-restraints excluded: chain A residue 1361 LYS Chi-restraints excluded: chain A residue 1569 CYS Chi-restraints excluded: chain A residue 1688 THR Chi-restraints excluded: chain A residue 1705 GLU Chi-restraints excluded: chain A residue 1802 ILE Chi-restraints excluded: chain A residue 1859 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.092 > 50: distance: 17 - 34: 10.112 distance: 21 - 39: 27.731 distance: 25 - 47: 16.485 distance: 30 - 34: 8.054 distance: 31 - 54: 15.012 distance: 34 - 35: 24.176 distance: 35 - 36: 32.845 distance: 35 - 38: 11.314 distance: 36 - 39: 9.217 distance: 39 - 40: 24.158 distance: 40 - 41: 10.711 distance: 40 - 43: 24.390 distance: 41 - 42: 20.753 distance: 41 - 47: 11.290 distance: 43 - 44: 8.230 distance: 44 - 45: 13.038 distance: 44 - 46: 18.137 distance: 47 - 48: 16.387 distance: 48 - 49: 4.716 distance: 48 - 51: 10.648 distance: 49 - 50: 10.650 distance: 49 - 54: 3.915 distance: 51 - 52: 9.530 distance: 51 - 53: 9.319 distance: 54 - 55: 7.789 distance: 55 - 56: 4.107 distance: 55 - 58: 11.951 distance: 56 - 57: 4.595 distance: 56 - 62: 5.565 distance: 57 - 85: 9.941 distance: 58 - 59: 13.219 distance: 59 - 60: 11.202 distance: 59 - 61: 8.841 distance: 62 - 63: 4.265 distance: 63 - 66: 8.308 distance: 64 - 65: 11.706 distance: 64 - 70: 8.797 distance: 65 - 96: 20.188 distance: 66 - 67: 7.788 distance: 67 - 68: 11.586 distance: 67 - 69: 9.100 distance: 70 - 71: 10.928 distance: 71 - 72: 10.939 distance: 71 - 74: 13.606 distance: 72 - 73: 7.759 distance: 72 - 77: 7.483 distance: 73 - 101: 10.575 distance: 74 - 75: 10.788 distance: 74 - 76: 18.480 distance: 78 - 79: 7.046 distance: 78 - 81: 6.046 distance: 79 - 80: 13.673 distance: 79 - 85: 8.620 distance: 80 - 107: 13.314 distance: 81 - 82: 3.322 distance: 81 - 83: 26.813 distance: 82 - 84: 5.116 distance: 85 - 86: 6.939 distance: 86 - 87: 5.442 distance: 86 - 89: 6.903 distance: 87 - 88: 7.425 distance: 87 - 96: 3.337 distance: 88 - 115: 13.211 distance: 89 - 90: 10.440 distance: 90 - 91: 4.317 distance: 90 - 92: 3.270 distance: 91 - 93: 6.282 distance: 92 - 94: 9.725 distance: 93 - 95: 6.182 distance: 94 - 95: 11.124 distance: 96 - 97: 11.975 distance: 97 - 98: 8.517 distance: 97 - 100: 7.085 distance: 98 - 99: 5.813 distance: 98 - 101: 10.331 distance: 99 - 120: 12.729 distance: 101 - 102: 9.108 distance: 102 - 103: 9.885 distance: 102 - 105: 6.267 distance: 103 - 104: 10.677 distance: 103 - 107: 7.245 distance: 104 - 127: 16.881 distance: 105 - 106: 16.326