Starting phenix.real_space_refine on Wed Feb 4 14:19:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e4a_47503/02_2026/9e4a_47503.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e4a_47503/02_2026/9e4a_47503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e4a_47503/02_2026/9e4a_47503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e4a_47503/02_2026/9e4a_47503.map" model { file = "/net/cci-nas-00/data/ceres_data/9e4a_47503/02_2026/9e4a_47503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e4a_47503/02_2026/9e4a_47503.cif" } resolution = 2.74 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= 0.011 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 87 5.16 5 C 6945 2.51 5 N 1782 2.21 5 O 2028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 10842 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3614 Classifications: {'peptide': 451} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 432} Chain: "B" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3614 Classifications: {'peptide': 451} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 432} Chain: "C" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3614 Classifications: {'peptide': 451} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 432} Time building chain proxies: 2.65, per 1000 atoms: 0.24 Number of scatterers: 10842 At special positions: 0 Unit cell: (95.348, 99.288, 131.596, 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 87 16.00 O 2028 8.00 N 1782 7.00 C 6945 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 314 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 310 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 314 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 325 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 314 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS C 325 " - pdb=" SG CYS C 337 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 512.6 milliseconds 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 12 sheets defined 44.6% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 40 through 70 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 153 through 162 Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.525A pdb=" N ASP A 202 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 203 " --> pdb=" O GLY A 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 199 through 203' Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 338 through 345 removed outlier: 3.813A pdb=" N LYS A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 356 Processing helix chain 'A' and resid 357 through 361 removed outlier: 4.130A pdb=" N CYS A 361 " --> pdb=" O GLN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 395 removed outlier: 4.589A pdb=" N LYS A 388 " --> pdb=" O LYS A 384 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N TYR A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 404 removed outlier: 3.730A pdb=" N GLY A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 443 Processing helix chain 'A' and resid 446 through 465 Processing helix chain 'B' and resid 17 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 40 through 70 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 153 through 162 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.525A pdb=" N ASP B 202 " --> pdb=" O SER B 199 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY B 203 " --> pdb=" O GLY B 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 199 through 203' Processing helix chain 'B' and resid 213 through 216 Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'B' and resid 338 through 345 removed outlier: 3.813A pdb=" N LYS B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 356 Processing helix chain 'B' and resid 357 through 361 removed outlier: 4.130A pdb=" N CYS B 361 " --> pdb=" O GLN B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 395 removed outlier: 4.588A pdb=" N LYS B 388 " --> pdb=" O LYS B 384 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N TYR B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 404 removed outlier: 3.731A pdb=" N GLY B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 443 Processing helix chain 'B' and resid 446 through 465 Processing helix chain 'C' and resid 17 through 25 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 40 through 70 Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 