Starting phenix.real_space_refine on Wed Feb 4 01:40:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l5y_62848/02_2026/9l5y_62848.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l5y_62848/02_2026/9l5y_62848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l5y_62848/02_2026/9l5y_62848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l5y_62848/02_2026/9l5y_62848.map" model { file = "/net/cci-nas-00/data/ceres_data/9l5y_62848/02_2026/9l5y_62848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l5y_62848/02_2026/9l5y_62848.cif" } resolution = 3.81 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= 0.013 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: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 12 5.16 5 C 5039 2.51 5 N 1443 2.21 5 O 1595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8123 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3691 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 19, 'TRANS': 440} Chain breaks: 2 Chain: "B" Number of atoms: 3702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3702 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 19, 'TRANS': 441} Chain breaks: 1 Chain: "D" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 386 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 8} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain breaks: 1 Chain: "F" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 344 Classifications: {'RNA': 16} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 7} Link IDs: {'rna3p': 15} Chain breaks: 1 Time building chain proxies: 2.08, per 1000 atoms: 0.26 Number of scatterers: 8123 At special positions: 0 Unit cell: (175.497, 99.736, 68.089, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 34 15.00 O 1595 8.00 N 1443 7.00 C 5039 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: 0.54 Conformation dependent library (CDL) restraints added in 198.5 milliseconds 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1726 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 3 sheets defined 67.9% alpha, 4.6% beta 12 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.970A pdb=" N SER A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 50 through 67 Processing helix chain 'A' and resid 67 through 81 Processing helix chain 'A' and resid 85 through 96 removed outlier: 3.799A pdb=" N ALA A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 104 Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 137 through 151 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 167 through 176 Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 198 through 211 removed outlier: 3.542A pdb=" N MET A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 Processing helix chain 'A' and resid 225 through 233 Processing helix chain 'A' and resid 238 through 251 removed outlier: 5.034A pdb=" N ASN A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASN A 247 " --> pdb=" O ARG A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 256 through 269 removed outlier: 3.864A pdb=" N ARG A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 276 through 291 removed outlier: 3.555A pdb=" N TYR A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 306 removed outlier: 3.506A pdb=" N SER A 306 " --> pdb=" O GLU A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 355 Processing helix chain 'A' and resid 369 through 372 removed outlier: 3.684A pdb=" N THR A 372 " --> pdb=" O THR A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 375 through 387 Processing helix chain 'A' and resid 392 through 401 removed outlier: 3.610A pdb=" N ALA A 396 " --> pdb=" O TYR A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 433 Processing helix chain 'A' and resid 466 through 475 Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'B' and resid 26 through 35 Processing helix chain 'B' and resid 36 through 39 removed outlier: 3.529A pdb=" N PHE B 39 " --> pdb=" O SER B 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 36 through 39' Processing helix chain 'B' and resid 50 through 67 Processing helix chain 'B' and resid 67 through 79 removed outlier: 3.557A pdb=" N VAL B 71 " --> pdb=" O ASP B 67 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARG B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 96 Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.543A pdb=" N THR B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 133 removed outlier: 3.625A pdb=" N GLU B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 150 removed outlier: 3.617A pdb=" N ASP B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 167 through 176 removed outlier: 3.508A pdb=" N HIS B 176 " --> pdb=" O ILE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.620A pdb=" N SER B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 198 through 209 Processing helix chain 'B' and resid 214 through 223 Processing helix chain 'B' and