Starting phenix.real_space_refine on Thu Jul 2 02:50:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8snd_40623/07_2026/8snd_40623.cif Found real_map, /net/cci-nas-00/data/ceres_data/8snd_40623/07_2026/8snd_40623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8snd_40623/07_2026/8snd_40623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8snd_40623/07_2026/8snd_40623.map" model { file = "/net/cci-nas-00/data/ceres_data/8snd_40623/07_2026/8snd_40623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8snd_40623/07_2026/8snd_40623.cif" } resolution = 3.1 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= -0.002 sd= 0.119 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 Mn 2 7.51 5 P 3 5.49 5 S 35 5.16 5 C 3928 2.51 5 N 992 2.21 5 O 1130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 6090 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4077 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 13, 'TRANS': 486} Chain breaks: 1 Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 950 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "C" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 925 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain breaks: 1 Chain: "A" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 136 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'3PE': 1, 'NAG': 1, 'UGA': 1, 'Y01': 1} Classifications: {'undetermined': 4, 'water': 8} Link IDs: {None: 10} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Time building chain proxies: 1.40, per 1000 atoms: 0.23 Number of scatterers: 6090 At special positions: 0 Unit cell: (74.52, 75.6, 152.28, 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) Mn 2 24.99 S 35 16.00 P 3 15.00 O 1130 8.00 N 992 7.00 C 3928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " 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: 0.50 Conformation dependent library (CDL) restraints added in 336.5 milliseconds 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1376 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 6 sheets defined 45.6% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 38 through 74 removed outlier: 4.188A pdb=" N PHE A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 Processing helix chain 'A' and resid 125 through 138 removed outlier: 3.979A pdb=" N LYS A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 176 through 191 removed outlier: 3.801A pdb=" N SER A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 220 Processing helix chain 'A' and resid 238 through 254 removed outlier: 3.534A pdb=" N TRP A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 262 removed outlier: 3.558A pdb=" N ALA A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TRP A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 285 through 288 removed outlier: 3.992A pdb=" N ILE A 288 " --> pdb=" O ASP A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 285 through 288' Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 331 through 355 removed outlier: 3.648A pdb=" N SER A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 391 removed outlier: 4.152A pdb=" N PHE A 378 " --> pdb=" O GLN A 374 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 420 Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.679A pdb=" N ALA A 424 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 removed outlier: 3.930A pdb=" N VAL A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 448 Processing helix chain 'A' and resid 468 through 497 removed outlier: 5.199A pdb=" N GLN A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 476 " --> pdb=" O TRP A 472 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE A 478 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N THR A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 534 Processing helix chain 'A' and resid 539 through 552 Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.693A pdb=" N THR B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.925A pdb=" N THR C 90 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 143 removed outlier: 8.679A pdb=" N ILE A 168 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU A 116 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE A 170 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N CYS A 118 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N GLN A 172 " --> pdb=" O CYS A 118 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE A 120 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL A 84 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ILE A 117 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL A 86 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL A 119 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE A 88 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ASP A 121 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N GLY A 90 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 89 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A 273 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LEU A 272 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 229 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LYS A 225 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 12.549A pdb=" N ILE A 224 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 16.448A pdb=" N ALA A 226 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 12.541A pdb=" N ALA A 322 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ALA A 228 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N GLY A 324 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLU A 230 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N SER A 326 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LYS A 232 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 501 removed outlier: 5.961A pdb=" N PHE A 500 " --> pdb=" O GLY B 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 8 Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 13 removed outlier: 3.621A pdb=" N VAL B 12 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 123 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.814A pdb=" N THR C 68 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 46 through 52 removed outlier: 6.797A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR C 115 " --> pdb=" O LEU C 97 " (cutoff:3.500A) 303 hydrogen bonds defined for protein. 846 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: 1.01 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 943 1.31 - 1.44: 1867 1.44 - 1.56: 3363 1.56 - 1.69: 8 1.69 - 1.81: 53 Bond restraints: 6234 Sorted by residual: bond pdb=" C3D UGA A 603 " pdb=" C4D UGA A 603 " ideal model delta sigma weight residual 1.525 1.266 0.259 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C1D UGA A 603 " pdb=" C2D UGA A 603 " ideal model delta sigma weight residual 1.528 1.276 0.252 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C1D UGA A 603 " pdb=" O4D UGA A 603 " ideal model delta sigma weight residual 1.393 1.553 -0.160 2.00e-02 2.50e+03 6.41e+01 bond pdb=" C2D UGA A 603 " pdb=" C3D UGA A 603 " ideal model delta sigma weight residual 1.534 1.659 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C4D UGA A 603 " pdb=" O4D UGA A 603 " ideal model delta sigma weight residual 1.432 1.555 -0.123 2.00e-02 2.50e+03 3.81e+01 ... (remaining 6229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 8430 3.23 - 6.46: 25 6.46 - 9.68: 4 9.68 - 12.91: 2 12.91 - 16.14: 2 Bond angle restraints: 8463 Sorted by residual: angle pdb=" O3A UGA A 603 " pdb=" PA UGA A 603 " pdb=" O5D UGA A 603 " ideal model delta sigma weight residual 93.30 109.44 -16.14 3.00e+00 1.11e-01 2.89e+01 angle pdb=" O3A UGA A 603 " pdb=" PB UGA A 603 " pdb=" O3B UGA A 603 " ideal model delta sigma weight residual 94.34 109.55 -15.21 3.00e+00 1.11e-01 2.57e+01 angle pdb=" O1A UGA A 603 " pdb=" PA UGA A 603 " pdb=" O2A UGA A 603 " ideal model delta sigma weight residual 120.95 109.55 11.40 3.00e+00 1.11e-01 1.44e+01 angle pdb=" O1B UGA A 603 " pdb=" PB UGA A 603 " pdb=" O2B UGA A 603 " ideal model delta sigma weight residual 120.33 109.29 11.04 3.00e+00 1.11e-01 1.35e+01 angle pdb=" N ILE A 211 " pdb=" CA ILE A 211 " pdb=" C ILE A 211 " ideal model delta sigma weight residual 111.81 108.79 3.02 8.60e-01 1.35e+00 1.24e+01 ... (remaining 8458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.74: 3317 20.74 - 41.48: 335 41.48 - 62.22: 55 62.22 - 82.96: 16 82.96 - 103.70: 6 Dihedral angle restraints: 3729 sinusoidal: 1567 harmonic: 2162 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual -86.00 -36.87 -49.13 1 1.00e+01 1.00e-02 3.32e+01 dihedral pdb=" O21 3PE A 601 " pdb=" C2 3PE A 601 " pdb=" C3 3PE A 601 " pdb=" O31 3PE A 601 " ideal model delta sinusoidal sigma weight residual 60.47 -43.23 103.70 1 3.00e+01 1.11e-03 1.32e+01 dihedral