153 through 162 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.525A pdb=" N ASP C 202 " --> pdb=" O SER C 199 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY C 203 " --> pdb=" O GLY C 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 199 through 203' Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 338 through 345 removed outlier: 3.813A pdb=" N LYS C 343 " --> pdb=" O PRO C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 356 Processing helix chain 'C' and resid 357 through 361 removed outlier: 4.131A pdb=" N CYS C 361 " --> pdb=" O GLN C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 395 removed outlier: 4.587A pdb=" N LYS C 388 " --> pdb=" O LYS C 384 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N TYR C 389 " --> pdb=" O ALA C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 404 removed outlier: 3.730A pdb=" N GLY C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 443 Processing helix chain 'C' and resid 446 through 465 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 81 removed outlier: 7.546A pdb=" N ASN A 416 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU A 277 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 179 removed outlier: 4.194A pdb=" N CYS A 172 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU A 169 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASP A 223 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 171 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE A 269 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 189 removed outlier: 6.629A pdb=" N LYS A 193 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASN A 94 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 245 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 81 removed outlier: 7.545A pdb=" N ASN B 416 " --> pdb=" O CYS B 275 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLU B 277 " --> pdb=" O ASN B 416 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 177 through 179 removed outlier: 4.194A pdb=" N CYS B 172 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU B 169 " --> pdb=" O ASP B 223 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASP B 223 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER B 171 " --> pdb=" O MET B 221 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE B 269 " --> pdb=" O ILE B 405 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA8, first strand: chain 'B' and resid 184 through 189 removed outlier: 6.630A pdb=" N LYS B 193 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ASN B 94 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE B 245 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 73 through 81 removed outlier: 7.545A pdb=" N ASN C 416 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU C 277 " --> pdb=" O ASN C 416 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 177 through 179 removed outlier: 4.195A pdb=" N CYS C 172 " --> pdb=" O CYS C 179 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU C 169 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP C 223 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER C 171 " --> pdb=" O MET C 221 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE C 269 " --> pdb=" O ILE C 405 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AB3, first strand: chain 'C' and resid 184 through 189 removed outlier: 6.629A pdb=" N LYS C 193 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASN C 94 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE C 245 " --> pdb=" O VAL C 265 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1566 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: 1.85 Time building geometry restraints manager: 1.18 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: 3516 1.34 - 1.46: 2614 1.46 - 1.58: 4850 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 11100 Sorted by residual: bond pdb=" CA ILE B 381 " pdb=" CB ILE B 381 " ideal model delta sigma weight residual 1.537 1.547 -0.010 1.29e-02 6.01e+03 5.82e-01 bond pdb=" CA ILE C 381 " pdb=" CB ILE C 381 " ideal model delta sigma weight residual 1.537 1.546 -0.009 1.29e-02 6.01e+03 5.14e-01 bond pdb=" CA ILE A 381 " pdb=" CB ILE A 381 " ideal model delta sigma weight residual 1.537 1.546 -0.009 1.29e-02 6.01e+03 5.11e-01 bond pdb=" CA ILE C 381 " pdb=" C ILE C 381 " ideal model delta sigma weight residual 1.524 1.517 