resid 225 through 236 Proline residue: B 234 - end of helix Processing helix chain 'B' and resid 238 through 251 removed outlier: 5.192A pdb=" N ASN B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ASN B 247 " --> pdb=" O ARG B 243 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS B 251 " --> pdb=" O ASN B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 255 Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 276 through 290 removed outlier: 3.532A pdb=" N TYR B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 338 through 355 removed outlier: 3.560A pdb=" N ALA B 342 " --> pdb=" O HIS B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'B' and resid 375 through 387 Processing helix chain 'B' and resid 392 through 401 removed outlier: 3.586A pdb=" N ALA B 396 " --> pdb=" O TYR B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 433 Processing helix chain 'B' and resid 466 through 477 removed outlier: 4.063A pdb=" N VAL B 476 " --> pdb=" O GLU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 removed outlier: 4.486A pdb=" N PHE B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 367 removed outlier: 6.710A pdb=" N THR A 317 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TRP A 359 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N PHE A 319 " --> pdb=" O TRP A 359 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE A 361 " --> pdb=" O PHE A 319 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL A 321 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 414 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A 411 " --> pdb=" O HIS A 440 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE A 442 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE A 413 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA A 439 " --> pdb=" O ALA A 458 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ILE A 457 " --> pdb=" O PRO A 453 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 365 through 367 removed outlier: 6.660A pdb=" N THR B 317 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N TRP B 359 " --> pdb=" O THR B 317 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N PHE B 319 " --> pdb=" O TRP B 359 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE B 361 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL B 321 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL B 411 " --> pdb=" O VAL B 438 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 414 through 415 386 hydrogen bonds defined for protein. 1140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2466 1.34 - 1.45: 1383 1.45 - 1.57: 4430 1.57 - 1.69: 64 1.69 - 1.81: 24 Bond restraints: 8367 Sorted by residual: bond pdb=" CG GLN B 366 " pdb=" CD GLN B 366 " ideal model delta sigma weight residual 1.516 1.470 0.046 2.50e-02 1.60e+03 3.38e+00 bond pdb=" CB ARG A 184 " pdb=" CG ARG A 184 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.56e+00 bond pdb=" CA ILE B 413 " pdb=" CB ILE B 413 " ideal model delta sigma weight residual 1.531 1.543 -0.012 1.11e-02 8.12e+03 1.21e+00 bond pdb=" N MET A 339 " pdb=" CA MET A 339 " ideal model delta sigma weight residual 1.459 1.472 -0.012 1.19e-02 7.06e+03 1.09e+00 bond pdb=" C ARG A 212 " pdb=" O ARG A 212 " ideal model delta sigma weight residual 1.235 1.230 0.005 4.70e-03 4.53e+04 1.02e+00 ... (remaining 8362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 11307 2.62 - 5.25: 150 5.25 - 7.87: 22 7.87 - 10.49: 5 10.49 - 13.12: 2 Bond angle restraints: 11486 Sorted by residual: angle pdb=" CA MET B 327 " pdb=" CB MET B 327 " pdb=" CG MET B 327 " ideal model delta sigma weight residual 114.10 123.57 -9.47 2.00e+00 2.50e-01 2.24e+01 angle pdb=" N ALA B 362 " pdb=" CA ALA B 362 " pdb=" C ALA B 362 " ideal model delta sigma weight residual 112.72 107.16 5.56 1.28e+00 6.10e-01 1.89e+01 angle pdb=" CA ARG B 105 " pdb=" CB ARG B 105 " pdb=" CG ARG B 105 " ideal model delta sigma weight residual 114.10 121.85 -7.75 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CA LEU B 187 " pdb=" CB LEU B 187 " pdb=" CG LEU B 187 " ideal model delta sigma weight residual 116.30 129.42 -13.12 3.50e+00 8.16e-02 1.40e+01 angle pdb=" CA GLU A 183 " pdb=" CB GLU A 183 " pdb=" CG GLU A 183 " ideal model delta sigma weight residual 114.10 120.65 -6.55 2.00e+00 2.50e-01 1.07e+01 ... (remaining 11481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4235 17.94 - 35.89: 577 35.89 - 53.83: 173 53.83 - 71.78: 65 71.78 - 89.72: 27 Dihedral angle restraints: 5077 sinusoidal: 2403 harmonic: 2674 Sorted by residual: dihedral pdb=" CA HIS A 338 " pdb=" C HIS A 338 " pdb=" N MET A 339 " pdb=" CA MET A 339 " ideal model delta harmonic sigma weight residual -180.00 -154.46 -25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA LEU B 304 " pdb=" C LEU B 304 " pdb=" N GLU B 305 " pdb=" CA GLU B 305 " ideal model delta harmonic sigma weight residual 180.00 155.08 24.92 