pdb=" CB GLU A 255 " pdb=" CG GLU A 255 " pdb=" CD GLU A 255 " pdb=" OE1 GLU A 255 " ideal model delta sinusoidal sigma weight residual 0.00 89.52 -89.52 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 3726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 756 0.051 - 0.102: 139 0.102 - 0.153: 25 0.153 - 0.204: 1 0.204 - 0.255: 2 Chirality restraints: 923 Sorted by residual: chirality pdb=" C3D UGA A 603 " pdb=" C2D UGA A 603 " pdb=" C4D UGA A 603 " pdb=" O3D UGA A 603 " both_signs ideal model delta sigma weight residual False -2.71 -2.46 -0.25 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" C2' UGA A 603 " pdb=" C1' UGA A 603 " pdb=" C3' UGA A 603 " pdb=" O2' UGA A 603 " both_signs ideal model delta sigma weight residual False -2.23 -2.44 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C2D UGA A 603 " pdb=" C1D UGA A 603 " pdb=" C3D UGA A 603 " pdb=" O2D UGA A 603 " both_signs ideal model delta sigma weight residual False -2.62 -2.44 -0.18 2.00e-01 2.50e+01 8.41e-01 ... (remaining 920 not shown) Planarity restraints: 1038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 270 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.93e+00 pdb=" N PRO A 271 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 40 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO B 41 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 41 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 41 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 172 " 0.019 5.00e-02 4.00e+02 2.90e-02 1.34e+00 pdb=" N PRO A 173 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 173 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 173 " 0.016 5.00e-02 4.00e+02 ... (remaining 1035 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1301 2.78 - 3.31: 5501 3.31 - 3.84: 9722 3.84 - 4.37: 11432 4.37 - 4.90: 20464 Nonbonded interactions: 48420 Sorted by model distance: nonbonded pdb=" O TRP A 234 " pdb=" OG1 THR A 539 " model vdw 2.254 3.040 nonbonded pdb=" OE2 GLU A 93 " pdb="MN MN A 605 " model vdw 2.262 3.060 nonbonded pdb=" O ALA B 24 " pdb=" ND2 ASN B 76 " model vdw 2.297 3.120 nonbonded pdb=" NE2 GLN A 338 " pdb=" O2B UGA A 603 " model vdw 2.309 3.120 nonbonded pdb=" O PHE B 29 " pdb=" NH2 ARG B 71 " model vdw 2.324 3.120 ... (remaining 48415 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: 1.370 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.420 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.259 6236 Z= 0.337 Angle : 0.595 16.141 8467 Z= 0.290 Chirality : 0.042 0.255 923 Planarity : 0.003 0.035 1038 Dihedral : 17.167 103.702 2347 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.64 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 18.51 % Favored : 81.49 % 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: 1.20 (0.31), residues: 732 helix: 1.67 (0.30), residues: 311 sheet: 1.43 (0.40), residues: 161 loop : -0.70 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 247 TYR 0.015 0.001 TYR C 106 PHE 0.013 0.001 PHE A 49 TRP 0.013 0.001 TRP A 41 HIS 0.001 0.000 HIS A 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.34 ( 6234) covalent geometry : angle 0.59491 / 0.29 ( 8463) SS BOND : bond 0.00232 / 0.11 ( 2) SS BOND : angle 0.84019 / 0.46 ( 4) hydrogen bonds : bond 0.13669 / 9.69 ( 303) hydrogen bonds : angle 5.07342 / 3.75 ( 846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.221 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0741 time to fit residues: 7.8499 Evaluate side-chains 69 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 397 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.168565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.132952 restraints weight = 6704.209| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.47 r_work: 0.3426 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6236 Z= 0.189 Angle : 0.517 5.439 8467 Z= 0.278 Chirality : 0.043 0.166 923 Planarity : 0.004 0.050 1038 Dihedral : 8.961 92.430 1019 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.60 % Favored : 97.27 % Rotamer: Outliers : 2.53 % Allowed : 16.77 % Favored : 80.70 % 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: 1.06 (0.31), residues: 732 helix: 1.58 (0.30), residues: 309 sheet: 1.09 (0.40), residues: 165 loop : -0.60 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 508 TYR 0.012 0.001 TYR A 414 PHE 0.014 0.002 PHE B 47 TRP 0.012 0.001 TRP A 472 HIS 0.002 