Starting phenix.real_space_refine on Sat May 2 15:30:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rqf_19440/05_2026/8rqf_19440.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rqf_19440/05_2026/8rqf_19440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rqf_19440/05_2026/8rqf_19440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rqf_19440/05_2026/8rqf_19440.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rqf_19440/05_2026/8rqf_19440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rqf_19440/05_2026/8rqf_19440.map" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 4466 2.51 5 N 1137 2.21 5 O 1303 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6950 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2315 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 16, 'TRANS': 284} Chain: "H" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1690 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "L" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1630 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 10, 'TRANS': 201} Chain: "K" Number of atoms: 930 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Conformer: "B" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} bond proxies already assigned to first conformer: 931 Chain: "B" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 365 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 7, 'TRANS': 38} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'BJU': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'BJU:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.96, per 1000 atoms: 0.28 Number of scatterers: 6950 At special positions: 0 Unit cell: (81.9, 75.4, 139.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1303 8.00 N 1137 7.00 C 4466 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 335.2 milliseconds 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1670 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 14 sheets defined 32.3% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 21 through 43 removed outlier: 3.933A pdb=" N VAL A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 57 Processing helix chain 'A' and resid 59 through 83 removed outlier: 3.860A pdb=" N ILE A 63 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 86 through 98 Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 115 through 129 Processing helix chain 'A' and resid 129 through 142 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 155 through 180 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 183 through 211 removed outlier: 3.599A pdb=" N VAL A 204 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.626A pdb=" N PHE A 216 " --> pdb=" O SER A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 244 Proline residue: A 230 - end of helix removed outlier: 3.696A pdb=" N PHE A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 removed outlier: 3.821A pdb=" N CYS A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 removed outlier: 3.615A pdb=" N SER A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.515A pdb=" N GLY A 280 " --> pdb=" O PRO A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 311 removed outlier: 3.883A pdb=" N GLY A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.133A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 187 through 192 removed outlier: 4.084A pdb=" N GLN H 192 " --> pdb=" O LEU H 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 182 through 189 Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 7 removed outlier: 3.659A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.991A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER H 58 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 97 through 98 removed outlier: 3.616A pdb=" N TYR H 100C" --> pdb=" O ASP H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 120 through 123 removed outlier: 6.194A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 120 through 123 removed outlier: 6.194A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 136 through 137 Processing sheet with id=AA7, first strand: chain 'H' and resid 151 through 154 removed outlier: 3.537A pdb=" N THR H 151 " --> pdb=" O ASN H 199 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL H 198 " --> pdb=" O VAL H 207 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL H 207 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS H 200 " --> pdb=" O THR H 