Starting phenix.real_space_refine on Sun Apr 5 00:25:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xca_66727/04_2026/9xca_66727.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xca_66727/04_2026/9xca_66727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xca_66727/04_2026/9xca_66727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xca_66727/04_2026/9xca_66727.map" model { file = "/net/cci-nas-00/data/ceres_data/9xca_66727/04_2026/9xca_66727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xca_66727/04_2026/9xca_66727.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 4192 2.51 5 N 992 2.21 5 O 1138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6360 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3111 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 15, 'TRANS': 391} Chain breaks: 1 Chain: "C" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3111 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 15, 'TRANS': 391} Chain breaks: 1 Chain: "B" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.54, per 1000 atoms: 0.24 Number of scatterers: 6360 At special positions: 0 Unit cell: (76.5, 75.65, 90.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 1138 8.00 N 992 7.00 C 4192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 269.4 milliseconds 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 0 sheets defined 86.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'B' and resid 6 through 42 removed outlier: 5.112A pdb=" N PHE B 31 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N SER B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Proline residue: B 36 - end of helix removed outlier: 3.899A pdb=" N GLU B 40 " --> pdb=" O PRO B 36 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU B 41 " --> pdb=" O SER B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 72 removed outlier: 3.873A pdb=" N PHE B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 70 " --> pdb=" O VAL B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 96 removed outlier: 3.608A pdb=" N SER B 81 " --> pdb=" O ARG B 77 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER B 82 " --> pdb=" O TRP B 78 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 84 " --> pdb=" O PHE B 80 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP B 96 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 114 Processing helix chain 'B' and resid 117 through 129 removed outlier: 3.913A pdb=" N CYS B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 142 removed outlier: 4.490A pdb=" N GLY B 135 " --> pdb=" O PRO B 131 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N THR B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 151 removed outlier: 4.443A pdb=" N ASN B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 160 removed outlier: 4.413A pdb=" N ILE B 158 " --> pdb=" O ILE B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 187 removed outlier: 4.065A pdb=" N LEU B 169 " --> pdb=" O TRP B 165 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE B 181 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 195 removed outlier: 3.774A pdb=" N VAL B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 221 removed outlier: 3.556A pdb=" N LEU B 220 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 221' Processing helix chain 'B' and resid 225 through 254 removed outlier: 5.451A pdb=" N GLN B 248 " --> pdb=" O THR B 244 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N PHE B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 289 removed outlier: 3.793A pdb=" N ILE B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 321 removed outlier: 3.843A pdb=" N MET B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 357 removed outlier: 4.039A pdb=" N ILE B 331 " --> pdb=" O PRO B 327 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 332 " --> pdb=" O LYS B 328 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY B 344 " --> pdb=" O PHE B 340 " (cutoff:3.500A) Proline residue: B 345 - end of helix removed outlier: 3.633A pdb=" N GLY B 350 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 357 " --> pdb=" O