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA PHE B 361 " pdb=" C PHE B 361 " pdb=" N ALA B 362 " pdb=" CA ALA B 362 " ideal model delta harmonic sigma weight residual 180.00 157.05 22.95 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 5074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 812 0.031 - 0.062: 336 0.062 - 0.093: 98 0.093 - 0.123: 43 0.123 - 0.154: 14 Chirality restraints: 1303 Sorted by residual: chirality pdb=" CG LEU A 38 " pdb=" CB LEU A 38 " pdb=" CD1 LEU A 38 " pdb=" CD2 LEU A 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA PRO A 423 " pdb=" N PRO A 423 " pdb=" C PRO A 423 " pdb=" CB PRO A 423 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CG LEU B 126 " pdb=" CB LEU B 126 " pdb=" CD1 LEU B 126 " pdb=" CD2 LEU B 126 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 1300 not shown) Planarity restraints: 1333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 366 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" CD GLN B 366 " 0.038 2.00e-02 2.50e+03 pdb=" OE1 GLN B 366 " -0.014 2.00e-02 2.50e+03 pdb=" NE2 GLN B 366 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 463 " 0.011 2.00e-02 2.50e+03 1.19e-02 3.53e+00 pdb=" CG TRP A 463 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 463 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 463 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 463 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 463 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 463 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 463 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 463 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 463 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 89 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C ALA B 89 " 0.032 2.00e-02 2.50e+03 pdb=" O ALA B 89 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA B 90 " -0.011 2.00e-02 2.50e+03 ... (remaining 1330 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 3378 2.93 - 3.42: 8956 3.42 - 3.92: 14649 3.92 - 4.41: 16291 4.41 - 4.90: 24517 Nonbonded interactions: 67791 Sorted by model distance: nonbonded pdb=" O ASN B 99 " pdb=" OD1 ASN B 99 " model vdw 2.438 3.040 nonbonded pdb=" O SER B 405 " pdb=" OG SER B 405 " model vdw 2.468 3.040 nonbonded pdb=" N1 A F 12 " pdb=" O6 G F 51 " model vdw 2.502 2.496 nonbonded pdb=" OD1 ASN B 99 " pdb=" OE2 GLU B 103 " model vdw 2.519 3.040 nonbonded pdb=" O SER A 405 " pdb=" OG SER A 405 " model vdw 2.556 3.040 ... (remaining 67786 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 25 through 117 or resid 119 through 492)) } ncs_group { reference = (chain 'D' and resid 8 through 55) selection = chain 'F' } 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 group one per residue 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: 1.890 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.790 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5094 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 : 0.003 0.046 8367 Z= 0.149 Angle : 0.769 13.119 11486 Z= 0.397 Chirality : 0.041 0.154 1303 Planarity : 0.005 0.056 1333 Dihedral : 19.336 89.721 3351 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.56 % Allowed : 28.34 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.27), residues: 911 helix: 0.03 (0.22), residues: 547 sheet: -2.58 (0.61), residues: 62 loop : -0.86 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 105 TYR 0.024 0.002 TYR B 128 PHE 0.020 0.002 PHE A 56 TRP 0.032 0.002 TRP A 463 HIS 0.012 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8367) covalent geometry : angle 0.76916 (11486) hydrogen bonds : bond 0.12874 ( 417) hydrogen bonds : angle 6.44303 ( 1186) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ASN cc_start: 0.7152 (t0) cc_final: 0.6817 (t0) REVERT: B 77 TYR cc_start: 0.5035 (OUTLIER) cc_final: 0.2495 (p90) REVERT: B 99 ASN cc_start: 0.8087 (t0) cc_final: 0.7772 (t0) REVERT: B 105 ARG cc_start: 0.6959 (tpt90) cc_final: 0.6672 (tpt90) REVERT: B 137 ARG cc_start: 0.7442 (mmp80) cc_final: 0.6270 (tpp80) REVERT: B 209 MET cc_start: -0.0028 (OUTLIER) cc_final: -0.1101 (tpt) REVERT: B 472 GLU cc_start: 0.5150 (tm-30) cc_final: 0.4695 (tt0) outliers start: 28 outliers final: 22 residues processed: 132 average time/residue: 0.0862 time to fit residues: 15.1730 Evaluate side-chains 123 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS B 99 ASN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5124 r_free = 0.5124 target = 0.230683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.193815 restraints weight = 15282.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.199407 restraints weight = 9920.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.203472 restraints weight = 7162.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.206293 restraints weight = 5565.