Starting phenix.real_space_refine on Thu Jul 2 06:11:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1n_36796/07_2026/8k1n_36796.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1n_36796/07_2026/8k1n_36796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k1n_36796/07_2026/8k1n_36796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1n_36796/07_2026/8k1n_36796.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1n_36796/07_2026/8k1n_36796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1n_36796/07_2026/8k1n_36796.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.070 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 2 5.49 5 S 23 5.16 5 C 4591 2.51 5 N 1255 2.21 5 O 1304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7175 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 3858 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 20, 'TRANS': 509} Chain: "E" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1589 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 8, 'TRANS': 202} Chain: "D" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1589 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 8, 'TRANS': 202} Chain: "C" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 139 Unusual residues: {'CDL': 1, 'RFP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'RFP:plan-4': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.65, per 1000 atoms: 0.23 Number of scatterers: 7175 At special positions: 0 Unit cell: (68.224, 84.864, 109.824, 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 23 16.00 P 2 15.00 O 1304 8.00 N 1255 7.00 C 4591 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: 0.50 Conformation dependent library (CDL) restraints added in 426.2 milliseconds 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 0 sheets defined 56.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 78 through 82 removed outlier: 4.491A pdb=" N ARG D 82 " --> pdb=" O VAL D 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 78 through 82' Processing helix chain 'D' and resid 99 through 109 removed outlier: 3.501A pdb=" N MET D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 125 removed outlier: 3.620A pdb=" N GLU D 120 " --> pdb=" O ALA D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 150 removed outlier: 3.671A pdb=" N GLN D 142 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS D 143 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 144 " --> pdb=" O ASN D 140 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 183 removed outlier: 3.909A pdb=" N GLN D 183 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 201 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 40 through 63 removed outlier: 3.686A pdb=" N LEU C 48 " --> pdb=" O TRP C 44 " (cutoff:3.500A) Proline residue: C 51 - end of helix removed outlier: 3.751A pdb=" N THR C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ALA C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 79 Processing helix chain 'C' and resid 81 through 87 Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 101 through 125 removed outlier: 5.365A pdb=" N MET C 105 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N PHE C 106 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N HIS C 107 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALA C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ASP C 125 " --> pdb=" O HIS C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 135 removed outlier: 4.603A pdb=" N ASP C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 169 removed outlier: 3.593A pdb=" N ALA C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 200 removed outlier: 3.534A pdb=" N VAL C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN C 200 " --> pdb=" O ALA C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 