Starting phenix.real_space_refine on Fri Aug 22 21:57:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z29_14458/08_2025/7z29_14458.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z29_14458/08_2025/7z29_14458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z29_14458/08_2025/7z29_14458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z29_14458/08_2025/7z29_14458.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z29_14458/08_2025/7z29_14458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z29_14458/08_2025/7z29_14458.map" } resolution = 3.38 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= 0.022 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 35 5.49 5 S 12 5.16 5 C 5264 2.51 5 N 1388 2.21 5 O 1608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 8307 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4268 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 494} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3298 Classifications: {'peptide': 405} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 30, 'TRANS': 374} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 721 Classifications: {'DNA': 34, 'RNA': 2} Modifications used: {'5*END': 1, 'rna3p': 2} Link IDs: {'rna3p': 35} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan': 1, ' DA%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'NVP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.70, per 1000 atoms: 0.20 Number of scatterers: 8307 At special positions: 0 Unit cell: (98.94, 109.61, 95.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 35 15.00 O 1608 8.00 N 1388 7.00 C 5264 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: 0.64 Conformation dependent library (CDL) restraints added in 226.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1766 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 38.8% alpha, 15.2% beta 13 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 30 through 44 removed outlier: 3.892A pdb=" N LEU A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 121 through 128 removed outlier: 3.969A pdb=" N LYS A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.516A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 296 through 311 Processing helix chain 'A' and resid 363 through 383 Processing helix chain 'A' and resid 394 through 404 removed outlier: 3.734A pdb=" N GLU A 404 " --> pdb=" O THR A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 removed outlier: 4.220A pdb=" N ILE A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.604A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.740A pdb=" N ASN A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.713A pdb=" N VAL A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP A 549 " --> pdb=" O ASN A 545 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 551 " --> pdb=" O GLN A 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 43 removed outlier: 4.121A pdb=" N LEU B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 89 removed outlier: 5.543A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 103 removed outlier: 3.527A pdb=" N LYS B 101 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 102 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS B 103 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.852A pdb=" N LYS B 126 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.641A pdb=" N ASN B 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 138 " --> pdb=" O ILE B 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 134 through 138' Processing helix chain 'B' and resid 154 through 175 removed outlier: 4.081A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 212 removed outlier: 3.802A pdb=" N THR B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.525A pdb=" N TRP B 239 " --> pdb=" O PRO B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 271 removed outlier: 4.186A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE B 270 " --> pdb=" O TRP B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 403 through 406 removed outlier: 3.568A pdb=" N TRP B 406 " --> pdb=" O THR B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 406' Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 131 Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 354 removed outlier: 7.228A pdb=" N LYS A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN A 343 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR A 351 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TYR A 339 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS A 353 " --> pdb=" O TRP A 337 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP A 337 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 340 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A 328 " --> pdb=" O GLN A 340 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A 390 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE A 389 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.706A pdb=" N THR A 362 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 512 " --> pdb=" O THR A 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 464 through 470 removed outlier: 3.968A pdb=" N GLY A 456 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 443 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU A 438 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 493 " --> pdb=" O LYS A 530 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AA8, first strand: chain 'B' and resid 61 through 64 Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 183 removed outlier: 3.582A pdb=" N SER B 191 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 105 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 252 through 253 removed outlier: 4.305A pdb=" N TRP B 252 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 347 through 348 removed outlier: 4.139A pdb=" N GLU B 344 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 339 " --> pdb=" O GLY B 352 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 347 through 348 removed outlier: 4.139A pdb=" N GLU B 344 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA B 327 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) 287 hydrogen bonds defined for protein. 