205 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR H 205 " --> pdb=" O HIS H 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.561A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.608A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.743A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER L 176 " --> pdb=" O SER L 162 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER L 162 " --> pdb=" O SER L 176 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 153 through 154 removed outlier: 3.569A pdb=" N TYR L 192 " --> pdb=" O PHE L 209 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL L 196 " --> pdb=" O VAL L 205 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.842A pdb=" N VAL K 12 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA K 33 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.842A pdb=" N VAL K 12 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TYR K 102 " --> pdb=" O ILE K 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 18 through 22 removed outlier: 3.773A pdb=" N LEU K 18 " --> pdb=" O MET K 82 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 863 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: 0.93 Time building geometry restraints manager: 0.63 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: 1088 1.30 - 1.43: 1915 1.43 - 1.56: 4043 1.56 - 1.68: 5 1.68 - 1.81: 65 Bond restraints: 7116 Sorted by residual: bond pdb=" C CYS A 125 " pdb=" O CYS A 125 " ideal model delta sigma weight residual 1.237 1.176 0.060 1.17e-02 7.31e+03 2.65e+01 bond pdb=" CA SER A 119 " pdb=" CB SER A 119 " ideal model delta sigma weight residual 1.528 1.451 0.078 1.59e-02 3.96e+03 2.39e+01 bond pdb=" C ILE A 120 " pdb=" O ILE A 120 " ideal model delta sigma weight residual 1.237 1.188 0.049 1.19e-02 7.06e+03 1.67e+01 bond pdb=" C VAL A 121 " pdb=" O VAL A 121 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.11e-02 8.12e+03 1.61e+01 bond pdb=" CA SER A 126 " pdb=" CB SER A 126 " ideal model delta sigma weight residual 1.531 1.469 0.061 1.72e-02 3.38e+03 1.27e+01 ... (remaining 7111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 9392 1.52 - 3.04: 177 3.04 - 4.55: 56 4.55 - 6.07: 33 6.07 - 7.59: 6 Bond angle restraints: 9664 Sorted by residual: angle pdb=" CA MET A 122 " pdb=" C MET A 122 " pdb=" N THR A 123 " ideal model delta sigma weight residual 117.07 124.66 -7.59 1.14e+00 7.69e-01 4.43e+01 angle pdb=" CA THR A 123 " pdb=" C THR A 123 " pdb=" N THR A 124 " ideal model delta sigma weight residual 117.07 123.35 -6.28 1.14e+00 7.69e-01 3.03e+01 angle pdb=" N SER A 119 " pdb=" CA SER A 119 " pdb=" C SER A 119 " ideal model delta sigma weight residual 111.36 105.69 5.67 1.09e+00 8.42e-01 2.71e+01 angle pdb=" CA MET A 122 " pdb=" C MET A 122 " pdb=" O MET A 122 " ideal model delta sigma weight residual 120.82 115.42 5.40 1.05e+00 9.07e-01 2.65e+01 angle pdb=" CA VAL A 121 " pdb=" C VAL A 121 " pdb=" N MET A 122 " ideal model delta sigma weight residual 116.72 122.24 -5.52 1.10e+00 8.26e-01 2.51e+01 ... (remaining 9659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.70: 3755 19.70 - 39.41: 394 39.41 - 59.11: 77 59.11 - 78.81: 7 78.81 - 98.52: 6 Dihedral angle restraints: 4239 sinusoidal: 1619 harmonic: 2620 Sorted by residual: dihedral pdb=" CA LEU A 246 " pdb=" C LEU A 246 " pdb=" N ASN A 247 " pdb=" CA ASN A 247 " ideal model delta harmonic sigma weight residual -180.00 -154.59 -25.41 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CB CYS H 140 " pdb=" SG CYS H 140 " pdb=" SG CYS H 196 " pdb=" CB CYS H 196 " ideal model delta sinusoidal sigma weight residual 93.00 135.07 -42.07 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CA HIS B 40 " pdb=" C HIS B 40 " pdb=" N TRP B 41 " pdb=" CA TRP B 41 " ideal model delta harmonic sigma weight residual -180.00 -157.94 -22.06 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 4236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 888 0.051 - 0.103: 168 0.103 - 0.154: 31 0.154 - 0.206: 2 0.206 - 0.257: 4 Chirality restraints: 1093 Sorted by residual: chirality pdb=" CA THR A 123 " pdb=" N THR A 123 " pdb=" C THR A 123 " pdb=" CB THR A 123 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA GLU A 257 " pdb=" N GLU A 257 " pdb=" C GLU A 257 " pdb=" CB GLU A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA SER A 119 " pdb=" N SER A 119 " pdb=" C SER A 119 " pdb=" CB SER A 119 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1090 