228 Processing helix chain 'C' and resid 232 through 236 removed outlier: 4.274A pdb=" N CYS C 236 " --> pdb=" O THR C 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 232 through 236' Processing helix chain 'C' and resid 238 through 244 removed outlier: 3.776A pdb=" N SER C 242 " --> pdb=" O PRO C 238 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 275 removed outlier: 4.143A pdb=" N LEU C 257 " --> pdb=" O TRP C 253 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU C 258 " --> pdb=" O TRP C 254 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 306 Processing helix chain 'C' and resid 309 through 329 removed outlier: 4.010A pdb=" N SER C 328 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 336 removed outlier: 7.416A pdb=" N ASP C 335 " --> pdb=" O HIS C 331 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLN C 336 " --> pdb=" O GLY C 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 331 through 336' Processing helix chain 'C' and resid 344 through 350 removed outlier: 4.844A pdb=" N THR C 348 " --> pdb=" O ARG C 344 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG C 349 " --> pdb=" O ASP C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 388 removed outlier: 3.706A pdb=" N PHE C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 362 " --> pdb=" O GLN C 358 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N MET C 370 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU C 383 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS C 384 " --> pdb=" O THR C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 397 Processing helix chain 'C' and resid 405 through 436 removed outlier: 6.820A pdb=" N HIS C 409 " --> pdb=" O TRP C 405 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 467 removed outlier: 3.910A pdb=" N GLN C 453 " --> pdb=" O THR C 449 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU C 454 " --> pdb=" O ALA C 450 " (cutoff:3.500A) Proline residue: C 455 - end of helix removed outlier: 3.574A pdb=" N LEU C 459 " --> pdb=" O PRO C 455 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LEU C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER C 461 " --> pdb=" O VAL C 457 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL C 463 " --> pdb=" O LEU C 459 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 493 Proline residue: C 476 - end of helix removed outlier: 5.026A pdb=" N TRP C 479 " --> pdb=" O THR C 475 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY C 480 " --> pdb=" O PRO C 476 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER C 493 " --> pdb=" O TYR C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 503 removed outlier: 5.278A pdb=" N ASN C 503 " --> pdb=" O GLN C 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 499 through 503' Processing helix chain 'C' and resid 507 through 510 No H-bonds generated for 'chain 'C' and resid 507 through 510' Processing helix chain 'C' and resid 522 through 540 Processing helix chain 'E' and resid 48 through 55 Processing helix chain 'E' and resid 78 through 82 removed outlier: 4.480A pdb=" N ARG E 82 " --> pdb=" O VAL E 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 78 through 82' Processing helix chain 'E' and resid 99 through 109 removed outlier: 3.511A pdb=" N LEU E 106 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA E 107 " --> pdb=" O ILE E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 125 removed outlier: 3.621A pdb=" N GLU E 120 " --> pdb=" O ALA E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 150 removed outlier: 3.680A pdb=" N LYS E 143 " --> pdb=" O GLY E 139 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL E 144 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER E 145 " --> pdb=" O ARG E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 183 removed outlier: 3.910A pdb=" N GLN E 183 " --> pdb=" O GLY E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 201 304 hydrogen bonds defined for protein. 