ALA B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'B' and resid 361 through 372 Processing helix chain 'B' and resid 372 through 380 removed outlier: 4.016A pdb=" N GLY B 376 " --> pdb=" O MET B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 391 removed outlier: 3.530A pdb=" N ILE B 387 " --> pdb=" O PRO B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 414 removed outlier: 3.595A pdb=" N ALA B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 34 removed outlier: 3.538A pdb=" N VAL C 12 " --> pdb=" O TYR C 8 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS C 29 " --> pdb=" O TYR C 25 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N PHE C 31 " --> pdb=" O ASN C 27 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N SER C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 42 Processing helix chain 'C' and resid 45 through 71 removed outlier: 3.701A pdb=" N LEU C 49 " --> pdb=" O ASP C 45 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE C 51 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE C 65 " --> pdb=" O ALA C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 96 removed outlier: 4.023A pdb=" N TRP C 96 " --> pdb=" O ILE C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 117 through 129 removed outlier: 3.844A pdb=" N CYS C 121 " --> pdb=" O GLY C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 142 Processing helix chain 'C' and resid 143 through 160 Proline residue: C 153 - end of helix removed outlier: 4.267A pdb=" N THR C 157 " --> pdb=" O PRO C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 183 Processing helix chain 'C' and resid 190 through 195 removed outlier: 4.449A pdb=" N VAL C 194 " --> pdb=" O GLU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 221 Processing helix chain 'C' and resid 223 through 254 removed outlier: 3.976A pdb=" N TRP C 227 " --> pdb=" O SER C 223 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLN C 248 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N PHE C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU C 254 " --> pdb=" O PHE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 290 removed outlier: 3.820A pdb=" N ILE C 278 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS C 290 " --> pdb=" O ARG C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 321 removed outlier: 3.858A pdb=" N LEU C 304 " --> pdb=" O ARG C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 356 removed outlier: 3.667A pdb=" N ILE C 331 " --> pdb=" O PRO C 327 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY C 344 " --> pdb=" O PHE C 340 " (cutoff:3.500A) Proline residue: C 345 - end of helix removed outlier: 3.591A pdb=" N ASN C 354 " --> pdb=" O GLY C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 362 removed outlier: 3.945A pdb=" N CYS C 362 " --> pdb=" O PRO C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 391 removed outlier: 3.652A pdb=" N ALA C 373 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN C 374 " --> pdb=" O GLY C 370 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL C 375 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA C 380 " --> pdb=" O GLY C 376 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY C 381 " --> pdb=" O GLY C 377 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU C 382 " --> pdb=" O PHE C 378 " (cutoff:3.500A) Proline residue: C 383 - end of helix Processing helix chain 'C' and resid 392 through 414 473 hydrogen bonds defined for protein. 1416 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: 1.13 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1863 1.34 - 1.46: 1314 1.46 - 1.57: 3290 1.57 - 1.69: 11 1.69 - 1.81: 62 Bond restraints: 6540 Sorted by residual: bond pdb=" CBT LMN B 701 " pdb=" CCM LMN B 701 " ideal model delta sigma weight residual 1.533 1.606 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" CBS LMN C 701 " pdb=" CCM LMN C 701 " ideal model delta sigma weight residual 1.529 1.600 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" CBS LMN B 701 " pdb=" CCM LMN B 701 " ideal model delta sigma weight residual 1.529 1.599 