not shown) Planarity restraints: 1216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 119 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C SER A 119 " -0.059 2.00e-02 2.50e+03 pdb=" O SER A 119 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE A 120 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 256 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" C MET A 256 " -0.045 2.00e-02 2.50e+03 pdb=" O MET A 256 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU A 257 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 291 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.65e+00 pdb=" C ILE A 291 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE A 291 " -0.016 2.00e-02 2.50e+03 pdb=" N PHE A 292 " -0.016 2.00e-02 2.50e+03 ... (remaining 1213 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 828 2.75 - 3.29: 6516 3.29 - 3.83: 10964 3.83 - 4.36: 12627 4.36 - 4.90: 22981 Nonbonded interactions: 53916 Sorted by model distance: nonbonded pdb=" OD1 ASP A 24 " pdb=" O HOH A 401 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.224 3.040 nonbonded pdb=" O PRO L 8 " pdb=" OG1 THR L 102 " model vdw 2.275 3.040 nonbonded pdb=" NH1 ARG L 66 " pdb=" O GLY L 68 " model vdw 2.281 3.120 nonbonded pdb=" OE1 GLN L 27 " pdb=" OH TYR L 93 " model vdw 2.301 3.040 ... (remaining 53911 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=0.37 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: 4.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.740 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 7120 Z= 0.232 Angle : 0.647 7.590 9670 Z= 0.387 Chirality : 0.044 0.257 1093 Planarity : 0.004 0.035 1216 Dihedral : 16.179 98.517 2560 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.26 % Allowed : 23.03 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.28), residues: 895 helix: 0.43 (0.31), residues: 276 sheet: 0.69 (0.38), residues: 203 loop : -1.26 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 52 TYR 0.019 0.001 TYR L 93 PHE 0.023 0.001 PHE H 122 TRP 0.009 0.001 TRP B 32 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 7116) covalent geometry : angle 0.64675 ( 9664) SS BOND : bond 0.00220 ( 3) SS BOND : angle 0.89135 ( 6) hydrogen bonds : bond 0.20210 ( 307) hydrogen bonds : angle 7.84019 ( 863) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 116 MET cc_start: 0.8299 (tpp) cc_final: 0.8097 (mmm) REVERT: A 151 LYS cc_start: 0.8365 (pttt) cc_final: 0.7221 (tttp) REVERT: A 180 ARG cc_start: 0.7034 (mmt-90) cc_final: 0.6023 (mtm180) REVERT: A 184 MET cc_start: 0.4806 (tmt) cc_final: 0.3438 (mtm) REVERT: A 192 MET cc_start: 0.4945 (tpt) cc_final: 0.4315 (mtt) REVERT: K 34 MET cc_start: 0.8444 (mtt) cc_final: 0.8195 (mtt) REVERT: K 82 SER cc_start: 0.7009 (m) cc_final: 0.6763 (t) REVERT: B 46 LYS cc_start: 0.8173 (mmtm) cc_final: 0.7527 (mtpt) outliers start: 2 outliers final: 2 residues processed: 106 average time/residue: 0.1027 time to fit residues: 14.0301 Evaluate side-chains 97 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 198 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 124 GLN ** 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 = 0.3877 r_free = 0.3877 target = 0.165572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.124867 restraints weight = 14156.141| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.93 r_work: 0.3203 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7120 Z= 0.153 Angle : 0.579 6.743 9670 Z= 0.298 Chirality : 0.043 0.133 1093 Planarity : 0.004 0.041 1216 Dihedral : 5.460 55.024 998 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.46 % Allowed : 22.25 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.29), residues: 895 helix: 0.57 (0.31), residues: 277 sheet: 0.90 (0.37), residues: 213 loop : -1.30 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 52 TYR 0.020 0.001 TYR L 93 PHE 0.013 0.001 PHE H 146 TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 7116) covalent geometry : angle 0.57874 ( 9664) SS BOND : bond 0.00425 ( 3) SS BOND : angle 1.17520 ( 6) hydrogen bonds : bond 0.04510 ( 307) hydrogen bonds : angle 5.57603 ( 863) Misc. bond : bond 0.00086 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.280 Fit side-chains REVERT: A 34 MET cc_start: 0.7936 (tpp) cc_final: 0.7693 (ttm) REVERT: A 151 LYS cc_start: 0.8428 (pttt) cc_final: 0.7297 (tttp) REVERT: A 180 ARG cc_start: 0.7108 (mmt-90) cc_final: 0.5930 (mtm180) REVERT: A 184 MET cc_start: 0.4964 (tmt) cc_final: 0.3545 (mtm) REVERT: A 192 MET cc_start: 0.4906 (tpt) cc_final: 0.4295 (mtt) REVERT: L 156 SER cc_start: 0.8256 (OUTLIER) cc_final: 0.8039 (t) REVERT: L 176 SER cc_start: 0.8619 (p) cc_final: 0.8340 (m) REVERT: K 82 SER cc_start: 0.7069 (m) cc_final: 0.6827 (t) REVERT: B 46 LYS cc_start: 0.8146 (mmtm) cc_final: 0.7510 (mtpt) outliers start: 19 outliers final: 12 residues processed: 113 average time/residue: 0.0890 time to fit residues: 13.2552 Evaluate side-chains 106 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 156 SER Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain B residue 7 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 3 optimal weight: 0.0070 chunk 72 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.167053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.128328 restraints weight = 24650.366| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 6.87 r_work: 0.3051 rms_B_bonded: 5.62 restraints_weight: 2.0000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7120 Z= 0.116 Angle : 0.522 6.821 9670 Z= 0.267 Chirality : 0.041 0.128 1093 Planarity : 0.004 0.038 1216 Dihedral : 5.236 57.040 998 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.33 % Allowed : 23.03 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.29), residues: 895 helix: 0.77 (0.31), residues: 277 sheet: 0.83 (0.37), residues: 218 loop : -1.23 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 52 TYR 0.015 0.001 TYR L 93 PHE 0.009 0.001 PHE H 146 TRP 0.007 0.001 TRP H 103 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 7116) covalent geometry : angle 0.52205 ( 9664) SS BOND : bond 0.00211 ( 3) SS BOND : angle 1.01211 ( 6) hydrogen bonds : bond 0.03858 ( 307) hydrogen bonds : angle 5.10766 ( 863) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.267 Fit side-chains REVERT: A 34 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7755 (ttm) REVERT: A 151 LYS cc_start: 0.8568 (pttt) cc_final: 0.7366 (tttp) REVERT: A 180 ARG cc_start: 0.7114 (mmt-90) cc_final: 0.5868 (mtm180) REVERT: A 184 MET cc_start: 0.4618 (tmt) cc_final: 0.3526 (mtm) REVERT: A 192 MET cc_start: 0.4973 (tpt) cc_final: 0.4270 (mtt) REVERT: A 213 SER cc_start: 0.8092 (OUTLIER) cc_final: 0.7760 (t) REVERT: L 91 TYR cc_start: 0.7237 (m-10) cc_final: 0.7010 (m-10) REVERT: L 106 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8666 (mt) REVERT: L 176 SER cc_start: 0.8614 (p) cc_final: 0.8383 (m) REVERT: B 46 LYS cc_start: 0.8259 (mmtm) cc_final: 0.7564 (mtpt) outliers start: 18 outliers final: 11 residues processed: 102 average time/residue: 0.0970 time to fit residues: 12.9044 Evaluate side-chains 101 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 211 ARG Chi-restraints excluded: chain B residue 7 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.163868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.125221 restraints weight = 22654.493| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 6.22 r_work: 0.3028 rms_B_bonded: 5.23 restraints_weight: 2.0000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7120 Z= 0.176 Angle : 0.561 6.792 9670 Z= 0.286 Chirality : 0.043 0.127 1093 Planarity : 0.004 0.045 1216 Dihedral : 5.388 57.450 998 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.98 % Allowed : 23.03 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.29), residues: 895 helix: 0.65 (0.31), residues: 278 sheet: 0.84 (0.37), residues: 219 loop : -1.31 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 52 TYR 0.022 0.002 TYR L 93 PHE 0.015 0.001 PHE A 285 TRP 0.009 0.001 TRP B 41 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 7116) covalent geometry : angle 0.56024 ( 9664) SS BOND : bond 0.00263 ( 3) SS BOND : angle 1.16983 ( 6) hydrogen bonds : bond 0.04168 ( 307) hydrogen bonds : angle 5.02505 ( 863) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.241 Fit side-chains REVERT: A 34 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7849 (ttm) REVERT: A 151 LYS cc_start: 0.8579 (pttt) cc_final: 0.7417 (tttp) REVERT: A 180 ARG cc_start: 0.7144 (mmt-90) cc_final: 0.5911 (mtm180) REVERT: A 184 MET cc_start: 0.4970 (tmt) cc_final: 0.3977 (ttp) REVERT: A 192 MET cc_start: 0.5040 (tpt) cc_final: 0.4335 (mtt) REVERT: A 213 SER cc_start: 0.8134 (OUTLIER) cc_final: 0.7788 (t) REVERT: L 176 SER cc_start: 0.8637 (p) cc_final: 0.8399 (m) REVERT: B 46 LYS cc_start: 0.8293 (mmtm) cc_final: 0.7612 (mtpt) outliers start: 23 outliers final: 18 residues processed: 111 average time/residue: 0.0926 time to fit residues: 13.4663 Evaluate side-chains 114 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain B residue 7 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.166296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.126299 restraints weight = 20511.146| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 5.41 r_work: 0.3094 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7120 Z= 0.122 Angle : 0.519 6.855 9670 Z= 0.263 Chirality : 0.041 0.132 1093 Planarity : 0.004 0.040 1216 Dihedral : 5.244 58.331 998 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.59 % Allowed : 24.19 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.29), residues: 895 helix: 0.83 (0.32), residues: 277 sheet: 0.90 (0.37), residues: 219 loop : -1.32 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 52 TYR 0.016 0.001 TYR L 93 PHE 0.010 0.001 PHE A 285 TRP 0.007 0.001 TRP B 32 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7116) covalent geometry : angle 0.51813 ( 9664) SS BOND : bond 0.00382 ( 3) SS BOND : angle 1.09355 ( 6) hydrogen bonds : bond 0.03667 ( 307) hydrogen bonds : angle 4.80691 ( 863) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.248 Fit side-chains REVERT: A 34 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7755 (ttm) REVERT: A 151 LYS cc_start: 0.8521 (pttt) cc_final: 0.7304 (tttp) REVERT: A 180 ARG cc_start: 0.7151 (mmt-90) cc_final: 0.5908 (mtm180) REVERT: A 184 MET cc_start: 0.4937 (tmt) cc_final: 0.4071 (ttp) REVERT: A 192 MET cc_start: 0.5009 (tpt) cc_final: 0.4330 (mtt) REVERT: A 213 SER cc_start: 0.8100 (OUTLIER) cc_final: 0.7732 (t) REVERT: L 106 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8654 (mt) REVERT: L 176 SER cc_start: 0.8614 (p) cc_final: 0.8353 (m) REVERT: B 46 LYS cc_start: 0.8253 (mmtm) cc_final: 0.7570 (mtpt) outliers start: 20 outliers final: 16 residues processed: 101 average time/residue: 0.1035 time to fit residues: 13.5524 Evaluate side-chains 106 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 211 ARG Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 33 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.162099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121717 restraints weight = 16465.814| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.83 r_work: 0.3119 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7120 Z= 0.215 Angle : 0.599 6.800 9670 Z= 0.304 Chirality : 0.044 0.132 1093 Planarity : 0.004 0.045 1216 Dihedral : 5.549 59.158 998 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.88 % Allowed : 23.29 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.29), residues: 895 helix: 0.57 (0.31), residues: 278 sheet: 0.82 (0.37), residues: 221 loop : -1.46 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 52 TYR 0.023 0.002 TYR L 93 PHE 0.018 0.002 PHE A 285 TRP 0.010 0.001 TRP B 41 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 7116) covalent geometry : angle 0.59808 ( 9664) SS BOND : bond 0.00430 ( 3) SS BOND : angle 1.32050 ( 6) hydrogen bonds : bond 0.04408 ( 307) hydrogen bonds : angle 4.93738 ( 863) Misc. bond : bond 0.00047 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.178 Fit side-chains REVERT: A 34 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7789 (ttm) REVERT: A 151 LYS cc_start: 0.8508 (pttt) cc_final: 0.7378 (tttp) REVERT: A 180 ARG cc_start: 0.7169 (mmt-90) cc_final: 0.5950 (mtm180) REVERT: A 184 MET cc_start: 0.5109 (tmt) cc_final: 0.4184 (ttp) REVERT: A 192 MET cc_start: 0.4901 (tpt) cc_final: 0.4259 (mtt) REVERT: A 213 SER cc_start: 0.8125 (OUTLIER) cc_final: 0.7763 (t) REVERT: L 78 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7505 (mp) REVERT: L 176 SER cc_start: 0.8653 (p) cc_final: 0.8365 (m) REVERT: B 46 LYS cc_start: 0.8252 (mmtm) cc_final: 0.7593 (mtpt) outliers start: 30 outliers final: 26 residues processed: 116 average time/residue: 0.0867 time to fit residues: 13.3711 Evaluate side-chains 123 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 211 ARG Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain B residue 7 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 63 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 44 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.163812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122744 restraints