912 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.65 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1143 1.28 - 1.41: 1704 1.41 - 1.54: 4375 1.54 - 1.67: 42 1.67 - 1.81: 39 Bond restraints: 7303 Sorted by residual: bond pdb=" C ARG E 53 " pdb=" O ARG E 53 " ideal model delta sigma weight residual 1.236 1.144 0.092 1.32e-02 5.74e+03 4.85e+01 bond pdb=" C ALA E 107 " pdb=" O ALA E 107 " ideal model delta sigma weight residual 1.236 1.159 0.078 1.25e-02 6.40e+03 3.85e+01 bond pdb=" C ARG D 53 " pdb=" O ARG D 53 " ideal model delta sigma weight residual 1.236 1.156 0.080 1.32e-02 5.74e+03 3.65e+01 bond pdb=" CA ALA D 107 " pdb=" CB ALA D 107 " ideal model delta sigma weight residual 1.532 1.450 0.083 1.53e-02 4.27e+03 2.93e+01 bond pdb=" CA ALA D 154 " pdb=" CB ALA D 154 " ideal model delta sigma weight residual 1.529 1.447 0.082 1.54e-02 4.22e+03 2.85e+01 ... (remaining 7298 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 9300 2.36 - 4.72: 480 4.72 - 7.09: 103 7.09 - 9.45: 29 9.45 - 11.81: 9 Bond angle restraints: 9921 Sorted by residual: angle pdb=" N ARG D 110 " pdb=" CA ARG D 110 " pdb=" C ARG D 110 " ideal model delta sigma weight residual 113.23 102.03 11.20 1.24e+00 6.50e-01 8.16e+01 angle pdb=" C ILE E 113 " pdb=" N ASP E 114 " pdb=" CA ASP E 114 " ideal model delta sigma weight residual 122.42 132.66 -10.24 1.33e+00 5.65e-01 5.92e+01 angle pdb=" N ILE C 346 " pdb=" CA ILE C 346 " pdb=" C ILE C 346 " ideal model delta sigma weight residual 111.56 105.21 6.35 8.60e-01 1.35e+00 5.45e+01 angle pdb=" N VAL E 22 " pdb=" CA VAL E 22 " pdb=" C VAL E 22 " ideal model delta sigma weight residual 112.90 105.83 7.07 9.60e-01 1.09e+00 5.42e+01 angle pdb=" C LYS E 131 " pdb=" N LYS E 132 " pdb=" CA LYS E 132 " ideal model delta sigma weight residual 120.94 109.62 11.32 1.57e+00 4.06e-01 5.20e+01 ... (remaining 9916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 3850 17.25 - 34.50: 382 34.50 - 51.75: 89 51.75 - 69.00: 39 69.00 - 86.25: 6 Dihedral angle restraints: 4366 sinusoidal: 1722 harmonic: 2644 Sorted by residual: dihedral pdb=" C PRO D 43 " pdb=" N PRO D 43 " pdb=" CA PRO D 43 " pdb=" CB PRO D 43 " ideal model delta harmonic sigma weight residual -120.70 -106.66 -14.04 0 2.50e+00 1.60e-01 3.16e+01 dihedral pdb=" CA GLY C 282 " pdb=" C GLY C 282 " pdb=" N LEU C 283 " pdb=" CA LEU C 283 " ideal model delta harmonic sigma weight residual 180.00 152.23 27.77 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" C VAL D 22 " pdb=" N VAL D 22 " pdb=" CA VAL D 22 " pdb=" CB VAL D 22 " ideal model delta harmonic sigma weight residual -122.00 -135.83 13.83 0 2.50e+00 1.60e-01 3.06e+01 ... (remaining 4363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1028 0.092 - 0.183: 126 0.183 - 0.275: 20 0.275 - 0.367: 6 0.367 - 0.458: 2 Chirality restraints: 1182 Sorted by residual: chirality pdb=" CB VAL E 91 " pdb=" CA VAL E 91 " pdb=" CG1 VAL E 91 " pdb=" CG2 VAL E 91 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CA GLU D 203 " pdb=" N GLU D 203 " pdb=" C GLU D 203 " pdb=" CB GLU D 203 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA VAL D 22 " pdb=" N VAL D 22 " pdb=" C VAL D 22 " pdb=" CB VAL D 22 " both_signs ideal model delta sigma weight residual False 2.44 2.08 0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 1179 not shown) Planarity restraints: 1245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 RFP C 601 " 0.111 2.00e-02 2.50e+03 2.52e-01 6.33e+02 pdb=" C18 RFP C 601 " -0.344 2.00e-02 2.50e+03 pdb=" C19 RFP C 601 " 0.335 2.00e-02 2.50e+03 pdb=" C20 RFP C 601 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 RFP