798 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 0.88 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1309 1.31 - 1.44: 2388 1.44 - 1.56: 4808 1.56 - 1.68: 69 1.68 - 1.81: 21 Bond restraints: 8595 Sorted by residual: bond pdb=" CA LYS B 138 " pdb=" C LYS B 138 " ideal model delta sigma weight residual 1.523 1.472 0.052 1.30e-02 5.92e+03 1.58e+01 bond pdb=" N ILE B 132 " pdb=" CA ILE B 132 " ideal model delta sigma weight residual 1.460 1.489 -0.029 7.50e-03 1.78e+04 1.52e+01 bond pdb=" CA LEU A 260 " pdb=" C LEU A 260 " ideal model delta sigma weight residual 1.524 1.481 0.042 1.26e-02 6.30e+03 1.13e+01 bond pdb=" C4' DG E 19 " pdb=" O4' DG E 19 " ideal model delta sigma weight residual 1.450 1.515 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O3' DC E 3 " pdb=" P OMC E 4 " ideal model delta sigma weight residual 1.607 1.558 0.049 1.50e-02 4.44e+03 1.05e+01 ... (remaining 8590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 11646 2.85 - 5.70: 177 5.70 - 8.55: 18 8.55 - 11.40: 1 11.40 - 14.25: 2 Bond angle restraints: 11844 Sorted by residual: angle pdb=" C5' DG E 19 " pdb=" C4' DG E 19 " pdb=" O4' DG E 19 " ideal model delta sigma weight residual 109.40 121.13 -11.73 1.50e+00 4.44e-01 6.12e+01 angle pdb=" N PRO A 412 " pdb=" CA PRO A 412 " pdb=" C PRO A 412 " ideal model delta sigma weight residual 112.47 126.72 -14.25 2.06e+00 2.36e-01 4.79e+01 angle pdb=" C5' DC E 3 " pdb=" C4' DC E 3 " pdb=" O4' DC E 3 " ideal model delta sigma weight residual 109.40 119.40 -10.00 1.50e+00 4.44e-01 4.45e+01 angle pdb=" CA GLY B 333 " pdb=" C GLY B 333 " pdb=" O GLY B 333 " ideal model delta sigma weight residual 122.24 117.62 4.62 8.70e-01 1.32e+00 2.82e+01 angle pdb=" C THR B 131 " pdb=" N ILE B 132 " pdb=" CA ILE B 132 " ideal model delta sigma weight residual 122.59 118.81 3.78 7.20e-01 1.93e+00 2.76e+01 ... (remaining 11839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4309 17.69 - 35.38: 544 35.38 - 53.07: 126 53.07 - 70.76: 45 70.76 - 88.46: 10 Dihedral angle restraints: 5034 sinusoidal: 2301 harmonic: 2733 Sorted by residual: dihedral pdb=" C TYR A 183 " pdb=" N TYR A 183 " pdb=" CA TYR A 183 " pdb=" CB TYR A 183 " ideal model delta harmonic sigma weight residual -122.60 -111.33 -11.27 0 2.50e+00 1.60e-01 2.03e+01 dihedral pdb=" C LYS B 424 " pdb=" N LYS B 424 " pdb=" CA LYS B 424 " pdb=" CB LYS B 424 " ideal model delta harmonic sigma weight residual -122.60 -133.72 11.12 0 2.50e+00 1.60e-01 1.98e+01 dihedral pdb=" CA GLU B 44 " pdb=" C GLU B 44 " pdb=" N GLY B 45 " pdb=" CA GLY B 45 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 5031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1110 0.074 - 0.148: 150 0.148 - 0.222: 28 0.222 - 0.297: 10 0.297 - 0.371: 6 Chirality restraints: 1304 Sorted by residual: chirality pdb=" CA GLU B 415 " pdb=" N GLU B 415 " pdb=" C GLU B 415 " pdb=" CB GLU B 415 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA TYR A 183 " pdb=" N TYR A 183 " pdb=" C TYR A 183 " pdb=" CB TYR A 183 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA LYS B 101 " pdb=" N LYS B 101 " pdb=" C LYS B 101 " pdb=" CB LYS B 101 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 1301 not shown) Planarity restraints: 1371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 307 " 0.465 9.50e-02 1.11e+02 2.09e-01 2.66e+01 pdb=" NE ARG A 307 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 307 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 307 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 307 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 156 " 0.059 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO B 157 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 130 " 0.018 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C PHE B 130 " -0.060 2.00e-02 2.50e+03 pdb=" O PHE B 130 " 0.022 2.00e-02 2.50e+03 pdb=" N THR B 131 " 0.020 2.00e-02 2.50e+03 ... (remaining 1368 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2406 2.82 - 3.34: 7260 3.34 - 3.86: 13458 3.86 - 4.38: 15856 4.38 - 4.90: 26301 Nonbonded interactions: 65281 Sorted by model distance: nonbonded pdb=" O LYS B 323 " pdb=" NZ LYS B 385 " model vdw 2.304 3.120 nonbonded pdb=" OH TYR A 457 " pdb=" OD2 ASP A 488 " model vdw 2.361 3.040 nonbonded pdb=" NZ LYS A 104 " pdb=" O LEU A 193 " model vdw 2.364 3.120 nonbonded pdb=" OD1 ASP B 17 " pdb=" N GLY B 18 " model vdw 2.369 3.120 nonbonded pdb=" OE1 GLN A 547 " pdb=" OG1 THR B 286 " model vdw 2.372 3.040 ... (remaining 65276 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 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: 0.110 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.740 Find NCS groups from input model: 0.020 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8595 Z= 0.322 Angle : 0.836 14.254 11844 Z= 0.523 Chirality : 0.061 0.371 1304 Planarity : 0.008 0.209 1371 Dihedral : 17.032 88.455 3268 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.04 % Favored : 96.85 % Rotamer: Outliers : 1.96 % Allowed : 1.96 % Favored : 96.09 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 3.08 % 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 aren not related in a simple way. whole: -0.47 (0.28), residues: 921 helix: 0.95 (0.31), residues: 325 sheet: -1.19 (0.39), residues: 171 loop : -0.85 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 284 TYR 0.030 0.002 TYR A 319 PHE 0.007 0.001 PHE A 389 TRP 0.029 0.002 TRP A 402 HIS 0.003 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 8595) covalent geometry : angle 0.83599 (11844) hydrogen bonds : bond 0.13815 ( 322) hydrogen bonds : angle 6.32394 ( 870) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.310 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 132 average time/residue: 0.0825 time to fit residues: 15.3482 Evaluate side-chains 99 