Starting phenix.real_space_refine on Sat Aug 23 00:27:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zip_60125/08_2025/8zip_60125.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zip_60125/08_2025/8zip_60125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zip_60125/08_2025/8zip_60125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zip_60125/08_2025/8zip_60125.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zip_60125/08_2025/8zip_60125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zip_60125/08_2025/8zip_60125.map" } resolution = 4.9 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= 0.001 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 52 5.16 5 C 5511 2.51 5 N 1465 2.21 5 O 1632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8662 Number of models: 1 Model: "" Number of chains: 3 Chain: "J" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2887 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "C" Number of atoms: 5748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5748 Classifications: {'peptide': 714} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 24, 'TRANS': 687} Chain breaks: 6 Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.65, per 1000 atoms: 0.19 Number of scatterers: 8662 At special positions: 0 Unit cell: (127.82, 95.45, 112.88, 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 52 16.00 P 2 15.00 O 1632 8.00 N 1465 7.00 C 5511 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 219.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 13 sheets defined 51.2% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 80 through 94 Processing helix chain 'J' and resid 99 through 103 removed outlier: 3.639A pdb=" N HIS J 103 " --> pdb=" O PRO J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 129 removed outlier: 4.175A pdb=" N ARG J 118 " --> pdb=" O PRO J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 148 Processing helix chain 'J' and resid 174 through 177 removed outlier: 3.703A pdb=" N ILE J 177 " --> pdb=" O PRO J 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 174 through 177' Processing helix chain 'J' and resid 183 through 195 Processing helix chain 'J' and resid 196 through 199 Processing helix chain 'J' and resid 204 through 219 removed outlier: 3.538A pdb=" N CYS J 219 " --> pdb=" O LYS J 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 235 Processing helix chain 'J' and resid 254 through 259 Processing helix chain 'J' and resid 260 through 264 Processing helix chain 'J' and resid 265 through 270 removed outlier: 3.537A pdb=" N ILE J 269 " --> pdb=" O PRO J 266 " (cutoff:3.500A) Processing helix chain 'J' and resid 275 through 286 Processing helix chain 'J' and resid 291 through 296 Processing helix chain 'J' and resid 303 through 307 Processing helix chain 'J' and resid 310 through 323 Processing helix chain 'J' and resid 336 through 338 No H-bonds generated for 'chain 'J' and resid 336 through 338' Processing helix chain 'J' and resid 339 through 351 Processing helix chain 'J' and resid 352 through 355 Processing helix chain 'J' and resid 361 through 368 Processing helix chain 'J' and resid 370 through 376 Processing helix chain 'C' and resid 6 through 11 removed outlier: 6.927A pdb=" N ALA C 11 " --> pdb=" O ASP C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 17 Processing helix chain 'C' and resid 19 through 27 removed outlier: 3.695A pdb=" N ARG C 23 " --> pdb=" O SER C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.710A pdb=" N ASP C 85 " --> pdb=" O PRO C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.578A pdb=" N MET C 92 " --> pdb=" O ASP C 89 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 93 " --> pdb=" O MET C 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 93' Processing helix chain 'C' and resid 97 through 111 Processing helix chain 'C' and resid 136 through 141 removed outlier: 3.753A pdb=" N ALA C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 169 Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 216 through 232 removed outlier: 3.867A pdb=" N ALA C 224 " --> pdb=" O GLN C 220 " (cutoff:3.500A) Proline residue: C 226 - end of helix Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 284 through 292 removed outlier: 4.475A pdb=" N TYR C 288 " --> pdb=" O TYR C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 302 removed outlier: 3.724A pdb=" N LEU C 299 " --> pdb=" O LYS C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 311 removed outlier: 3.585A pdb=" N ASP C 310 " --> pdb=" O