Starting phenix.real_space_refine on Thu Jul 2 02:43:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kmi_62434/07_2026/9kmi_62434.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kmi_62434/07_2026/9kmi_62434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kmi_62434/07_2026/9kmi_62434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kmi_62434/07_2026/9kmi_62434.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kmi_62434/07_2026/9kmi_62434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kmi_62434/07_2026/9kmi_62434.map" } resolution = 3.05 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= -0.001 sd= 0.027 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 S 42 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 3949 2.51 5 N 957 2.21 5 O 1075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6026 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4289 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 25, 'TRANS': 512} Chain breaks: 1 Chain: "H" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 922 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 804 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 8 Ad-hoc single atom residues: {' CL': 1, ' NA': 2} Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1, 'water': 1} Chain breaks: 3 Time building chain proxies: 1.13, per 1000 atoms: 0.19 Number of scatterers: 6026 At special positions: 0 Unit cell: (74.62, 81.18, 109.06, 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) Cl 1 17.00 S 42 16.00 Na 2 11.00 O 1075 8.00 N 957 7.00 C 3949 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.38 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " 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=0, symmetry=0 Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 140.2 milliseconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1386 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 7 sheets defined 55.4% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 47 through 56 removed outlier: 4.174A pdb=" N VAL A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.572A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.806A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 90 through 105 Processing helix chain 'A' and resid 110 through 116 removed outlier: 3.620A pdb=" N LYS A 115 " --> pdb=" O CYS A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 Processing helix chain 'A' and resid 121 through 151 removed outlier: 3.523A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.660A pdb=" N ARG A 177 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 247 through 266 Proline residue: A 253 - end of helix removed outlier: 3.547A pdb=" N THR A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.814A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.326A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 315 removed outlier: 3.630A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 4.211A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 372 through 379 Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.629A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 444 removed outlier: 3.676A pdb=" N ILE A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ILE A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.909A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 484 through 496 removed outlier: 3.895A pdb=" N MET A 495 " --> pdb=" O ASP A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 removed outlier: 3.526A pdb=" N TYR A 506 " --> pdb=" O PRO A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 526 removed outlier: 3.585A pdb=" N LEU A 524 " --> pdb=" O PHE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 555 Processing helix chain 'A' and resid 555 through 567 Processing helix chain 'A' and resid 571 through 581 removed outlier: 3.603A pdb=" N LYS A 577 " --> pdb=" O ARG A 573 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.573A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.568A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.892A pdb=" N ALA L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 7 removed outlier: 5.562A pdb=" N GLY H 16 " --> pdb=" O SER H 85 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.735A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.826A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.677A pdb=" N SER L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.354A pdb=" N MET L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'L' and