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" CBT LMN C 701 " pdb=" CCM LMN C 701 " ideal model delta sigma weight residual 1.533 1.601 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" CBI LMN C 701 " pdb=" CBK LMN C 701 " ideal model delta sigma weight residual 1.524 1.584 -0.060 2.00e-02 2.50e+03 9.12e+00 ... (remaining 6535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 8772 2.83 - 5.66: 106 5.66 - 8.50: 15 8.50 - 11.33: 6 11.33 - 14.16: 3 Bond angle restraints: 8902 Sorted by residual: angle pdb=" C4 LMN B 701 " pdb=" O4 LMN B 701 " pdb=" CCR LMN B 701 " ideal model delta sigma weight residual 120.22 106.06 14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" C4 LMN C 701 " pdb=" O4 LMN C 701 " pdb=" CCR LMN C 701 " ideal model delta sigma weight residual 120.22 106.13 14.09 3.00e+00 1.11e-01 2.21e+01 angle pdb=" CBK LMN B 701 " pdb=" CBQ LMN B 701 " pdb=" CCM LMN B 701 " ideal model delta sigma weight residual 117.54 104.83 12.71 3.00e+00 1.11e-01 1.80e+01 angle pdb=" CCQ LMN C 701 " pdb=" OCB LMN C 701 " pdb=" CCS LMN C 701 " ideal model delta sigma weight residual 119.65 109.24 10.41 3.00e+00 1.11e-01 1.21e+01 angle pdb=" CBL LMN B 701 " pdb=" CBR LMN B 701 " pdb=" CCM LMN B 701 " ideal model delta sigma weight residual 117.04 106.66 10.38 3.00e+00 1.11e-01 1.20e+01 ... (remaining 8897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.94: 3651 27.94 - 55.87: 158 55.87 - 83.81: 33 83.81 - 111.75: 17 111.75 - 139.68: 19 Dihedral angle restraints: 3878 sinusoidal: 1568 harmonic: 2310 Sorted by residual: dihedral pdb=" CCC LMN B 701 " pdb=" CCR LMN B 701 " pdb=" OBY LMN B 701 " pdb=" O4 LMN B 701 " ideal model delta sinusoidal sigma weight residual 60.74 -159.58 -139.68 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" CCC LMN B 701 " pdb=" CCR LMN B 701 " pdb=" OBY LMN B 701 " pdb=" CCV LMN B 701 " ideal model delta sinusoidal sigma weight residual -59.74 78.09 -137.83 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" CAA LMN C 701 " pdb=" CAW LMN C 701 " pdb=" CAY LMN C 701 " pdb=" CBA LMN C 701 " ideal model delta sinusoidal sigma weight residual -179.97 -42.93 -137.04 1 3.00e+01 1.11e-03 1.85e+01 ... (remaining 3875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 836 0.050 - 0.099: 171 0.099 - 0.149: 14 0.149 - 0.199: 3 0.199 - 0.248: 2 Chirality restraints: 1026 Sorted by residual: chirality pdb=" CCV LMN B 701 " pdb=" CCR LMN B 701 " pdb=" CCT LMN B 701 " pdb=" OAU LMN B 701 " both_signs ideal model delta sigma weight residual False 2.28 2.53 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CCV LMN C 701 " pdb=" CCR LMN C 701 " pdb=" CCT LMN C 701 " pdb=" OAU LMN C 701 " both_signs ideal model delta sigma weight residual False 2.28 2.52 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CCW LMN B 701 " pdb=" CCS LMN B 701 " pdb=" CCU LMN B 701 " pdb=" OAV LMN B 701 " both_signs ideal model delta sigma weight residual False 2.30 2.49 -0.19 2.00e-01 2.50e+01 8.74e-01 ... (remaining 1023 not shown) Planarity restraints: 1066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 35 " -0.032 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO B 36 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 344 " 0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO C 345 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 345 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 345 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 298 " 0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO B 299 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 299 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 299 " 0.020 5.00e-02 4.00e+02 ... (remaining 1063 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1341 2.77 - 3.31: 6261 3.31 - 3.84: 10616 3.84 - 4.37: 11242 4.37 - 4.90: 20465 Nonbonded interactions: 49925 Sorted by model distance: nonbonded pdb=" O ASN C 298 " pdb=" N ARG C 300 " model vdw 2.244 3.120 nonbonded pdb=" O LEU C 317 " pdb=" OG1 THR C 321 " model vdw 2.249 3.040 nonbonded pdb=" OD1 ASN B 27 " pdb=" OG SER B 172 " model vdw 2.267 3.040 nonbonded pdb=" O ASN C 295 " pdb=" OG1 THR C 419 " model vdw 2.280 3.040 nonbonded pdb=" O SER C 215 " pdb=" OG1 THR C 216 " model vdw 2.318 3.040 ... (remaining 49920 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: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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: 3.450 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.290 Find NCS groups from input model: 0.090 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:1.