ASN C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 340 Processing helix chain 'C' and resid 344 through 361 removed outlier: 4.896A pdb=" N VAL C 350 " --> pdb=" O GLU C 346 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY C 361 " --> pdb=" O ILE C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 390 Processing helix chain 'C' and resid 392 through 402 Processing helix chain 'C' and resid 417 through 448 Processing helix chain 'C' and resid 473 through 505 Processing helix chain 'C' and resid 516 through 521 removed outlier: 4.051A pdb=" N CYS C 521 " --> pdb=" O ASP C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 541 Processing helix chain 'C' and resid 545 through 558 Processing helix chain 'C' and resid 593 through 599 Processing helix chain 'C' and resid 603 through 611 Processing helix chain 'C' and resid 615 through 622 Processing helix chain 'C' and resid 648 through 666 removed outlier: 3.759A pdb=" N THR C 666 " --> pdb=" O THR C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 699 Processing helix chain 'C' and resid 699 through 708 Processing helix chain 'C' and resid 716 through 724 removed outlier: 4.052A pdb=" N PHE C 720 " --> pdb=" O LEU C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 750 Processing sheet with id=AA1, first strand: chain 'J' and resid 31 through 34 removed outlier: 6.870A pdb=" N LEU J 10 " --> pdb=" O LEU J 106 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N THR J 108 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N CYS J 12 " --> pdb=" O THR J 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 55 through 56 Processing sheet with id=AA3, first strand: chain 'J' and resid 171 through 172 Processing sheet with id=AA4, first strand: chain 'J' and resid 171 through 172 removed outlier: 6.369A pdb=" N ASN J 299 " --> pdb=" O ILE J 332 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 240 through 244 removed outlier: 3.704A pdb=" N LEU J 244 " --> pdb=" O GLN J 248 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLN J 248 " --> pdb=" O LEU J 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 47 through 49 Processing sheet with id=AA7, first strand: chain 'C' and resid 62 through 64 Processing sheet with id=AA8, first strand: chain 'C' and resid 115 through 118 removed outlier: 3.559A pdb=" N SER C 118 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N CYS C 122 " --> pdb=" O ARG C 673 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE C 675 " --> pdb=" O CYS C 122 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR C 124 " --> pdb=" O ILE C 675 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N SER C 173 " --> pdb=" O HIS C 670 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL C 672 " --> pdb=" O SER C 173 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU C 175 " --> pdb=" O VAL C 672 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N CYS C 674 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N THR C 177 " --> pdb=" O CYS C 674 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN C 172 " --> pdb=" O GLY C 459 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU C 461 " --> pdb=" O GLN C 172 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ILE C 174 " --> pdb=" O LEU C 461 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE C 463 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE C 176 " --> pdb=" O ILE C 463 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY C 246 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR C 266 " --> pdb=" O GLY C 246 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N PHE C 248 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ILE C 264 " --> pdb=" O PHE C 248 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ARG C 250 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA C 262 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N HIS C 252 " --> pdb=" O ALA C 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 233 through 234 removed outlier: 3.608A pdb=" N ALA C 234 " --> pdb=" O SER C 242 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER C 242 " --> pdb=" O ALA C 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 365 through 367 Processing sheet with id=AB2, first strand: chain 'C' and resid 404 through 407 removed outlier: 3.566A pdb=" N VAL C 412 " --> pdb=" O VAL C 405 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 564 through 565 removed outlier: 3.654A pdb=" N PHE C 578 " --> pdb=" O TYR C 589 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY C 585 " --> pdb=" O HIS C 582 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 713 through 715 411 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 0.97 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: 2815 1.34 - 1.46: 1599 1.46 - 1.58: 4338 1.58 - 1.69: 3 1.69 - 1.81: 90 Bond restraints: 8845 Sorted by residual: bond pdb=" N GLU C 410 " pdb=" CA GLU C 410 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.25e-02 6.40e+03 5.38e+00 bond pdb=" C GLN C 452 " pdb=" N PRO C 453 " ideal model delta sigma weight residual 1.331 1.353 -0.022 1.20e-02 6.94e+03 3.33e+00 bond pdb=" C GLN J 265 " pdb=" N PRO J 266 " ideal model delta sigma weight residual 1.337 1.319 0.018 9.80e-03 1.04e+04 3.19e+00 bond pdb=" C4 ADP J 401 " pdb=" C5 ADP J 401 " ideal model delta sigma weight residual 1.490 1.457 0.033 2.00e-02 2.50e+03 2.67e+00 bond pdb=" CB ARG J 64 " pdb=" CG ARG J 64 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.52e+00 ... (remaining 8840 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 11630 1.80 - 3.59: 273 3.59 - 5.39: 32 5.39 - 7.19: 6 7.19 - 8.98: 2 Bond angle restraints: 11943 Sorted by residual: angle pdb=" N GLY C 66 " pdb=" CA GLY C 66 " pdb=" C GLY C 66 " ideal model delta sigma weight residual 114.85 107.98 6.87 1.35e+00 5.49e-01 2.59e+01 angle pdb=" C GLY C 710 " pdb=" N PHE C 711 " pdb=" CA PHE C 711 " ideal model delta sigma weight residual 121.70 127.94 -6.24 1.80e+00 3.09e-01 1.20e+01 angle pdb=" N ASN C 688 " pdb=" CA ASN C 688 " pdb=" C ASN C 688 " ideal model delta sigma weight residual 109.81 117.31 -7.50 2.21e+00 2.05e-01 1.15e+01 angle pdb=" CA GLY C 710 " pdb=" C GLY C 710 " pdb=" N PHE C 711 " ideal model delta sigma weight residual 115.50 120.35 -4.85 1.45e+00 4.76e-01 1.12e+01 angle pdb=" N PHE C 711 " pdb=" CA PHE C 711 " pdb=" C PHE C 711 " ideal model delta sigma weight residual 111.00 119.98 -8.98 2.80e+00 1.28e-01 1.03e+01 ... (remaining 11938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 4968 21.62 - 43.25: 311 43.25 - 64.87: 36 64.87 - 86.49: 13 86.49 - 108.12: 4 Dihedral angle restraints: 5332 sinusoidal: 2179 harmonic: 3153 Sorted by residual: dihedral pdb=" C5' ADP J 401 " pdb=" O5' ADP J 401 " pdb=" PA ADP J 401 " pdb=" O2A ADP J 401 " ideal model delta sinusoidal sigma weight residual -60.00 48.12 -108.12 1 2.00e+01 2.50e-03 3.15e+01 dihedral pdb=" CA ALA C 111 " pdb=" C ALA C 111 " pdb=" N TRP C 112 " pdb=" CA TRP C 112 " ideal model delta harmonic sigma weight residual 180.00 -153.24 -26.76 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA ASP J 181 " pdb=" C ASP J 181 " pdb=" N LEU J 182 " pdb=" CA LEU J 182 " ideal model delta harmonic sigma weight residual 180.00 160.70 19.30 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 5329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 942 0.047 - 0.094: 288 0.094 - 0.141: 69 0.141 - 0.188: 2 0.188 - 0.235: 1 Chirality restraints: 1302 Sorted by residual: chirality pdb=" CA ASN C 688 " pdb=" N ASN C 688 " pdb=" C ASN C 688 " pdb=" CB ASN C 688 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA PHE C 711 " pdb=" N PHE C 711 " pdb=" C PHE C 711 " pdb=" CB PHE C 711 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA PRO J 114 " pdb=" N PRO J 114 " pdb=" C PRO J 114 " pdb=" CB PRO J 114 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 1299 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 98 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO C 99 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 225 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO C 226 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 226 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 226 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 409 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C ASN C 409 " -0.026 2.00e-02 2.50e+03 pdb=" O ASN C 409 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU C 410 " 0.009 2.00e-02 2.50e+03 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.09: 2 2.09 - 2.79: 2259 2.79 - 3.49: 12294 3.49 - 4.20: 20711 4.20 - 4.90: 36440 Nonbonded interactions: 71706 Sorted by model distance: nonbonded pdb=" OD2 ASP J 27 " pdb=" OG SER C 644 " model vdw 1.384 3.040 nonbonded pdb=" N THR J 353 " pdb=" OE2 GLU C 537 " model vdw 1.995 3.120 nonbonded pdb=" O HIS C 153 " pdb=" OG SER C 156 " model vdw 2.106 3.040 nonbonded pdb=" O MET C 389 " pdb=" OG SER C 613 " model vdw 2.157 3.040 nonbonded pdb=" OD1 ASP J 159 " pdb=" O3' ADP J 401 " model vdw 2.183 3.040 ... (remaining 71701 