resid 45 through 49 removed outlier: 5.570A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 930 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: 0.65 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1739 1.34 - 1.46: 1347 1.46 - 1.57: 3048 1.57 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 6195 Sorted by residual: bond pdb=" CB VAL A 227 " pdb=" CG1 VAL A 227 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.49e+00 bond pdb=" CB TRP A 228 " pdb=" CG TRP A 228 " ideal model delta sigma weight residual 1.498 1.440 0.058 3.10e-02 1.04e+03 3.47e+00 bond pdb=" CB VAL A 378 " pdb=" CG1 VAL A 378 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.41e+00 bond pdb=" CB ILE A 139 " pdb=" CG2 ILE A 139 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.14e+00 bond pdb=" CG1 ILE A 479 " pdb=" CD1 ILE A 479 " ideal model delta sigma weight residual 1.513 1.446 0.067 3.90e-02 6.57e+02 2.97e+00 ... (remaining 6190 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 8060 2.13 - 4.27: 296 4.27 - 6.40: 43 6.40 - 8.53: 11 8.53 - 10.67: 10 Bond angle restraints: 8420 Sorted by residual: angle pdb=" C SER L 51 " pdb=" N THR L 52 " pdb=" CA THR L 52 " ideal model delta sigma weight residual 121.54 131.81 -10.27 1.91e+00 2.74e-01 2.89e+01 angle pdb=" C ALA A 303 " pdb=" N ILE A 304 " pdb=" CA ILE A 304 " ideal model delta sigma weight residual 122.88 115.74 7.14 1.76e+00 3.23e-01 1.65e+01 angle pdb=" C GLU A 107 " pdb=" N GLY A 108 " pdb=" CA GLY A 108 " ideal model delta sigma weight residual 122.73 118.98 3.75 9.30e-01 1.16e+00 1.62e+01 angle pdb=" CB ILE A 304 " pdb=" CG1 ILE A 304 " pdb=" CD1 ILE A 304 " ideal model delta sigma weight residual 113.80 106.04 7.76 2.10e+00 2.27e-01 1.37e+01 angle pdb=" C ALA A 189 " pdb=" N ASN A 190 " pdb=" CA ASN A 190 " ideal model delta sigma weight residual 121.54 128.50 -6.96 1.91e+00 2.74e-01 1.33e+01 ... (remaining 8415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 3191 17.85 - 35.71: 294 35.71 - 53.56: 54 53.56 - 71.41: 10 71.41 - 89.26: 5 Dihedral angle restraints: 3554 sinusoidal: 1362 harmonic: 2192 Sorted by residual: dihedral pdb=" CA ALA A 303 " pdb=" C ALA A 303 " pdb=" N ILE A 304 " pdb=" CA ILE A 304 " ideal model delta harmonic sigma weight residual -180.00 -150.42 -29.58 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA ARG A 428 " pdb=" C ARG A 428 " pdb=" N GLU A 429 " pdb=" CA GLU A 429 " ideal model delta harmonic sigma weight residual 180.00 153.29 26.71 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA TYR L 95 " pdb=" C TYR L 95 " pdb=" N PRO L 96 " pdb=" CA PRO L 96 " ideal model delta harmonic sigma weight residual 180.00 154.14 25.86 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 3551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 851 0.104 - 0.209: 64 0.209 - 0.313: 4 0.313 - 0.418: 0 0.418 - 0.522: 1 Chirality restraints: 920 Sorted by residual: chirality pdb=" CB VAL A 447 " pdb=" CA VAL A 447 " pdb=" CG1 VAL A 447 " pdb=" CG2 VAL A 447 " both_signs ideal model delta sigma weight residual False -2.63 -2.11 -0.52 2.00e-01 2.50e+01 6.81e+00 chirality pdb=" CB THR A 249 " pdb=" CA THR A 249 " pdb=" OG1 THR A 249 " pdb=" CG2 THR A 249 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB VAL A 357 " pdb=" CA VAL A 357 " pdb=" CG1 VAL A 357 " pdb=" CG2 VAL A 357 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 917 not shown) Planarity restraints: 1037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 92 " 0.025 2.00e-02 2.50e+03 2.72e-02 1.30e+01 pdb=" CG PHE L 92 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE L 92 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE L 92 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE L 92 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE L 92 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE L 92 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 129 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C VAL A 129 " 0.056 2.00e-02 2.50e+03 pdb=" O VAL A 129 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE A 130 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 168 " -0.047 5.00e-02 4.00e+02 7.25e-02 8.42e+00 pdb=" N PRO A 169 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 169 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 169 " -0.039 5.00e-02 4.00e+02 ... (remaining 1034 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1504 2.79 - 3.31: 5588 3.31 - 3.84: 10857 3.84 - 4.37: 13203 4.37 - 4.90: 