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 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 : 0.005 0.073 6540 Z= 0.239 Angle : 0.769 14.160 8902 Z= 0.328 Chirality : 0.040 0.248 1026 Planarity : 0.004 0.049 1066 Dihedral : 20.747 139.684 2410 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: 2.16 (0.31), residues: 806 helix: 2.27 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -1.76 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 319 TYR 0.013 0.001 TYR C 24 PHE 0.014 0.001 PHE C 411 TRP 0.016 0.001 TRP B 107 HIS 0.003 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 6540) covalent geometry : angle 0.76942 ( 8902) hydrogen bonds : bond 0.10325 ( 473) hydrogen bonds : angle 3.78096 ( 1416) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.225 Fit side-chains REVERT: B 126 ARG cc_start: 0.7056 (tpt-90) cc_final: 0.6738 (ttt180) REVERT: B 189 ASN cc_start: 0.6589 (t0) cc_final: 0.6249 (m110) REVERT: B 237 PHE cc_start: 0.8274 (t80) cc_final: 0.7916 (t80) REVERT: C 74 MET cc_start: 0.4837 (tpt) cc_final: 0.4509 (ptm) REVERT: C 86 LEU cc_start: 0.7294 (tp) cc_final: 0.7065 (mp) REVERT: C 219 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6961 (mt-10) REVERT: C 389 LYS cc_start: 0.7068 (ttpt) cc_final: 0.6773 (tttm) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.0910 time to fit residues: 14.9115 Evaluate side-chains 99 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.0770 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN B 91 ASN B 146 ASN B 360 ASN C 27 ASN C 91 ASN C 198 ASN C 366 HIS C 374 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.192026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.166991 restraints weight = 6710.478| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.76 r_work: 0.3765 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6540 Z= 0.132 Angle : 0.633 8.310 8902 Z= 0.300 Chirality : 0.041 0.289 1026 Planarity : 0.005 0.056 1066 Dihedral : 17.226 122.290 1118 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.08 % Favored : 93.67 % Rotamer: Outliers : 0.30 % Allowed : 9.57 % 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: 2.22 (0.30), residues: 806 helix: 2.24 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -1.59 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 418 TYR 0.020 0.001 TYR C 316 PHE 0.011 0.001 PHE C 80 TRP 0.013 0.001 TRP C 96 HIS 0.003 0.001 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6540) covalent geometry : angle 0.63290 ( 8902) hydrogen bonds : bond 0.04246 ( 473) hydrogen bonds : angle 3.39270 ( 1416) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.216 Fit side-chains REVERT: B 189 ASN cc_start: 0.7073 (t0) cc_final: 0.6832 (m110) REVERT: B 329 LEU cc_start: 0.7633 (mm) cc_final: 0.7409 (tt) REVERT: C 86 LEU cc_start: 0.7794 (tp) cc_final: 0.7452 (mp) outliers start: 2 outliers final: 2 residues processed: 111 average time/residue: 0.0803 time to fit residues: 11.8566 Evaluate side-chains 107 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.185135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.159678 restraints weight = 6578.203| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.61 r_work: 0.3700 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6540 Z= 0.147 Angle : 0.636 8.524 8902 Z= 0.307 Chirality : 0.040 0.231 1026 Planarity : 0.005 0.055 1066 Dihedral : 14.105 115.702 1118 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.96 % Favored : 93.80 % Rotamer: Outliers : 0.91 % Allowed : 12.46 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.06 (0.30), residues: 806 helix: 2.14 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -1.77 