weight = 19106.523| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 4.31 r_work: 0.3092 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7120 Z= 0.177 Angle : 0.569 6.816 9670 Z= 0.289 Chirality : 0.043 0.137 1093 Planarity : 0.004 0.044 1216 Dihedral : 5.521 59.956 998 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.88 % Allowed : 23.42 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.28), residues: 895 helix: 0.63 (0.31), residues: 277 sheet: 0.78 (0.37), residues: 220 loop : -1.43 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 52 TYR 0.026 0.002 TYR L 91 PHE 0.014 0.001 PHE A 285 TRP 0.008 0.001 TRP B 32 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 7116) covalent geometry : angle 0.56835 ( 9664) SS BOND : bond 0.00268 ( 3) SS BOND : angle 1.24112 ( 6) hydrogen bonds : bond 0.04115 ( 307) hydrogen bonds : angle 4.84350 ( 863) Misc. bond : bond 0.00037 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.201 Fit side-chains REVERT: A 34 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7824 (ttm) REVERT: A 151 LYS cc_start: 0.8533 (pttt) cc_final: 0.7368 (tttp) REVERT: A 180 ARG cc_start: 0.7187 (mmt-90) cc_final: 0.5946 (mtm180) REVERT: A 184 MET cc_start: 0.5068 (tmt) cc_final: 0.4200 (ttp) REVERT: A 192 MET cc_start: 0.4940 (tpt) cc_final: 0.4265 (mtt) REVERT: A 213 SER cc_start: 0.8103 (OUTLIER) cc_final: 0.7757 (t) REVERT: L 78 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7515 (mp) REVERT: L 176 SER cc_start: 0.8662 (p) cc_final: 0.8335 (m) REVERT: B 46 LYS cc_start: 0.8259 (mmtm) cc_final: 0.7592 (mtpt) outliers start: 30 outliers final: 25 residues processed: 114 average time/residue: 0.0905 time to fit residues: 13.5233 Evaluate side-chains 121 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 43 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.2952 > 50: distance: 134 - 138: 6.006 distance: 138 - 139: 15.039 distance: 139 - 140: 10.182 distance: 139 - 142: 21.232 distance: 140 - 141: 18.303 distance: 140 - 147: 10.793 distance: 142 - 143: 6.275 distance: 143 - 144: 3.813 distance: 144 - 145: 4.072 distance: 144 - 146: 3.289 distance: 147 - 148: 6.352 distance: 148 - 149: 29.195 distance: 148 - 151: 12.925 distance: 149 - 150: 39.601 distance: 149 - 156: 69.295 distance: 151 - 152: 21.657 distance: 152 - 153: 20.245 distance: 153 - 154: 5.982 distance: 153 - 155: 4.345 distance: 156 - 157: 63.235 distance: 157 - 158: 29.190 distance: 157 - 160: 33.966 distance: 158 - 159: 27.924 distance: 158 - 168: 16.505 distance: 160 - 161: 16.445 distance: 161 - 162: 7.402 distance: 161 - 163: 9.089 distance: 162 - 164: 17.018 distance: 163 - 165: 9.122 distance: 164 - 166: 5.888 distance: 165 - 166: 7.425 distance: 166 - 167: 6.910 distance: 168 - 169: 9.415 distance: 169 - 170: 16.625 distance: 169 - 172: 7.228 distance: 170 - 171: 10.745 distance: 170 - 179: 17.711 distance: 172 - 173: 11.169 distance: 174 - 175: 3.909 distance: 175 - 176: 3.759 distance: 176 - 177: 4.433 distance: 176 - 178: 6.613 distance: 179 - 180: 8.513 distance: 180 - 181: 7.193 distance: 180 - 183: 6.088 distance: 181 - 182: 15.852 distance: 181 - 191: 9.852 distance: 183 - 184: 5.253 distance: 184 - 185: 4.743 distance: 184 - 186: 4.861 distance: 185 - 187: 6.348 distance: 186 - 188: 8.065 distance: 187 - 189: 3.401 distance: 188 - 189: 7.513 distance: 189 - 190: 3.752 distance: 191 - 192: 8.487 distance: 192 - 193: 9.293 distance: 192 - 195: 8.248 distance: 193 - 194: 13.479 distance: 193 - 197: 4.726 distance: 195 - 196: 10.580 distance: 197 - 198: 8.282 distance: 198 - 199: 20.382 distance: 198 - 201: 7.217 distance: 199 - 200: 25.634 distance: 199 - 205: 19.094 distance: 201 - 202: 8.571 distance: 202 - 203: 13.964 distance: 202 - 204: 14.076 distance: 205 - 206: 10.832 distance: 206 - 207: 16.269 distance: 206 - 209: 23.320 distance: 207 - 208: 9.299 distance: 207 - 213: 28.706 distance: 209 - 210: 10.629 distance: 209 - 211: 26.497 distance: 210 - 212: 15.276 distance: 213 - 214: 22.622 distance: 214 - 215: 6.399 distance: 214 - 217: 19.379 distance: 215 - 216: 22.319 distance: 215 - 220: 23.229 distance: 217 - 218: 16.356 distance: 217 - 219: 16.404 distance: 220 - 221: 5.279 distance: 221 - 222: 8.691 distance: 222 - 223: 12.346 distance: 222 - 231: 4.189 distance: 224 - 225: 8.440 distance: 225 - 226: 8.928 distance: 225 - 227: 4.115 distance: 226 - 228: 4.525 distance: 227 - 229: 5.899 distance: 229 - 230: 7.056