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 ( 6234) covalent geometry : angle 0.51647 / 0.28 ( 8463) SS BOND : bond 0.00307 / 0.15 ( 2) SS BOND : angle 0.66359 / 0.36 ( 4) hydrogen bonds : bond 0.04944 / 3.42 ( 303) hydrogen bonds : angle 4.10703 / 2.90 ( 846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.231 Fit side-chains REVERT: A 124 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6815 (mm-30) REVERT: A 438 MET cc_start: 0.7580 (mtp) cc_final: 0.7316 (mtp) outliers start: 16 outliers final: 12 residues processed: 91 average time/residue: 0.0709 time to fit residues: 8.9666 Evaluate side-chains 91 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 102 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 542 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.176507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.141950 restraints weight = 6789.149| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.33 r_work: 0.3550 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6236 Z= 0.114 Angle : 0.436 5.034 8467 Z= 0.238 Chirality : 0.040 0.157 923 Planarity : 0.003 0.051 1038 Dihedral : 8.304 86.550 1019 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.46 % Favored : 97.40 % Rotamer: Outliers : 3.64 % Allowed : 17.09 % Favored : 79.27 % 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 (0.31), residues: 732 helix: 1.92 (0.30), residues: 305 sheet: 1.06 (0.40), residues: 165 loop : -0.66 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 71 TYR 0.007 0.001 TYR A 91 PHE 0.012 0.001 PHE B 47 TRP 0.008 0.001 TRP A 472 HIS 0.002 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 6234) covalent geometry : angle 0.43568 / 0.24 ( 8463) SS BOND : bond 0.00281 / 0.13 ( 2) SS BOND : angle 0.53693 / 0.29 ( 4) hydrogen bonds : bond 0.03926 / 2.70 ( 303) hydrogen bonds : angle 3.85562 / 2.71 ( 846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.230 Fit side-chains REVERT: A 358 TRP cc_start: 0.7900 (p-90) cc_final: 0.7682 (p-90) outliers start: 23 outliers final: 16 residues processed: 102 average time/residue: 0.0681 time to fit residues: 9.5580 Evaluate side-chains 95 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 102 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 56 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.176312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.142748 restraints weight = 6790.077| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.29 r_work: 0.3566 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6236 Z= 0.099 Angle : 0.416 5.057 8467 Z= 0.228 Chirality : 0.040 0.157 923 Planarity : 0.003 0.052 1038 Dihedral : 8.181 83.409 1019 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.46 % Favored : 97.40 % Rotamer: Outliers : 3.80 % Allowed : 17.25 % Favored : 78.96 % 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: 1.28 (0.31), residues: 732 helix: 2.01 (0.30), residues: 307 sheet: 1.12 (0.40), residues: 165 loop : -0.75 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 348 TYR 0.015 0.001 TYR C 106 PHE 0.010 0.001 PHE A 49 TRP 0.007 0.001 TRP A 472 HIS 0.001 0.000 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 6234) covalent geometry : angle 0.41619 / 0.23 ( 8463) SS BOND : bond 0.00305 / 0.15 ( 2) SS BOND : angle 0.36468 / 0.20 ( 4) hydrogen bonds : bond 0.03555 / 2.44 ( 303) hydrogen bonds : angle 3.73410 / 2.61 ( 846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.167 Fit side-chains REVERT: A 62 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7069 (tt0) REVERT: A 239 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.8038 (tt) outliers start: 24 outliers final: 20 residues processed: 99 average time/residue: 0.0710 time to fit residues: 9.5687 Evaluate side-chains 100 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 17 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.176417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.141581 restraints weight = 6957.694| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.37 r_work: 0.3539 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6236 Z= 0.118 Angle : 0.435 5.127 8467 Z= 0.236 Chirality : 0.040 0.159 923 Planarity : 0.003 0.053 1038 Dihedral : 8.218 84.241 1019 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.60 % Favored : 97.27 % Rotamer: Outliers : 4.27 % Allowed : 17.56 % Favored : 78.16 % 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: 