0.007 1.05e-02 9.07e+03 4.95e-01 bond pdb=" CA ILE A 381 " pdb=" C ILE A 381 " ideal model delta sigma weight residual 1.524 1.518 0.007 1.05e-02 9.07e+03 4.42e-01 ... (remaining 11095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 14434 1.00 - 2.00: 468 2.00 - 3.00: 71 3.00 - 4.00: 27 4.00 - 5.00: 9 Bond angle restraints: 15009 Sorted by residual: angle pdb=" CA MET C 129 " pdb=" C MET C 129 " pdb=" N ALA C 130 " ideal model delta sigma weight residual 114.90 117.63 -2.73 1.37e+00 5.33e-01 3.97e+00 angle pdb=" CA MET A 129 " pdb=" C MET A 129 " pdb=" N ALA A 130 " ideal model delta sigma weight residual 114.90 117.62 -2.72 1.37e+00 5.33e-01 3.94e+00 angle pdb=" CA MET B 129 " pdb=" C MET B 129 " pdb=" N ALA B 130 " ideal model delta sigma weight residual 114.90 117.54 -2.64 1.37e+00 5.33e-01 3.73e+00 angle pdb=" N MET B 129 " pdb=" CA MET B 129 " pdb=" C MET B 129 " ideal model delta sigma weight residual 110.70 113.31 -2.61 1.55e+00 4.16e-01 2.83e+00 angle pdb=" N PRO C 331 " pdb=" CA PRO C 331 " pdb=" C PRO C 331 " ideal model delta sigma weight residual 110.40 113.09 -2.69 1.61e+00 3.86e-01 2.79e+00 ... (remaining 15004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 6077 16.63 - 33.27: 472 33.27 - 49.90: 102 49.90 - 66.53: 33 66.53 - 83.17: 21 Dihedral angle restraints: 6705 sinusoidal: 2742 harmonic: 3963 Sorted by residual: dihedral pdb=" CB CYS C 290 " pdb=" SG CYS C 290 " pdb=" SG CYS C 367 " pdb=" CB CYS C 367 " ideal model delta sinusoidal sigma weight residual -86.00 -148.66 62.66 1 1.00e+01 1.00e-02 5.19e+01 dihedral pdb=" CB CYS A 290 " pdb=" SG CYS A 290 " pdb=" SG CYS A 367 " pdb=" CB CYS A 367 " ideal model delta sinusoidal sigma weight residual -86.00 -148.61 62.61 1 1.00e+01 1.00e-02 5.18e+01 dihedral pdb=" CB CYS B 290 " pdb=" SG CYS B 290 " pdb=" SG CYS B 367 " pdb=" CB CYS B 367 " ideal model delta sinusoidal sigma weight residual -86.00 -148.59 62.59 1 1.00e+01 1.00e-02 5.18e+01 ... (remaining 6702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1015 0.029 - 0.057: 431 0.057 - 0.086: 106 0.086 - 0.114: 59 0.114 - 0.143: 9 Chirality restraints: 1620 Sorted by residual: chirality pdb=" CA ILE A 381 " pdb=" N ILE A 381 " pdb=" C ILE A 381 " pdb=" CB ILE A 381 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA ILE B 381 " pdb=" N ILE B 381 " pdb=" C ILE B 381 " pdb=" CB ILE B 381 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE C 381 " pdb=" N ILE C 381 " pdb=" C ILE C 381 " pdb=" CB ILE C 381 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 1617 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 284 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO C 285 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO C 285 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 285 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 284 " -0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO B 285 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 285 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 285 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 284 " 0.018 5.00e-02 4.00e+02 2.76e-02 1.21e+00 pdb=" N PRO A 285 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " 0.015 5.00e-02 4.00e+02 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1666 2.76 - 3.29: 10299 3.29 - 3.83: 17685 3.83 - 4.36: 21574 4.36 - 4.90: 36804 Nonbonded interactions: 88028 Sorted by model distance: nonbonded pdb=" OG1 THR C 214 " pdb=" OD2 ASP C 409 " model vdw 2.223 3.040 nonbonded pdb=" OG1 THR B 214 " pdb=" OD2 ASP B 409 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR A 214 " pdb=" OD2 ASP A 409 " model vdw 2.224 3.040 nonbonded pdb=" OE1 GLU B 235 " pdb=" OH TYR C 389 " model vdw 2.325 3.040 nonbonded pdb=" OE1 GLU A 235 " pdb=" OH TYR B 389 " model vdw 2.347 3.040 ... (remaining 88023 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = 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: 3.580 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.400 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:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 : 0.002 0.015 11121 Z= 0.094 Angle : 0.460 4.995 15051 Z= 0.258 Chirality : 0.036 0.143 1620 Planarity : 0.002 0.028 1944 Dihedral : 13.086 83.168 4098 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.22), residues: 1347 helix: 1.30 (0.23), residues: 453 sheet: 0.26 (0.29), residues: 291 