22377 Nonbonded interactions: 53529 Sorted by model distance: nonbonded pdb=" O ILE A 101 " pdb=" OG1 THR A 105 " model vdw 2.256 3.040 nonbonded pdb=" O SER A 464 " pdb=" OG SER A 464 " model vdw 2.272 3.040 nonbonded pdb=" O TYR A 148 " pdb=" OG SER A 152 " model vdw 2.286 3.040 nonbonded pdb=" OD1 ASP A 494 " pdb=" OH TYR H 59 " model vdw 2.293 3.040 nonbonded pdb=" O VAL A 485 " pdb=" OG SER A 489 " model vdw 2.312 3.040 ... (remaining 53524 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.080 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 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 : 0.009 0.348 6198 Z= 0.387 Angle : 1.007 13.772 8426 Z= 0.540 Chirality : 0.059 0.522 920 Planarity : 0.008 0.073 1037 Dihedral : 14.304 89.263 2159 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.15 % Allowed : 0.62 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.32 (0.27), residues: 756 helix: -1.29 (0.23), residues: 375 sheet: -1.48 (0.48), residues: 111 loop : -1.63 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 56 TYR 0.029 0.002 TYR A 137 PHE 0.062 0.003 PHE L 92 TRP 0.016 0.002 TRP A 218 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00766 / 0.32 ( 6195) covalent geometry : angle 0.99446 / 0.54 ( 8420) SS BOND : bond 0.20106 / 13.40 ( 3) SS BOND : angle 6.08944 / 4.30 ( 6) hydrogen bonds : bond 0.14365 / 9.36 ( 326) hydrogen bonds : angle 7.95679 / 5.45 ( 930) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.155 Fit side-chains REVERT: A 96 PHE cc_start: 0.7973 (t80) cc_final: 0.7771 (t80) REVERT: A 191 PHE cc_start: 0.8247 (m-80) cc_final: 0.7911 (m-80) REVERT: A 256 MET cc_start: 0.8790 (tpt) cc_final: 0.8447 (tpt) REVERT: A 408 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6704 (mt-10) REVERT: L 90 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8080 (tm-30) outliers start: 1 outliers final: 0 residues processed: 91 average time/residue: 0.0607 time to fit residues: 7.4616 Evaluate side-chains 81 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 chunk 27 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.152883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.122087 restraints weight = 6822.630| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.08 r_work: 0.3304 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6198 Z= 0.168 Angle : 0.607 8.873 8426 Z= 0.321 Chirality : 0.042 0.155 920 Planarity : 0.006 0.055 1037 Dihedral : 5.625 48.207 840 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.93 % Allowed : 5.40 % Favored : 93.67 % 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: -1.23 (0.29), residues: 756 helix: -0.18 (0.25), residues: 381 sheet: -1.45 (0.47), residues: 115 loop : -1.24 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 56 TYR 0.022 0.001 TYR A 137 PHE 0.016 0.002 PHE L 92 TRP 0.018 0.001 TRP A 470 HIS 0.002 0.001 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 6195) covalent geometry : angle 0.60627 / 0.32 ( 8420) SS BOND : bond 0.00911 / 0.61 ( 3) SS BOND : angle 1.21591 / 0.86 ( 6) hydrogen bonds : bond 0.04029 / 2.66 ( 326) hydrogen bonds : angle 5.52417 / 3.83 ( 930) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.156 Fit side-chains REVERT: A 191 PHE cc_start: 0.8244 (m-80) cc_final: 0.7964 (m-80) REVERT: A 256 MET cc_start: 0.8798 (tpt) cc_final: 0.8299 (tpt) REVERT: A 408 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7289 (mt-10) REVERT: L 90 GLN cc_start: 0.8970 (tm-30) cc_final: 0.8248 (tt0) outliers start: 6 outliers final: 4 residues processed: 98 average time/residue: 0.0613 time to fit residues: 7.9148 Evaluate side-chains 90 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 23 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 0.0670 chunk 4 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 ASN ** 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 = 0.3779 r_free = 0.3779 target = 0.155097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.124337 restraints weight = 6693.056| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.07 r_work: 0.3165 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6198 Z= 0.172 Angle : 0.595 9.997 8426 Z= 0.311 Chirality : 0.043 0.163 920 Planarity : 0.005 0.048 1037 Dihedral : 5.480 50.170 840 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.70 % Allowed : 8.18 % Favored : 90.12 % 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: -0.75 (0.31), residues: 756 helix: 0.28 (0.26), residues: 375 sheet: -1.29 (0.48), residues: 115 