1.26 (0.32), residues: 732 helix: 1.97 (0.30), residues: 307 sheet: 1.15 (0.41), residues: 165 loop : -0.76 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 348 TYR 0.014 0.001 TYR C 106 PHE 0.010 0.001 PHE A 49 TRP 0.008 0.001 TRP A 472 HIS 0.001 0.000 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 6234) covalent geometry : angle 0.43460 / 0.24 ( 8463) SS BOND : bond 0.00309 / 0.15 ( 2) SS BOND : angle 0.25216 / 0.14 ( 4) hydrogen bonds : bond 0.03687 / 2.53 ( 303) hydrogen bonds : angle 3.73059 / 2.61 ( 846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.228 Fit side-chains outliers start: 27 outliers final: 23 residues processed: 103 average time/residue: 0.0530 time to fit residues: 7.6174 Evaluate side-chains 100 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 102 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 46 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 63 optimal weight: 0.0010 chunk 71 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.177694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.143656 restraints weight = 6769.627| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.31 r_work: 0.3561 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6236 Z= 0.097 Angle : 0.417 5.091 8467 Z= 0.227 Chirality : 0.040 0.155 923 Planarity : 0.003 0.053 1038 Dihedral : 8.064 85.437 1019 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.19 % Favored : 97.68 % Rotamer: Outliers : 4.11 % Allowed : 18.04 % Favored : 77.85 % 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: 1.32 (0.31), residues: 732 helix: 2.07 (0.30), residues: 307 sheet: 1.23 (0.42), residues: 155 loop : -0.77 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 348 TYR 0.018 0.001 TYR B 105 PHE 0.010 0.001 PHE A 49 TRP 0.007 0.001 TRP A 472 HIS 0.001 0.000 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 6234) covalent geometry : angle 0.41664 / 0.23 ( 8463) SS BOND : bond 0.00427 / 0.21 ( 2) SS BOND : angle 0.61556 / 0.34 ( 4) hydrogen bonds : bond 0.03379 / 2.32 ( 303) hydrogen bonds : angle 3.66241 / 2.56 ( 846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.223 Fit side-chains REVERT: A 426 TYR cc_start: 0.8493 (m-10) cc_final: 0.7930 (m-10) outliers start: 26 outliers final: 22 residues processed: 97 average time/residue: 0.0703 time to fit residues: 9.3937 Evaluate side-chains 98 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 102 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 497 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 = 0.4077 r_free = 0.4077 target = 0.175640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.140781 restraints weight = 6876.901| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.36 r_work: 0.3524 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6236 Z= 0.121 Angle : 0.436 5.134 8467 Z= 0.238 Chirality : 0.040 0.159 923 Planarity : 0.003 0.054 1038 Dihedral : 8.048 86.094 1019 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.73 % Favored : 97.13 % Rotamer: Outliers : 4.43 % Allowed : 18.20 % Favored : 77.37 % 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: 1.26 (0.31), residues: 732 helix: 2.02 (0.30), residues: 307 sheet: 1.19 (0.42), residues: 155 loop : -0.80 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 348 TYR 0.017 0.001 TYR C 106 PHE 0.011 0.001 PHE B 47 TRP 0.009 0.001 TRP A 472 HIS 0.001 0.000 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 6234) covalent geometry : angle 0.43608 / 0.24 ( 8463) SS BOND : bond 0.00309 / 0.15 ( 2) SS BOND : angle 0.64316 / 0.35 ( 4) hydrogen bonds : bond 0.03685 / 2.53 ( 303) hydrogen bonds : angle 3.71581 / 2.60 ( 846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.230 Fit side-chains REVERT: A 62 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7120 (tt0) REVERT: A 426 TYR cc_start: 0.8546 (m-10) cc_final: 0.7946 (m-10) REVERT: C 102 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7999 (t0) outliers start: 28 outliers final: 23 residues processed: 100 average time/residue: 0.0681 time to fit residues: 9.5479 Evaluate side-chains 102 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 102 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 34 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 497 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 = 0.4076 r_free = 0.4076 target = 0.175646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.141008 