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.208579 restraints weight = 4588.266| |-----------------------------------------------------------------------------| r_work (final): 0.4905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5122 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8367 Z= 0.153 Angle : 0.680 11.185 11486 Z= 0.335 Chirality : 0.040 0.315 1303 Planarity : 0.005 0.050 1333 Dihedral : 15.989 86.286 1596 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 22.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 6.48 % Allowed : 23.89 % Favored : 69.63 % 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: -0.69 (0.28), residues: 911 helix: 0.12 (0.22), residues: 558 sheet: -2.83 (0.57), residues: 62 loop : -0.76 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 104 TYR 0.020 0.002 TYR B 128 PHE 0.035 0.002 PHE A 39 TRP 0.013 0.002 TRP A 273 HIS 0.008 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8367) covalent geometry : angle 0.68031 (11486) hydrogen bonds : bond 0.04488 ( 417) hydrogen bonds : angle 5.43741 ( 1186) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 98 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ARG cc_start: 0.7178 (mmm160) cc_final: 0.5768 (tpp-160) REVERT: A 203 LYS cc_start: 0.7390 (ptmm) cc_final: 0.6990 (mmtm) REVERT: A 237 ASN cc_start: 0.7166 (t0) cc_final: 0.6741 (m-40) REVERT: A 424 TRP cc_start: 0.2347 (OUTLIER) cc_final: -0.0143 (m-90) REVERT: B 203 LYS cc_start: 0.7847 (mmmt) cc_final: 0.7343 (ptmm) REVERT: B 209 MET cc_start: 0.0079 (ppp) cc_final: -0.0564 (tpp) outliers start: 51 outliers final: 34 residues processed: 136 average time/residue: 0.0844 time to fit residues: 15.4544 Evaluate side-chains 121 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 86 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 424 TRP Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 75 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 84 optimal weight: 0.0570 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS ** B 338 HIS ** 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 = 0.5125 r_free = 0.5125 target = 0.230694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.197358 restraints weight = 15251.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.201454 restraints weight = 9257.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.207789 restraints weight = 6455.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.208731 restraints weight = 4622.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.210722 restraints weight = 4013.796| |-----------------------------------------------------------------------------| r_work (final): 0.4927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5101 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8367 Z= 0.128 Angle : 0.640 14.304 11486 Z= 0.313 Chirality : 0.039 0.221 1303 Planarity : 0.004 0.046 1333 Dihedral : 15.783 90.622 1584 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 6.35 % Allowed : 23.13 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.28), residues: 911 helix: 0.10 (0.22), residues: 561 sheet: -2.77 (0.56), residues: 64 loop : -0.78 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 105 TYR 0.017 0.002 TYR B 128 PHE 0.032 0.002 PHE A 39 TRP 0.013 0.001 TRP A 273 HIS 0.009 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8367) covalent geometry : angle 0.63974 (11486) hydrogen bonds : bond 0.03962 ( 417) hydrogen bonds : angle 5.13571 ( 1186) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 99 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.6385 (mm) cc_final: 0.5932 (tt) REVERT: A 203 LYS cc_start: 0.7312 (ptmm) cc_final: 0.7006 (mmtm) REVERT: A 237 ASN cc_start: 0.7333 (t0) cc_final: 0.7047 (t0) REVERT: A 358 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6735 (tm) REVERT: A 422 MET cc_start: 0.2081 (tpp) cc_final: 0.1179 (tmm) REVERT: A 424 TRP cc_start: 0.2314 (OUTLIER) cc_final: -0.0300 (m-90) REVERT: B 77 TYR cc_start: 0.4981 (OUTLIER) cc_final: 0.2549 (p90) REVERT: B 104 ARG cc_start: 0.2577 (mtp180) cc_final: 0.2343 (mtp180) REVERT: B 114 LYS cc_start: 0.6644 (mmtp) cc_final: 0.6429 (mptt) REVERT: B 209 MET cc_start: 0.0060 (OUTLIER) cc_final: -0.0546 (tpp) outliers start: 50 outliers final: 34 residues processed: 135 average time/residue: 0.0956 time to fit residues: 17.1104 Evaluate side-chains 130 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 92 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 424 TRP Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 20 optimal weight: 0.9980 chunk 90 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 18 optimal weight: 0.0980 chunk 82 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 251 HIS ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5155 r_free = 0.5155 target = 0.233180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.197090 restraints weight = 16155.