loop : -1.08 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 428 TYR 0.018 0.001 TYR A 137 PHE 0.018 0.002 PHE L 92 TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 6195) covalent geometry : angle 0.59413 / 0.31 ( 8420) SS BOND : bond 0.00320 / 0.22 ( 3) SS BOND : angle 1.42254 / 0.75 ( 6) hydrogen bonds : bond 0.03834 / 2.53 ( 326) hydrogen bonds : angle 5.22940 / 3.64 ( 930) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 98 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7561 (mt-10) REVERT: A 172 MET cc_start: 0.7638 (ttp) cc_final: 0.7345 (ttm) REVERT: A 191 PHE cc_start: 0.8218 (m-80) cc_final: 0.7937 (m-80) REVERT: A 256 MET cc_start: 0.8777 (tpt) cc_final: 0.8252 (tpt) REVERT: A 304 ILE cc_start: 0.7346 (OUTLIER) cc_final: 0.6727 (tp) REVERT: A 408 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7291 (mt-10) REVERT: H 40 SER cc_start: 0.8095 (t) cc_final: 0.7859 (p) REVERT: L 90 GLN cc_start: 0.8973 (tm-30) cc_final: 0.8288 (tt0) outliers start: 11 outliers final: 7 residues processed: 97 average time/residue: 0.0662 time to fit residues: 8.4273 Evaluate side-chains 94 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.5980 chunk 61 optimal weight: 0.0470 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 53 optimal weight: 0.0010 chunk 29 optimal weight: 0.5980 chunk 49 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 overall best weight: 0.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 ASN ** 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 = 0.3779 r_free = 0.3779 target = 0.155637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.125080 restraints weight = 6729.429| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.08 r_work: 0.3191 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6198 Z= 0.132 Angle : 0.552 8.802 8426 Z= 0.289 Chirality : 0.041 0.137 920 Planarity : 0.005 0.046 1037 Dihedral : 5.308 54.119 840 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.85 % Allowed : 10.19 % Favored : 87.96 % 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: -0.44 (0.31), residues: 756 helix: 0.56 (0.26), residues: 379 sheet: -1.11 (0.47), residues: 118 loop : -1.00 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 428 TYR 0.017 0.001 TYR A 137 PHE 0.012 0.001 PHE A 392 TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 6195) covalent geometry : angle 0.55188 / 0.29 ( 8420) SS BOND : bond 0.00271 / 0.18 ( 3) SS BOND : angle 1.08078 / 0.64 ( 6) hydrogen bonds : bond 0.03539 / 2.33 ( 326) hydrogen bonds : angle 4.92984 / 3.44 ( 930) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 172 MET cc_start: 0.7458 (ttp) cc_final: 0.7056 (ttm) REVERT: A 191 PHE cc_start: 0.8272 (m-80) cc_final: 0.7842 (m-80) REVERT: A 256 MET cc_start: 0.8762 (tpt) cc_final: 0.8287 (tpt) REVERT: A 327 MET cc_start: 0.8714 (mmm) cc_final: 0.8387 (mmp) REVERT: A 486 ASN cc_start: 0.7964 (m-40) cc_final: 0.7619 (m110) REVERT: H 40 SER cc_start: 0.8051 (t) cc_final: 0.7836 (p) REVERT: H 60 TYR cc_start: 0.8857 (m-80) cc_final: 0.8648 (m-80) REVERT: L 90 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8293 (tt0) outliers start: 12 outliers final: 6 residues processed: 100 average time/residue: 0.0572 time to fit residues: 7.7680 Evaluate side-chains 96 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 528 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 71 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 43 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 ASN ** 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 = 0.3753 r_free = 0.3753 target = 0.153290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122412 restraints weight = 6865.418| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.08 r_work: 0.3209 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6198 Z= 0.199 Angle : 0.599 9.142 8426 Z= 0.315 Chirality : 0.043 0.166 920 Planarity : 0.005 0.049 1037 Dihedral : 5.434 55.623 840 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.93 % Allowed : 10.96 % Favored : 86.11 % 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: -0.47 (0.31), residues: 756 helix: 0.51 (0.26), residues: 380 sheet: -1.03 (0.48), residues: 115 loop : -1.02 (0.41), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 428 TYR 0.019 0.002 TYR A 137 PHE 0.018 0.002 PHE L 92 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 ( 6195) covalent geometry : angle 0.59834 / 0.31 ( 8420) SS BOND : bond 0.00337 / 0.23 ( 3) SS BOND : angle 1.33441 / 0.72 ( 