loop : 0.84 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 371 TYR 0.013 0.001 TYR C 426 PHE 0.007 0.001 PHE B 394 TRP 0.007 0.001 TRP C 233 HIS 0.003 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00174 (11100) covalent geometry : angle 0.45993 (15009) SS BOND : bond 0.00177 ( 21) SS BOND : angle 0.53786 ( 42) hydrogen bonds : bond 0.22093 ( 552) hydrogen bonds : angle 8.06518 ( 1566) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8884 (mt) cc_final: 0.8586 (mp) REVERT: A 201 ARG cc_start: 0.7817 (ptm160) cc_final: 0.7509 (ppt-90) REVERT: A 333 ASP cc_start: 0.8393 (p0) cc_final: 0.7980 (t0) REVERT: A 351 ASP cc_start: 0.8945 (m-30) cc_final: 0.8493 (m-30) REVERT: A 399 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8139 (tp-100) REVERT: A 458 TYR cc_start: 0.7295 (t80) cc_final: 0.6707 (t80) REVERT: B 45 LEU cc_start: 0.8896 (mt) cc_final: 0.8510 (mp) REVERT: B 201 ARG cc_start: 0.7811 (ptm160) cc_final: 0.7493 (ppt-90) REVERT: B 333 ASP cc_start: 0.8379 (p0) cc_final: 0.7949 (t0) REVERT: B 399 GLN cc_start: 0.8647 (tm-30) cc_final: 0.8114 (tp-100) REVERT: B 458 TYR cc_start: 0.7410 (t80) cc_final: 0.6787 (t80) REVERT: C 45 LEU cc_start: 0.8875 (mt) cc_final: 0.8610 (mt) REVERT: C 201 ARG cc_start: 0.7876 (ptm160) cc_final: 0.7545 (ppt-90) REVERT: C 333 ASP cc_start: 0.8360 (p0) cc_final: 0.7930 (t0) REVERT: C 356 LYS cc_start: 0.8902 (mmmm) cc_final: 0.8592 (mmtm) REVERT: C 399 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8117 (tp-100) REVERT: C 458 TYR cc_start: 0.7453 (t80) cc_final: 0.6836 (t80) outliers start: 0 outliers final: 1 residues processed: 169 average time/residue: 0.6550 time to fit residues: 118.6802 Evaluate side-chains 108 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 227 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.094898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.066859 restraints weight = 17366.216| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.81 r_work: 0.2767 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 11121 Z= 0.298 Angle : 0.612 5.464 15051 Z= 0.329 Chirality : 0.045 0.147 1620 Planarity : 0.004 0.026 1944 Dihedral : 4.315 16.369 1478 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.69 % Allowed : 7.36 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.23), residues: 1347 helix: 1.72 (0.23), residues: 489 sheet: 0.29 (0.29), residues: 288 loop : 1.12 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 166 TYR 0.021 0.002 TYR C 426 PHE 0.016 0.002 PHE C 257 TRP 0.008 0.002 TRP B 233 HIS 0.010 0.002 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00704 (11100) covalent geometry : angle 0.61146 (15009) SS BOND : bond 0.00446 ( 21) SS BOND : angle 0.90002 ( 42) hydrogen bonds : bond 0.04645 ( 552) hydrogen bonds : angle 5.72884 ( 1566) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.8469 (mt0) cc_final: 0.7999 (mt0) REVERT: A 201 ARG cc_start: 0.8134 (ptm160) cc_final: 0.7756 (ppt-90) REVERT: A 333 ASP cc_start: 0.8647 (p0) cc_final: 0.8218 (t0) REVERT: A 351 ASP cc_start: 0.8977 (m-30) cc_final: 0.8470 (m-30) REVERT: A 399 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8407 (tp-100) REVERT: A 458 TYR cc_start: 0.7593 (t80) cc_final: 0.7138 (t80) REVERT: B 48 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8723 (mp) REVERT: B 139 GLN cc_start: 0.8274 (mt0) cc_final: 0.7905 (mt0) REVERT: B 201 ARG cc_start: 0.8085 (ptm160) cc_final: 0.7750 (ppt-90) REVERT: B 333 ASP cc_start: 0.8669 (p0) cc_final: 0.8215 (t0) REVERT: B 351 ASP cc_start: 0.8927 (m-30) cc_final: 0.8454 (m-30) REVERT: B 392 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.9011 (tttm) REVERT: B 399 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8421 (tp-100) REVERT: B 458 TYR cc_start: 0.7668 (t80) cc_final: 0.7203 (t80) REVERT: C 48 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8718 (mp) REVERT: C 53 SER cc_start: 0.8829 (t) cc_final: 0.8629 (p) REVERT: C 139 GLN cc_start: 0.8315 (mt0) cc_final: 0.8021 (mt0) REVERT: C 201 ARG cc_start: 0.8146 (ptm160) cc_final: 0.7733 (ppt-90) REVERT: C 333 ASP cc_start: 0.8629 (p0) cc_final: 0.8216 (t0) REVERT: C 351 ASP cc_start: 0.8980 (m-30) cc_final: 0.8509 (m-30) REVERT: C 399 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8404 (tp-100) REVERT: C 458 TYR cc_start: 0.7698 (t80) cc_final: 0.7188 (t80) outliers start: 20 outliers final: 7 residues