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.202958 restraints weight = 10243.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.207143 restraints weight = 7232.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4932 r_free = 0.4932 target = 0.210129 restraints weight = 5539.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4953 r_free = 0.4953 target = 0.212244 restraints weight = 4492.711| |-----------------------------------------------------------------------------| r_work (final): 0.4929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5094 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8367 Z= 0.123 Angle : 0.627 13.705 11486 Z= 0.306 Chirality : 0.038 0.155 1303 Planarity : 0.004 0.046 1333 Dihedral : 15.668 93.058 1581 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 6.10 % Allowed : 24.14 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.28), residues: 911 helix: 0.13 (0.22), residues: 565 sheet: -2.75 (0.56), residues: 64 loop : -0.80 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 105 TYR 0.019 0.002 TYR B 377 PHE 0.032 0.002 PHE A 39 TRP 0.013 0.001 TRP A 463 HIS 0.008 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8367) covalent geometry : angle 0.62652 (11486) hydrogen bonds : bond 0.03775 ( 417) hydrogen bonds : angle 5.00174 ( 1186) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 102 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 PHE cc_start: 0.5430 (t80) cc_final: 0.5222 (t80) REVERT: A 57 ILE cc_start: 0.6428 (mm) cc_final: 0.5970 (tt) REVERT: A 128 TYR cc_start: 0.4587 (t80) cc_final: 0.4245 (t80) REVERT: A 203 LYS cc_start: 0.7311 (ptmm) cc_final: 0.7031 (mmtm) REVERT: A 237 ASN cc_start: 0.7334 (t0) cc_final: 0.7015 (t0) REVERT: A 358 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6670 (tm) REVERT: A 422 MET cc_start: 0.2292 (tpp) cc_final: 0.1337 (tmm) REVERT: A 424 TRP cc_start: 0.2292 (OUTLIER) cc_final: -0.0351 (m-90) REVERT: B 77 TYR cc_start: 0.4763 (OUTLIER) cc_final: 0.2288 (p90) REVERT: B 114 LYS cc_start: 0.6521 (mmtp) cc_final: 0.6284 (mptt) REVERT: B 186 LEU cc_start: 0.8568 (mm) cc_final: 0.8087 (mm) REVERT: B 209 MET cc_start: -0.0042 (OUTLIER) cc_final: -0.0588 (tpp) REVERT: B 305 GLU cc_start: 0.6164 (OUTLIER) cc_final: 0.5930 (mp0) outliers start: 48 outliers final: 33 residues processed: 133 average time/residue: 0.0870 time to fit residues: 15.6807 Evaluate side-chains 130 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 92 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 361 PHE Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 424 TRP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.4615 > 50: distance: 37 - 62: 19.261 distance: 42 - 67: 15.104 distance: 49 - 53: 4.396 distance: 50 - 75: 11.294 distance: 53 - 54: 6.892 distance: 54 - 55: 13.580 distance: 54 - 57: 14.349 distance: 55 - 56: 4.721 distance: 55 - 62: 5.763 distance: 56 - 80: 21.386 distance: 57 - 58: 11.812 distance: 58 - 59: 15.259 distance: 59 - 60: 3.327 distance: 60 - 61: 6.507 distance: 62 - 63: 6.608 distance: 63 - 64: 10.069 distance: 63 - 66: 11.966 distance: 64 - 65: 11.828 distance: 64 - 67: 8.903 distance: 65 - 89: 15.549 distance: 67 - 68: 4.371 distance: 68 - 69: 15.161 distance: 68 - 71: 15.810 distance: 69 - 70: 5.918 distance: 69 - 75: 25.700 distance: 70 - 100: 35.429 distance: 71 - 72: 15.721 distance: 71 - 73: 5.225 distance: 72 - 74: 36.666 distance: 75 - 76: 6.084 distance: 76 - 77: 9.952 distance: 76 - 79: 5.113 distance: 77 - 78: 5.805 distance: 78 - 108: 34.407 distance: 80 - 81: 11.554 distance: 81 - 82: 11.659 distance: 81 - 84: 8.811 distance: 82 - 83: 8.797 distance: 83 - 116: 13.322 distance: 84 - 85: 4.102 distance: 85 - 86: 12.555 distance: 86 - 87: 8.291 distance: 86 - 88: 3.388 distance: 89 - 90: 14.234 distance: 90 - 91: 5.056 distance: 90 - 93: 4.362 distance: 91 - 92: 14.352 distance: 91 - 100: 18.208 distance: 92 - 124: 34.613 distance: 93 - 94: 8.774 distance: 94 - 95: 25.621 distance: 96 - 97: 14.801 distance: 97 - 98: 14.343 distance: 97 - 99: 20.075 distance: 100 - 101: 3.797 distance: 101 - 102: 22.314 distance: 101 - 104: 19.909 distance: 102 - 103: 16.421 distance: 102 - 108: 17.197 distance: 104 - 105: 4.664 distance: 105 - 106: 18.195 distance: 105 - 107: 22.102 distance: 108 - 109: 17.039 distance: 109 - 110: 11.254 distance: 110 - 111: 20.575 distance: 110 - 116: 5.068 distance: 112 - 113: 6.102 distance: 113 - 114: 12.760 distance: 113 - 115: 6.271 distance: 116 - 117: 23.369 distance: 117 - 118: 15.693 distance: 117 - 120: 23.172 distance: 118 - 119: 6.859 distance: 118 - 124: 17.481 distance: 120 - 121: 19.225 distance: 121 - 122: 29.317 distance: 121 - 123: 9.227 distance: 124 - 125: 9.843 distance: 125 - 126: 10.491 distance: 125 - 128: 11.520 distance: 126 - 127: 7.885 distance: 126 - 132: 7.236 distance: 128 - 129: 23.508 distance: 128 - 130: 15.251 distance: 129 - 131: 28.913