6) hydrogen bonds : bond 0.03864 / 2.54 ( 326) hydrogen bonds : angle 5.06476 / 3.54 ( 930) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 172 MET cc_start: 0.7588 (ttp) cc_final: 0.7261 (ttm) REVERT: A 191 PHE cc_start: 0.8386 (m-80) cc_final: 0.8002 (m-80) REVERT: A 192 THR cc_start: 0.8805 (t) cc_final: 0.8593 (t) REVERT: A 212 ASN cc_start: 0.8220 (t0) cc_final: 0.7991 (t0) REVERT: A 256 MET cc_start: 0.8829 (tpt) cc_final: 0.8326 (tpt) REVERT: A 304 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.7300 (tp) REVERT: H 40 SER cc_start: 0.8087 (t) cc_final: 0.7878 (p) REVERT: H 78 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7765 (tt) outliers start: 19 outliers final: 12 residues processed: 104 average time/residue: 0.0608 time to fit residues: 8.4456 Evaluate side-chains 105 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 49 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 28 optimal weight: 0.5980 chunk 65 optimal weight: 0.1980 chunk 2 optimal weight: 0.0970 chunk 62 optimal weight: 0.9980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.158383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.127764 restraints weight = 6776.231| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.10 r_work: 0.3291 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6198 Z= 0.129 Angle : 0.553 9.829 8426 Z= 0.285 Chirality : 0.040 0.137 920 Planarity : 0.005 0.044 1037 Dihedral : 5.283 57.754 840 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.62 % Allowed : 11.73 % Favored : 85.65 % 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: -0.20 (0.31), residues: 756 helix: 0.75 (0.27), residues: 379 sheet: -1.00 (0.48), residues: 118 loop : -0.88 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 178 TYR 0.017 0.001 TYR A 137 PHE 0.012 0.001 PHE A 392 TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 6195) covalent geometry : angle 0.55215 / 0.29 ( 8420) SS BOND : bond 0.00180 / 0.11 ( 3) SS BOND : angle 0.98697 / 0.55 ( 6) hydrogen bonds : bond 0.03478 / 2.28 ( 326) hydrogen bonds : angle 4.80398 / 3.36 ( 930) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.191 Fit side-chains REVERT: A 172 MET cc_start: 0.7442 (ttp) cc_final: 0.7035 (ttm) REVERT: A 191 PHE cc_start: 0.8391 (m-80) cc_final: 0.8001 (m-80) REVERT: A 256 MET cc_start: 0.8804 (tpt) cc_final: 0.8360 (tpt) REVERT: A 327 MET cc_start: 0.8872 (mmm) cc_final: 0.8601 (mmp) REVERT: A 427 ARG cc_start: 0.6485 (mmm160) cc_final: 0.5727 (mmm160) REVERT: A 486 ASN cc_start: 0.7932 (m-40) cc_final: 0.7549 (m110) REVERT: A 495 MET cc_start: 0.8978 (ptt) cc_final: 0.8597 (ptt) REVERT: H 78 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7752 (tt) REVERT: L 90 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8528 (tm-30) outliers start: 17 outliers final: 11 residues processed: 105 average time/residue: 0.0590 time to fit residues: 8.3471 Evaluate side-chains 105 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain H residue 78 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 28 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 3 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 ASN ** 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 = 0.3772 r_free = 0.3772 target = 0.155137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124366 restraints weight = 6770.308| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.08 r_work: 0.3249 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6198 Z= 0.177 Angle : 0.592 10.756 8426 Z= 0.306 Chirality : 0.042 0.151 920 Planarity : 0.005 0.048 1037 Dihedral : 5.382 57.902 840 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.78 % Allowed : 12.19 % Favored : 85.03 % 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: -0.25 (0.32), residues: 756 helix: 0.69 (0.27), residues: 380 sheet: -0.86 (0.49), residues: 115 loop : -0.97 (0.42), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 428 TYR 0.017 0.001 TYR A 137 PHE 0.015 0.002 PHE A 392 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 6195) covalent geometry : angle 0.59109 / 0.31 ( 8420) SS BOND : bond 0.00212 / 0.15 ( 3) SS BOND : angle 1.14847 / 0.67 ( 6) hydrogen bonds : bond 0.03728 / 2.45 ( 326) hydrogen bonds : angle 4.92474 / 3.45 ( 930) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.178 Fit side-chains REVERT: A 69 TYR cc_start: 0.8919 (OUTLIER) cc_final: 0.8461 (p90) REVERT: A 191 PHE cc_start: 0.8429 (m-80) cc_final: 0.8088 (m-80) REVERT: A 256 MET cc_start: 0.8822 (tpt) cc_final: 0.8389 (tpt) REVERT: H 78 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7797 (tt) REVERT: L 90 GLN cc_start: 0.8962 (tm-30) cc_final: 0.8586 (tm-30) outliers start: 18 outliers final: 14 residues processed: 103 average time/residue: 0.0717 time to fit residues: 9.8123 Evaluate side-chains 107 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 236 TRP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 0.2980 chunk 54 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 167 ASN ** 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 = 0.3725 r_free = 0.3725 target = 0.151311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.120009 restraints weight = 6794.068| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.09 r_work: 0.3159 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6198 Z= 0.203 Angle : 0.615 11.101 8426 Z= 0.318 Chirality : 0.043 0.166 920 Planarity : 0.005 0.044 1037 Dihedral : 5.531 59.691 840 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.24 % Allowed : 13.27 % Favored : 83.49 % 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: -0.32 (0.31), residues: 756 helix: 0.59 (0.26), residues: 380 sheet: -0.84 (0.50), residues: 115 loop : -0.96 (0.42), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 428 TYR 0.017 0.002 TYR A 137 PHE 0.017 0.002 PHE A 392 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 ( 6195) covalent geometry : angle 0.61394 / 0.32 ( 8420) SS BOND : bond 0.00242 / 0.17 ( 3) SS BOND : angle 1.29885 / 0.69 ( 6) hydrogen bonds : bond 0.03841 / 2.52 ( 326) hydrogen bonds : angle 5.03240 / 3.52 ( 930) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.215 Fit side-chains REVERT: A 69 TYR cc_start: 0.8953 (OUTLIER) cc_final: 0.8224 (p90) REVERT: A 256 MET cc_start: 0.8834 (tpt) cc_final: 0.8346 (tpt) REVERT: A 486 ASN cc_start: 0.8073 (m-40) cc_final: 0.7787 (m-40) REVERT: A 495 MET cc_start: 0.9027 (ptt) cc_final: 0.8592 (ptt) REVERT: H 78 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7786 (tt) REVERT: L 90 GLN cc_start: 0.9009 (tm-30) cc_final: 0.8545 (tt0) outliers start: 21 outliers final: 16 residues processed: 103 average time/residue: 0.0556 time to fit residues: 7.8637 Evaluate side-chains 109 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 236 TRP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.0095 > 50: distance: 57 - 64: 4.300 distance: 64 - 65: 21.621 distance: 65 - 66: 51.705 distance: 65 - 68: 31.372 distance: 66 - 67: 22.072 distance: 66 - 75: 43.116 distance: 68 - 69: 26.866 distance: 69 - 70: 19.790 distance: 70 - 71: 16.166 distance: 71 - 72: 17.889 distance: 72 - 73: 14.808 distance: 72 - 74: 22.740 distance: 75 - 76: 26.417 distance: 76 - 77: 10.700 distance: 76 - 79: 10.969 distance: 77 - 78: 21.681 distance: 77 - 83: 5.539 distance: 79 - 80: 3.521 distance: 80 - 81: 11.075 distance: 80 - 82: 24.098 distance: 83 - 84: 7.890 distance: 84 - 85: 15.948 distance: 84 - 87: 14.117 distance: 85 - 86: 34.598 distance: 85 - 92: 30.063 distance: 87 - 88: 3.076 distance: 88 - 89: 21.560 distance: 89 - 90: 12.305 distance: 89 - 91: 10.998 distance: 92 - 93: 13.252 distance: 93 - 94: 15.547 distance: 93 - 96: 7.873 distance: 94 - 95: 11.154 distance: 96 - 97: 17.292 distance: 98 - 99: 41.669 distance: 99 - 100: 39.259 distance: 99 - 102: 23.118 distance: 100 - 101: 14.863 distance: 100 - 103: 18.346 distance: 103 - 104: 19.227 distance: 104 - 105: 22.861 distance: 104 - 107: 21.662 distance: 105 - 106: 24.738 distance: 105 - 111: 15.385 distance: 107 - 108: 44.580 distance: 108 - 109: 6.840 distance: 108 - 110: 9.549 distance: 111 - 112: 22.954 distance: 112 - 113: 14.178 distance: 112 - 115: 38.870 distance: 113 - 114: 26.552 distance: 113 - 122: 18.854 distance: 115 - 116: 15.954 distance: 116 - 117: 36.956 distance: 116 - 118: 34.622 distance: 119 - 121: 32.292 distance: 120 - 121: 39.533 distance: 122 - 123: 28.929 distance: 123 - 124: 21.816 distance: 123 - 126: 21.166 distance: 124 - 125: 20.271 distance: 124 - 129: 11.214 distance: 126 - 127: 22.737 distance: 126 - 128: 9.018 distance: 129 - 130: 9.696 distance: 130 - 131: 18.602 distance: 130 - 133: 3.237 distance: 131 - 132: 39.852 distance: 131 - 135: 22.411 distance: 132 - 157: 32.135 distance: 133 - 134: 32.657 distance: 135 - 136: 22.818 distance: 135 - 141: 22.172 distance: 136 - 137: 21.049 distance: 136 - 139: 14.349 distance: 137 - 138: 18.709 distance: 137 - 142: 14.242 distance: 138 - 166: 30.474 distance: 139 - 140: 10.788 distance: 140 - 141: 12.281