processed: 112 average time/residue: 0.5918 time to fit residues: 72.0089 Evaluate side-chains 94 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 460 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 67 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 GLN ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** 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 = 0.3454 r_free = 0.3454 target = 0.097512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.069188 restraints weight = 17297.268| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.89 r_work: 0.2802 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11121 Z= 0.138 Angle : 0.535 9.067 15051 Z= 0.279 Chirality : 0.040 0.135 1620 Planarity : 0.003 0.024 1944 Dihedral : 4.151 16.322 1476 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.61 % Allowed : 9.31 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.23), residues: 1347 helix: 2.08 (0.24), residues: 486 sheet: 0.01 (0.28), residues: 303 loop : 1.04 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 166 TYR 0.012 0.001 TYR C 426 PHE 0.008 0.001 PHE C 257 TRP 0.006 0.001 TRP C 46 HIS 0.009 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00314 (11100) covalent geometry : angle 0.52936 (15009) SS BOND : bond 0.00417 ( 21) SS BOND : angle 1.56605 ( 42) hydrogen bonds : bond 0.03828 ( 552) hydrogen bonds : angle 5.38558 ( 1566) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.5883 (pmm) cc_final: 0.5671 (pmm) REVERT: A 201 ARG cc_start: 0.8030 (ptm160) cc_final: 0.7665 (ppt-90) REVERT: A 333 ASP cc_start: 0.8637 (p0) cc_final: 0.8207 (t0) REVERT: A 351 ASP cc_start: 0.8945 (m-30) cc_final: 0.8422 (m-30) REVERT: A 399 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8295 (tp-100) REVERT: A 458 TYR cc_start: 0.7508 (t80) cc_final: 0.7058 (t80) REVERT: B 41 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8260 (tm) REVERT: B 48 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8776 (mp) REVERT: B 201 ARG cc_start: 0.8015 (ptm160) cc_final: 0.7671 (ppt-90) REVERT: B 333 ASP cc_start: 0.8666 (p0) cc_final: 0.8215 (t0) REVERT: B 351 ASP cc_start: 0.8892 (m-30) cc_final: 0.8410 (m-30) REVERT: B 392 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8940 (tttm) REVERT: B 399 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8302 (tp-100) REVERT: B 458 TYR cc_start: 0.7558 (t80) cc_final: 0.7099 (t80) REVERT: C 30 LEU cc_start: 0.8387 (tt) cc_final: 0.8175 (tt) REVERT: C 41 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8411 (tm) REVERT: C 53 SER cc_start: 0.8799 (t) cc_final: 0.8506 (p) REVERT: C 201 ARG cc_start: 0.8051 (ptm160) cc_final: 0.7654 (ppt-90) REVERT: C 333 ASP cc_start: 0.8618 (p0) cc_final: 0.8209 (t0) REVERT: C 344 GLU cc_start: 0.8498 (tt0) cc_final: 0.8132 (pp20) REVERT: C 351 ASP cc_start: 0.8959 (m-30) cc_final: 0.8493 (m-30) REVERT: C 399 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8309 (tp-100) REVERT: C 458 TYR cc_start: 0.7634 (t80) cc_final: 0.7169 (t80) outliers start: 19 outliers final: 5 residues processed: 111 average time/residue: 0.5689 time to fit residues: 68.6780 Evaluate side-chains 101 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 365 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 88 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 97 optimal weight: 0.1980 chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 71 optimal weight: 0.0170 chunk 58 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 ASN ** C 438 GLN ** 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 = 0.3465 r_free = 0.3465 target = 0.098175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.070213 restraints weight = 17386.189| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.86 r_work: 0.2825 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11121 Z= 0.112 Angle : 0.511 8.721 15051 Z= 0.262 Chirality : 0.039 0.134 1620 Planarity : 0.003 0.024 1944 Dihedral : 4.003 16.136 1476 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.69 % Allowed : 10.15 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.23), residues: 1347 helix: 2.10 (0.24), residues: 492 sheet: -0.04 (0.27), residues: 297 loop : 1.05 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 166 TYR 0.008 0.001 TYR C 426 PHE 0.007 0.001 PHE C 152 TRP 0.005 0.001 TRP A 46 HIS 0.008 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00253 (11100) covalent geometry : angle 0.50756 (15009) SS BOND : bond 0.00245 ( 21) SS BOND : angle 1.19424 ( 42) hydrogen bonds : bond 0.03338 ( 552) hydrogen bonds : angle 5.20458 ( 1566) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 ARG cc_start: 0.7995 (ptm160) cc_final: 0.7643 (ppt-90) REVERT: A 333 ASP cc_start: 0.8630 (p0) cc_final: 0.8208 (t0) REVERT: A 351 ASP cc_start: 0.8943 (m-30) cc_final: 0.8444 (m-30) REVERT: A 399 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8180 (tp-100) REVERT: A 458 TYR cc_start: 0.7482 (t80) cc_final: 0.7061 (t80) REVERT: B 201 ARG cc_start: 0.7961 (ptm160) cc_final: 0.7640 (ppt-90) REVERT: B 333 ASP cc_start: 0.8643 (p0) cc_final: 0.8200 (t0) REVERT: B 351 ASP cc_start: 0.8895 (m-30) cc_final: 0.8437 (m-30) REVERT: B 378 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8358 (ptp) REVERT: B 392 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8964 (tttm) REVERT: B 399 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8282 (tp-100) REVERT: C 30 LEU cc_start: 0.8327 (tt) cc_final: 0.8088 (tt) REVERT: C 48 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8739 (mp) REVERT: C 53 SER cc_start: 0.8775 (t) cc_final: 0.8520 (p) REVERT: C 201 ARG cc_start: 0.8002 (ptm160) cc_final: 0.7607 (ppt-90) REVERT: C 333 ASP cc_start: 0.8621 (p0) cc_final: 0.8223 (t0) REVERT: C 351 ASP cc_start: 0.8950 (m-30) cc_final: 0.8444 (m-30) REVERT: C 399 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8229 (tp-100) REVERT: C 458 TYR cc_start: 0.7607 (t80) cc_final: 0.7324 (t80) outliers start: 20 outliers final: 6 residues processed: 109 average time/residue: 0.5795 time to fit residues: 68.4670 Evaluate side-chains 101 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 365 MET 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: 53.3077 > 50: distance: 25 - 30: 22.239 distance: 30 - 31: 45.710 distance: 31 - 32: 23.671 distance: 31 - 34: 28.377 distance: 32 - 33: 26.882 distance: 32 - 35: 16.028 distance: 35 - 36: 8.801 distance: 35 - 215: 11.687 distance: 36 - 37: 5.535 distance: 36 - 39: 22.063 distance: 37 - 38: 8.743 distance: 37 - 41: 16.897 distance: 39 - 40: 15.852 distance: 41 - 42: 18.312 distance: 41 - 199: 18.592 distance: 42 - 43: 13.365 distance: 42 - 45: 14.028 distance: 43 - 44: 28.353 distance: 43 - 50: 23.617 distance: 44 - 196: 23.762 distance: 45 - 46: 25.186 distance: 46 - 47: 10.393 distance: 47 - 48: 12.852 distance: 47 - 49: 14.343 distance: 50 - 51: 11.973 distance: 51 - 52: 15.329 distance: 51 - 54: 23.933 distance: 52 - 53: 9.486 distance: 52 - 59: 20.649 distance: 53 - 253: 11.605 distance: 54 - 55: 20.687 distance: 55 - 56: 4.509 distance: 56 - 57: 13.711 distance: 56 - 58: 16.732 distance: 59 - 60: 12.945 distance: 59 - 177: 5.371 distance: 60 - 61: 15.203 distance: 60 - 63: 29.717 distance: 61 - 62: 13.411 distance: 61 - 68: 6.585 distance: 62 - 174: 18.941 distance: 63 - 64: 31.772 distance: 64 - 65: 14.477 distance: 65 - 66: 4.007 distance: 65 - 67: 8.340 distance: 68 - 69: 15.148 distance: 68 - 256: 19.640 distance: 69 - 70: 30.071 distance: 69 - 72: 13.743 distance: 70 - 71: 3.932 distance: 70 - 79: 30.415 distance: 71 - 268: 26.385 distance: 72 - 73: 18.734 distance: 73 - 74: 12.853 distance: 74 - 75: 21.615 distance: 75 - 76: 8.580 distance: 76 - 77: 9.861 distance: 76 - 78: 8.374 distance: 79 - 80: 20.884 distance: 79 - 163: 8.383 distance: 80 - 81: 31.890 distance: 80 - 83: 3.652 distance: 81 - 82: 11.057 distance: 81 - 87: 12.480 distance: 82 - 160: 24.221 distance: 83 - 84: 9.607 distance: 84 - 85: 38.126 distance: 84 - 86: 18.202 distance: 87 - 88: 7.084 distance: 87 - 271: 9.938 distance: 88 - 89: 25.598 distance: 88 - 91: 18.992 distance: 89 - 90: 11.603 distance: 89 - 95: 27.805 distance: 90 - 285: 15.255 distance: 91 - 92: 40.996 distance: 91 - 93: 35.696 distance: 92 - 94: 12.524 distance: 95 - 96: 31.532 distance: 96 - 97: 10.409 distance: 96 - 99: 17.171 distance: 97 - 98: 44.928 distance: 97 - 107: 23.761 distance: 99 - 100: 22.828 distance: 100 - 101: 6.120 distance: 100 - 102: 19.718 distance: 101 - 103: 12.393 distance: 102 - 104: 6.841 distance: 103 - 105: 10.557 distance: 104 - 105: 7.653 distance: 105 - 106: 13.363 distance: 107 - 108: 11.388 distance: 108 - 109: 20.450 distance: 108 - 111: 19.885 distance: 109 - 115: 34.012 distance: 111 - 112: 22.314 distance: 112 - 113: 31.633 distance: 112 - 114: 15.954