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 300 TYR 0.019 0.002 TYR C 24 PHE 0.014 0.002 PHE C 94 TRP 0.016 0.002 TRP C 96 HIS 0.004 0.001 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 6540) covalent geometry : angle 0.63568 ( 8902) hydrogen bonds : bond 0.04498 ( 473) hydrogen bonds : angle 3.46232 ( 1416) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.228 Fit side-chains REVERT: B 189 ASN cc_start: 0.7058 (t0) cc_final: 0.6826 (m110) REVERT: B 329 LEU cc_start: 0.7889 (mm) cc_final: 0.7636 (tt) REVERT: B 418 ARG cc_start: 0.6522 (ttp-110) cc_final: 0.6259 (ttp-110) REVERT: C 86 LEU cc_start: 0.7763 (tp) cc_final: 0.7423 (mp) outliers start: 6 outliers final: 2 residues processed: 112 average time/residue: 0.0831 time to fit residues: 12.2809 Evaluate side-chains 104 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 45 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN C 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.182861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.157440 restraints weight = 6576.556| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.60 r_work: 0.3674 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6540 Z= 0.151 Angle : 0.633 8.902 8902 Z= 0.307 Chirality : 0.041 0.309 1026 Planarity : 0.005 0.050 1066 Dihedral : 12.846 107.853 1118 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.71 % Favored : 94.04 % Rotamer: Outliers : 1.22 % Allowed : 13.22 % Favored : 85.56 % 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: 2.01 (0.30), residues: 806 helix: 2.11 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -1.80 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 300 TYR 0.020 0.001 TYR C 24 PHE 0.020 0.002 PHE B 340 TRP 0.016 0.002 TRP C 96 HIS 0.004 0.001 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6540) covalent geometry : angle 0.63329 ( 8902) hydrogen bonds : bond 0.04517 ( 473) hydrogen bonds : angle 3.50070 ( 1416) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.225 Fit side-chains REVERT: B 189 ASN cc_start: 0.7151 (t0) cc_final: 0.6927 (m110) REVERT: B 253 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7947 (mp10) REVERT: B 329 LEU cc_start: 0.7929 (mm) cc_final: 0.7690 (tt) REVERT: B 418 ARG cc_start: 0.6712 (ttp-110) cc_final: 0.6494 (ttp-110) REVERT: C 86 LEU cc_start: 0.7788 (tp) cc_final: 0.7452 (mp) outliers start: 8 outliers final: 5 residues processed: 107 average time/residue: 0.0871 time to fit residues: 12.2800 Evaluate side-chains 105 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 284 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.182208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.156663 restraints weight = 6699.174| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.62 r_work: 0.3676 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6540 Z= 0.141 Angle : 0.615 8.474 8902 Z= 0.300 Chirality : 0.040 0.313 1026 Planarity : 0.005 0.049 1066 Dihedral : 11.748 91.440 1118 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.46 % Favored : 94.29 % Rotamer: Outliers : 1.82 % Allowed : 14.13 % Favored : 84.04 % 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: 2.00 (0.30), residues: 806 helix: 2.12 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -1.88 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.018 0.001 TYR C 24 PHE 0.014 0.001 PHE B 412 TRP 0.015 0.002 TRP C 96 HIS 0.004 0.001 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6540) covalent geometry : angle 0.61495 ( 8902) hydrogen bonds : bond 0.04350 ( 473) hydrogen bonds : angle 3.47868 ( 1416) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.195 Fit side-chains REVERT: B 253 GLN cc_start: 0.8220 (mm-40) cc_final: 0.8003 (mp10) REVERT: B 329 LEU cc_start: 0.7948 (mm) cc_final: 0.7725 (tt) REVERT: C 86 LEU cc_start: 0.7752 (tp) cc_final: 0.7411 (mp) REVERT: C 107 TRP cc_start: 0.7290 (OUTLIER) cc_final: 0.5438 (t-100) outliers start: 12 outliers final: 8 residues processed: 113 average time/residue: 0.0859 time to fit residues: 12.6367 Evaluate side-chains 108 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 107 