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 11.500 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.850 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 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 : 0.006 0.058 8846 Z= 0.272 Angle : 0.694 8.983 11943 Z= 0.395 Chirality : 0.045 0.235 1302 Planarity : 0.004 0.051 1537 Dihedral : 14.309 108.115 3304 Min Nonbonded Distance : 1.384 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % 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 aren not related in a simple way. whole: -3.13 (0.22), residues: 1069 helix: -1.51 (0.21), residues: 471 sheet: -2.31 (0.43), residues: 132 loop : -2.52 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 258 TYR 0.013 0.001 TYR C 311 PHE 0.016 0.002 PHE C 253 TRP 0.016 0.002 TRP J 342 HIS 0.010 0.001 HIS C 359 Details of bonding type rmsd covalent geometry : bond 0.00613 ( 8845) covalent geometry : angle 0.69355 (11943) hydrogen bonds : bond 0.18014 ( 409) hydrogen bonds : angle 7.04546 ( 1131) Misc. bond : bond 0.00103 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 26 ASP cc_start: 0.8234 (m-30) cc_final: 0.7677 (t0) REVERT: J 113 ASN cc_start: 0.7586 (p0) cc_final: 0.7326 (p0) REVERT: J 159 ASP cc_start: 0.5642 (t70) cc_final: 0.4378 (t70) REVERT: J 218 LEU cc_start: 0.9000 (mt) cc_final: 0.8765 (tp) REVERT: J 252 ILE cc_start: 0.8076 (pt) cc_final: 0.7623 (mm) REVERT: J 300 VAL cc_start: 0.8962 (t) cc_final: 0.8207 (t) REVERT: J 347 ILE cc_start: 0.8946 (mt) cc_final: 0.8732 (mm) REVERT: C 75 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8287 (tm-30) REVERT: C 77 MET cc_start: 0.7941 (mpp) cc_final: 0.7735 (mpp) REVERT: C 113 MET cc_start: 0.7663 (mtp) cc_final: 0.7318 (mtt) REVERT: C 290 ILE cc_start: 0.9520 (mt) cc_final: 0.9304 (tp) REVERT: C 358 MET cc_start: 0.8844 (mtm) cc_final: 0.8590 (mtp) REVERT: C 363 MET cc_start: 0.9113 (mtp) cc_final: 0.8892 (tpp) REVERT: C 489 PHE cc_start: 0.9032 (t80) cc_final: 0.8798 (t80) REVERT: C 517 ASP cc_start: 0.8857 (m-30) cc_final: 0.8554 (t0) REVERT: C 547 MET cc_start: 0.9090 (tmm) cc_final: 0.8814 (tmm) REVERT: C 687 ASP cc_start: 0.8803 (m-30) cc_final: 0.8570 (m-30) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.0866 time to fit residues: 20.1801 Evaluate side-chains 105 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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-2.0-5787/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: 55.4503 > 50: distance: 43 - 48: 31.001 distance: 48 - 49: 9.942 distance: 49 - 50: 10.938 distance: 49 - 52: 4.761 distance: 50 - 51: 16.117 distance: 50 - 55: 11.416 distance: 52 - 53: 16.868 distance: 52 - 54: 10.796 distance: 55 - 56: 17.095 distance: 56 - 57: 5.022 distance: 56 - 59: 26.088 distance: 57 - 58: 10.929 distance: 57 - 67: 9.021 distance: 59 - 60: 4.893 distance: 60 - 61: 10.316 distance: 60 - 62: 44.021 distance: 61 - 63: 15.374 distance: 63 - 65: 37.468 distance: 64 - 65: 11.473 distance: 65 - 66: 10.362 distance: 67 - 68: 14.840 distance: 68 - 69: 8.264 distance: 68 - 71: 5.767 distance: 69 - 70: 6.032 distance: 69 - 75: 12.925 distance: 71 - 72: 6.825 distance: 72 - 73: 7.068 distance: 72 - 74: 12.382 distance: 75 - 76: 14.954 distance: 76 - 77: 8.355 distance: 76 - 79: 18.295 distance: 77 - 78: 9.009 distance: 77 - 80: 14.600 distance: 80 - 81: 13.724 distance: 81 - 82: 4.686 distance: 81 - 84: 20.412 distance: 82 - 83: 8.698 distance: 83 - 108: 30.751 distance: 84 - 85: 5.281 distance: 85 - 86: 10.786 distance: 86 - 87: 27.693 distance: 86 - 88: 29.032 distance: 89 - 90: 16.601 distance: 90 - 91: 6.107 distance: 90 - 93: 12.212 distance: 91 - 92: 15.656 distance: 91 - 96: 3.349 distance: 93 - 94: 11.575 distance: 93 - 95: 8.587 distance: 96 - 97: 13.035 distance: 97 - 98: 19.477 distance: 97 - 100: 16.664 distance: 98 - 99: 29.218 distance: 98 - 103: 16.057 distance: 100 - 101: 29.834 distance: 100 - 102: 28.248 distance: 103 - 104: 7.088 distance: 104 - 105: 9.787 distance: 104 - 107: 16.297 distance: 105 - 106: 21.260 distance: 105 - 108: 21.638 distance: 108 - 109: 21.388 distance: 109 - 110: 28.600 distance: 109 - 112: 12.281 distance: 110 - 111: 5.396 distance: 110 - 113: 15.392 distance: 113 - 114: 19.691 distance: 114 - 115: 32.218 distance: 114 - 117: 16.481 distance: 115 - 116: 16.358 distance: 115 - 125: 16.975 distance: 117 - 118: 9.243 distance: 118 - 119: 14.555 distance: 118 - 120: 12.275 distance: 119 - 121: 13.939 distance: 120 - 122: 13.515 distance: 121 - 123: 14.462 distance: 122 - 123: 16.225