C 601 " -0.014 2.00e-02 2.50e+03 2.18e-01 5.96e+02 pdb=" C16 RFP C 601 " 0.085 2.00e-02 2.50e+03 pdb=" C17 RFP C 601 " 0.364 2.00e-02 2.50e+03 pdb=" C18 RFP C 601 " -0.264 2.00e-02 2.50e+03 pdb=" C30 RFP C 601 " -0.171 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 RFP C 601 " 0.044 2.00e-02 2.50e+03 2.15e-01 5.79e+02 pdb=" C16 RFP C 601 " -0.057 2.00e-02 2.50e+03 pdb=" C2 RFP C 601 " -0.244 2.00e-02 2.50e+03 pdb=" N1 RFP C 601 " 0.387 2.00e-02 2.50e+03 pdb=" O11 RFP C 601 " -0.129 2.00e-02 2.50e+03 ... (remaining 1242 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1104 2.75 - 3.29: 6921 3.29 - 3.83: 11553 3.83 - 4.36: 14489 4.36 - 4.90: 24846 Nonbonded interactions: 58913 Sorted by model distance: nonbonded pdb=" O ILE C 134 " pdb=" OG1 THR C 137 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR C 33 " pdb=" OD1 ASN C 144 " model vdw 2.219 3.040 nonbonded pdb=" O PRO C 472 " pdb=" OG1 THR C 475 " model vdw 2.300 3.040 nonbonded pdb=" OG1 THR C 146 " pdb=" OH TYR C 271 " model vdw 2.336 3.040 nonbonded pdb=" OG SER E 192 " pdb=" OE2 GLU E 197 " model vdw 2.345 3.040 ... (remaining 58908 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 'D' selection = chain 'E' } 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: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.240 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:6.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 : 0.008 0.092 7303 Z= 0.535 Angle : 1.246 11.812 9921 Z= 0.806 Chirality : 0.066 0.458 1182 Planarity : 0.015 0.252 1245 Dihedral : 15.468 86.254 2686 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.70 % Allowed : 1.95 % Favored : 97.36 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.26), residues: 946 helix: -0.23 (0.22), residues: 524 sheet: -1.56 (0.75), residues: 56 loop : -2.61 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 544 TYR 0.026 0.002 TYR C 56 PHE 0.027 0.003 PHE E 19 TRP 0.017 0.001 TRP C 44 HIS 0.011 0.002 HIS E 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00831 / 0.53 ( 7303) covalent geometry : angle 1.24613 / 0.81 ( 9921) hydrogen bonds : bond 0.14881 / 10.25 ( 304) hydrogen bonds : angle 6.19566 / 4.66 ( 912) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 145 time to evaluate : 0.244 Fit side-chains REVERT: C 78 MET cc_start: 0.7808 (mmm) cc_final: 0.7594 (mmm) REVERT: C 93 ASP cc_start: 0.7902 (p0) cc_final: 0.7307 (p0) REVERT: C 135 ASP cc_start: 0.6707 (t0) cc_final: 0.6454 (t70) REVERT: C 473 ARG cc_start: 0.7541 (ptt-90) cc_final: 0.7151 (pmt-80) REVERT: E 161 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7250 (mm-30) REVERT: D 123 GLU cc_start: 0.7351 (tt0) cc_final: 0.6555 (mm-30) REVERT: D 128 ASP cc_start: 0.7309 (t0) cc_final: 0.6915 (t70) REVERT: D 131 LYS cc_start: 0.8071 (mtmt) cc_final: 0.7434 (mmtt) REVERT: D 171 GLU cc_start: 0.7887 (tp30) cc_final: 0.7198 (mt-10) REVERT: D 204 LYS cc_start: 0.6686 (mttp) cc_final: 0.5544 (tmtt) REVERT: D 209 ARG cc_start: 0.6572 (ttm170) cc_final: 0.6106 (tpm170) outliers start: 5 outliers final: 0 residues processed: 149 average time/residue: 0.5189 time to fit residues: 81.0663 Evaluate side-chains 95 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 244 GLN E 193 HIS D 38 HIS D 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.142285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.118217 restraints weight = 8634.430| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.03 r_work: 0.3251 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 7303 Z= 0.147 Angle : 0.718 19.553 9921 Z= 0.340 Chirality : 0.044 0.201 1182 Planarity : 0.005 0.068 1245 Dihedral : 13.236 124.628 1183 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.89 % Allowed : 10.99 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.27), residues: 