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 284 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 48 optimal weight: 0.0980 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.182381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.156930 restraints weight = 6672.521| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.61 r_work: 0.3683 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6540 Z= 0.136 Angle : 0.616 8.576 8902 Z= 0.299 Chirality : 0.041 0.357 1026 Planarity : 0.005 0.049 1066 Dihedral : 10.785 87.203 1118 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.46 % Favored : 94.29 % Rotamer: Outliers : 2.13 % Allowed : 14.44 % Favored : 83.43 % 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: 2.05 (0.30), residues: 806 helix: 2.16 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -1.88 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 418 TYR 0.018 0.001 TYR C 24 PHE 0.012 0.001 PHE B 412 TRP 0.014 0.002 TRP C 96 HIS 0.003 0.001 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6540) covalent geometry : angle 0.61648 ( 8902) hydrogen bonds : bond 0.04224 ( 473) hydrogen bonds : angle 3.45654 ( 1416) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.141 Fit side-chains REVERT: B 253 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7976 (mp10) REVERT: B 421 MET cc_start: 0.7379 (mtt) cc_final: 0.7161 (mtt) REVERT: C 86 LEU cc_start: 0.7785 (tp) cc_final: 0.7429 (mp) REVERT: C 107 TRP cc_start: 0.7285 (OUTLIER) cc_final: 0.5565 (t-100) outliers start: 14 outliers final: 8 residues processed: 115 average time/residue: 0.0805 time to fit residues: 12.2068 Evaluate side-chains 104 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 107 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.7274 > 50: distance: 44 - 61: 9.422 distance: 48 - 75: 27.065 distance: 53 - 82: 20.185 distance: 56 - 61: 5.881 distance: 57 - 87: 15.322 distance: 61 - 62: 15.944 distance: 62 - 63: 16.148 distance: 62 - 65: 25.393 distance: 63 - 64: 13.513 distance: 63 - 75: 7.379 distance: 64 - 96: 22.285 distance: 65 - 66: 13.397 distance: 66 - 67: 21.009 distance: 66 - 68: 19.451 distance: 67 - 69: 6.764 distance: 68 - 70: 5.247 distance: 68 - 71: 15.570 distance: 69 - 70: 15.367 distance: 70 - 72: 15.153 distance: 71 - 73: 8.238 distance: 72 - 74: 13.406 distance: 73 - 74: 12.394 distance: 75 - 76: 12.682 distance: 76 - 77: 12.268 distance: 76 - 79: 11.960 distance: 77 - 78: 17.671 distance: 77 - 82: 17.047 distance: 78 - 103: 17.518 distance: 79 - 80: 17.597 distance: 79 - 81: 6.483 distance: 82 - 83: 18.453 distance: 83 - 84: 20.004 distance: 83 - 86: 31.382 distance: 84 - 85: 9.404 distance: 84 - 87: 11.199 distance: 85 - 111: 30.779 distance: 87 - 88: 14.424 distance: 88 - 89: 10.203 distance: 88 - 91: 14.254 distance: 89 - 90: 18.039 distance: 89 - 96: 22.949 distance: 90 - 117: 26.525 distance: 91 - 92: 12.229 distance: 92 - 93: 11.817 distance: 93 - 94: 9.414 distance: 93 - 95: 25.656 distance: 96 - 97: 14.725 distance: 97 - 98: 6.846 distance: 97 - 100: 10.105 distance: 98 - 99: 6.841 distance: 99 - 122: 39.280 distance: 100 - 101: 10.595 distance: 100 - 102: 3.208 distance: 103 - 104: 26.485 distance: 104 - 105: 13.618 distance: 104 - 107: 8.310 distance: 105 - 106: 12.582 distance: 105 - 111: 29.783 distance: 106 - 127: 33.793 distance: 107 - 108: 4.729 distance: 107 - 109: 32.572 distance: 111 - 112: 8.406 distance: 112 - 113: 12.021 distance: 112 - 115: 14.923 distance: 113 - 114: 8.956 distance: 113 - 117: 13.210 distance: 114 - 133: 23.253 distance: 115 - 116: 15.188 distance: 117 - 118: 17.422 distance: 118 - 119: 26.599 distance: 118 - 121: 9.742 distance: 119 - 120: 27.901 distance: 119 - 122: 16.967 distance: 120 - 140: 34.035 distance: 122 - 123: 6.661 distance: 123 - 124: 15.375 distance: 123 - 126: 11.185 distance: 124 - 125: 41.131 distance: 124 - 127: 38.103 distance: 125 - 145: 29.399 distance: 127 - 128: 38.259 distance: 128 - 129: 28.640 distance: 128 - 131: 38.095 distance: 129 - 130: 11.254 distance: 129 - 133: 13.358 distance: 130 - 150: 10.409 distance: 131 - 132: 16.737 distance: 136 - 157: 3.064