restraints weight = 6832.186| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.35 r_work: 0.3526 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6236 Z= 0.121 Angle : 0.439 5.143 8467 Z= 0.240 Chirality : 0.040 0.158 923 Planarity : 0.003 0.054 1038 Dihedral : 8.013 86.459 1019 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.60 % Favored : 97.27 % Rotamer: Outliers : 3.96 % Allowed : 18.51 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.25 (0.32), residues: 732 helix: 2.00 (0.30), residues: 307 sheet: 1.12 (0.41), residues: 165 loop : -0.80 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 348 TYR 0.017 0.001 TYR C 106 PHE 0.012 0.001 PHE B 47 TRP 0.010 0.001 TRP A 472 HIS 0.001 0.000 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 6234) covalent geometry : angle 0.43850 / 0.24 ( 8463) SS BOND : bond 0.00297 / 0.14 ( 2) SS BOND : angle 0.51343 / 0.28 ( 4) hydrogen bonds : bond 0.03690 / 2.53 ( 303) hydrogen bonds : angle 3.72995 / 2.61 ( 846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.231 Fit side-chains REVERT: A 62 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7059 (tt0) REVERT: A 426 TYR cc_start: 0.8515 (m-10) cc_final: 0.7876 (m-10) REVERT: C 102 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.8025 (t0) outliers start: 25 outliers final: 24 residues processed: 97 average time/residue: 0.0733 time to fit residues: 9.9015 Evaluate side-chains 101 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 515 CYS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 102 ASP 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: 65.7016 > 50: distance: 68 - 81: 22.356 distance: 72 - 92: 31.696 distance: 77 - 81: 20.516 distance: 81 - 82: 19.297 distance: 82 - 83: 18.738 distance: 82 - 85: 9.712 distance: 83 - 84: 16.926 distance: 85 - 86: 14.061 distance: 86 - 87: 21.090 distance: 86 - 88: 12.279 distance: 87 - 89: 17.771 distance: 88 - 90: 26.660 distance: 89 - 91: 11.212 distance: 90 - 91: 15.809 distance: 92 - 93: 43.635 distance: 93 - 94: 31.764 distance: 93 - 96: 25.614 distance: 94 - 95: 13.671 distance: 94 - 99: 36.550 distance: 96 - 97: 29.231 distance: 99 - 100: 6.608 distance: 100 - 101: 43.653 distance: 100 - 103: 49.851 distance: 101 - 102: 23.519 distance: 101 - 107: 35.269 distance: 103 - 104: 14.334 distance: 104 - 106: 17.512 distance: 107 - 108: 3.080 distance: 108 - 109: 20.775 distance: 108 - 111: 15.494 distance: 109 - 110: 15.320 distance: 109 - 119: 8.408 distance: 110 - 145: 7.893 distance: 111 - 112: 17.983 distance: 112 - 113: 17.805 distance: 112 - 114: 18.192 distance: 113 - 115: 33.064 distance: 114 - 116: 29.007 distance: 115 - 117: 7.367 distance: 116 - 117: 24.011 distance: 117 - 118: 6.264 distance: 119 - 120: 16.041 distance: 120 - 123: 9.275 distance: 121 - 122: 18.209 distance: 121 - 126: 7.964 distance: 122 - 157: 23.103 distance: 123 - 124: 13.210 distance: 123 - 125: 7.060 distance: 126 - 127: 23.453 distance: 127 - 128: 11.826 distance: 127 - 130: 7.974 distance: 128 - 129: 16.266 distance: 128 - 138: 27.640 distance: 129 - 168: 11.160 distance: 130 - 131: 13.121 distance: 131 - 132: 12.262 distance: 131 - 133: 20.233 distance: 132 - 134: 24.900 distance: 133 - 135: 14.145 distance: 134 - 136: 17.757 distance: 135 - 136: 12.888 distance: 136 - 137: 11.331 distance: 139 - 140: 19.327 distance: 139 - 142: 5.425 distance: 140 - 145: 7.977 distance: 141 - 179: 34.728 distance: 142 - 143: 3.649 distance: 142 - 144: 15.031 distance: 145 - 146: 6.604 distance: 146 - 149: 16.984 distance: 147 - 157: 30.491 distance: 150 - 151: 7.193 distance: 150 - 152: 3.670 distance: 151 - 153: 17.891 distance: 152 - 154: 18.630 distance: 153 - 155: 15.597 distance: 154 - 155: 9.353 distance: 155 - 156: 23.685 distance: 157 - 158: 19.361 distance: 158 - 159: 5.993 distance: 158 - 161: 13.667 distance: 159 - 160: 29.255 distance: 159 - 168: 11.569 distance: 161 - 162: 7.986 distance: 162 - 163: 23.876 distance: 162 - 164: 37.035 distance: 163 - 165: 34.465 distance: 164 - 166: 36.122 distance: 166 - 167: 14.951 distance: 168 - 169: 12.204 distance: 169 - 170: 7.349 distance: 169 - 172: 21.280 distance: 170 - 171: 10.559 distance: 170 - 179: 10.799 distance: 172 - 173: 11.362 distance: 173 - 174: 20.631 distance: 173 - 175: 11.454 distance: 174 - 176: 25.021 distance: 175 - 177: 13.306 distance: 176 - 178: 15.259 distance: 177 - 178: 26.725