946 helix: 0.24 (0.23), residues: 542 sheet: -1.09 (0.74), residues: 58 loop : -2.41 (0.29), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 123 TYR 0.006 0.001 TYR C 56 PHE 0.021 0.002 PHE C 365 TRP 0.019 0.001 TRP C 44 HIS 0.003 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 7303) covalent geometry : angle 0.71794 / 0.34 ( 9921) hydrogen bonds : bond 0.03496 / 2.36 ( 304) hydrogen bonds : angle 3.84249 / 2.83 ( 912) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.268 Fit side-chains REVERT: C 93 ASP cc_start: 0.8285 (p0) cc_final: 0.7627 (p0) REVERT: C 125 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7447 (t70) REVERT: C 387 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: C 488 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7906 (tp) REVERT: E 161 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7662 (mm-30) REVERT: E 204 LYS cc_start: 0.7754 (mttp) cc_final: 0.7509 (ttmm) REVERT: D 128 ASP cc_start: 0.8010 (t0) cc_final: 0.7644 (t70) REVERT: D 131 LYS cc_start: 0.8643 (mtmt) cc_final: 0.7866 (mmtt) REVERT: D 171 GLU cc_start: 0.8426 (tp30) cc_final: 0.7794 (tt0) REVERT: D 209 ARG cc_start: 0.7252 (ttm170) cc_final: 0.6275 (tpm170) outliers start: 28 outliers final: 9 residues processed: 116 average time/residue: 0.5529 time to fit residues: 67.2825 Evaluate side-chains 113 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 34 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.8899 > 50: distance: 61 - 70: 34.135 distance: 70 - 71: 16.002 distance: 70 - 76: 41.894 distance: 71 - 72: 33.880 distance: 71 - 74: 36.758 distance: 72 - 73: 43.843 distance: 72 - 77: 36.305 distance: 74 - 75: 17.500 distance: 75 - 76: 46.259 distance: 77 - 78: 3.951 distance: 78 - 79: 30.667 distance: 78 - 81: 18.430 distance: 79 - 80: 31.555 distance: 79 - 86: 33.756 distance: 81 - 82: 10.440 distance: 82 - 83: 8.217 distance: 83 - 84: 6.426 distance: 83 - 85: 4.449 distance: 86 - 87: 33.461 distance: 87 - 88: 29.143 distance: 87 - 90: 11.629 distance: 88 - 89: 45.560 distance: 88 - 94: 44.072 distance: 90 - 91: 6.751 distance: 91 - 92: 18.453 distance: 92 - 93: 41.903 distance: 94 - 95: 48.230 distance: 95 - 96: 13.352 distance: 95 - 98: 14.576 distance: 96 - 97: 42.098 distance: 96 - 102: 42.172 distance: 98 - 99: 36.780 distance: 99 - 100: 17.975 distance: 99 - 101: 8.488 distance: 103 - 104: 20.223 distance: 103 - 106: 49.070 distance: 104 - 105: 40.460 distance: 104 - 110: 15.029 distance: 106 - 107: 39.786 distance: 107 - 108: 10.519 distance: 107 - 109: 41.123 distance: 110 - 111: 22.512 distance: 111 - 112: 19.589 distance: 111 - 114: 25.210 distance: 112 - 113: 40.958 distance: 112 - 118: 28.680 distance: 114 - 115: 17.223 distance: 115 - 116: 35.612 distance: 115 - 117: 39.201 distance: 118 - 119: 9.772 distance: 119 - 120: 54.618 distance: 119 - 122: 13.021 distance: 120 - 121: 22.981 distance: 120 - 126: 20.681 distance: 122 - 123: 18.011 distance: 123 - 124: 42.097 distance: 123 - 125: 53.538 distance: 126 - 127: 41.490 distance: 127 - 128: 4.284 distance: 127 - 130: 13.288 distance: 128 - 129: 21.716 distance: 128 - 135: 39.884 distance: 130 - 131: 26.564 distance: 131 - 132: 22.273 distance: 132 - 133: 12.589 distance: 132 - 134: 26.929 distance: 135 - 136: 27.384 distance: 135 - 141: 43.875 distance: 136 - 137: 9.137 distance: 136 - 139: 17.473 distance: 137 - 138: 7.002 distance: 137 - 142: 27.473 distance: 139 - 140: 26.565 distance: 140 - 141: 22.035 distance: 142 - 143: 11.330 distance: 143 - 144: 30.252 distance: 143 - 146: 23.645 distance: 144 - 145: 10.016 distance: 144 - 153: 28.238 distance: 146 - 147: 22.715 distance: 147 - 148: 14.158 distance: 147 - 149: 12.804 distance: 148 - 150: 20.639 distance: 149 - 151: 18.002 distance: 150 - 152: 18.777 distance: 151 - 152: 12.868