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.211243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.166892 restraints weight = 8842.640| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.83 r_work: 0.3676 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8595 Z= 0.168 Angle : 0.603 7.446 11844 Z= 0.317 Chirality : 0.044 0.240 1304 Planarity : 0.005 0.057 1371 Dihedral : 16.094 78.990 1365 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.47 % Favored : 96.31 % Rotamer: Outliers : 0.86 % Allowed : 9.90 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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 aren not related in a simple way. whole: -0.51 (0.27), residues: 921 helix: 0.96 (0.30), residues: 327 sheet: -1.11 (0.39), residues: 172 loop : -0.97 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 358 TYR 0.019 0.002 TYR A 339 PHE 0.008 0.001 PHE B 416 TRP 0.017 0.002 TRP A 406 HIS 0.003 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 8595) covalent geometry : angle 0.60291 (11844) hydrogen bonds : bond 0.04190 ( 322) hydrogen bonds : angle 4.31451 ( 870) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8036 (pt0) cc_final: 0.7657 (pt0) REVERT: B 102 LYS cc_start: 0.7378 (mppt) cc_final: 0.6724 (mppt) REVERT: B 382 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.7931 (mp) outliers start: 7 outliers final: 5 residues processed: 99 average time/residue: 0.0740 time to fit residues: 10.4557 Evaluate side-chains 99 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 43 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 73 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 chunk 8 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN A 547 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.205125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.160790 restraints weight = 8844.423| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.80 r_work: 0.3640 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8595 Z= 0.218 Angle : 0.638 7.076 11844 Z= 0.334 Chirality : 0.046 0.215 1304 Planarity : 0.005 0.052 1371 Dihedral : 16.215 77.861 1364 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.02 % Favored : 95.87 % Rotamer: Outliers : 2.08 % Allowed : 13.08 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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 aren not related in a simple way. whole: -0.80 (0.27), residues: 921 helix: 0.70 (0.29), residues: 324 sheet: -1.18 (0.40), residues: 162 loop : -1.18 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 358 TYR 0.021 0.002 TYR A 339 PHE 0.010 0.002 PHE B 130 TRP 0.017 0.002 TRP A 402 HIS 0.004 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00520 ( 8595) covalent geometry : angle 0.63808 (11844) hydrogen bonds : bond 0.04471 ( 322) hydrogen bonds : angle 4.33005 ( 870) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8193 (pt0) cc_final: 0.7867 (pt0) REVERT: A 281 LYS cc_start: 0.8213 (ttmt) cc_final: 0.7819 (tttt) REVERT: B 102 LYS cc_start: 0.7372 (mppt) cc_final: 0.6785 (mppt) REVERT: B 382 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8019 (mp) outliers start: 17 outliers final: 13 residues processed: 111 average time/residue: 0.0788 time to fit residues: 12.3271 Evaluate side-chains 101 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 32 optimal weight: 0.0770 chunk 73 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN A 480 GLN B 363 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.210021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.165318 restraints weight = 8830.713| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.83 r_work: 0.3685 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8595 Z= 0.151 Angle : 0.565 6.861 11844 Z= 0.295 Chirality : 0.043 0.148 1304 Planarity : 0.004 0.050 1371 Dihedral : 15.928 78.189 1364 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.74 % Rotamer: Outliers : 2.32 % Allowed : 15.40 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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 aren not related in a simple way. whole: -0.60 (0.27), residues: 921 helix: 0.96 (0.29), residues: 324 sheet: -1.33 (0.39), residues: 175 loop : -0.99 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 125 TYR 0.017 0.002 TYR A 339 PHE 0.006 0.001 PHE B 416 TRP 0.016 0.002 TRP A 402 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8595) covalent geometry : angle 0.56476 (11844) hydrogen bonds : bond 0.03603 ( 322) hydrogen bonds : angle 4.08152 ( 870) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8150 (pt0) cc_final: 0.7794 (pt0) REVERT: B 102 LYS cc_start: 0.7235 (mppt) cc_final: 0.6864 (mppt) REVERT: B 203 GLU cc_start: 0.7404 (pp20) cc_final: 0.7153 (pp20) REVERT: B 382 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.7931 (mp) outliers start: 19 outliers final: 11 residues processed: 113 average time/residue: 0.0868 time to fit residues: 13.8946 Evaluate side-chains 105 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 88 optimal weight: 8.9990 chunk 78 optimal weight: 0.5980 chunk 42 optimal weight: 40.0000 chunk 73 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN B 363 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.206175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.161473 restraints weight = 8815.975| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.80 r_work: 0.3664 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8595 Z= 0.181 Angle : 0.593 7.104 11844 Z= 0.308 Chirality : 0.044 0.234 1304 Planarity : 0.005 0.051 1371 Dihedral : 15.848 77.232 1364 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.34 % Favored : 95.55 % Rotamer: Outliers : 2.93 % Allowed : 16.50 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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 aren not related in a simple way. whole: -0.74 (0.27), residues: 921 helix: 0.84 (0.29), residues: 328 sheet: -1.44 (0.39), residues: 175 loop : -1.08 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 358 TYR 0.020 0.002 TYR A 339 PHE 0.008 0.001 PHE B 130 TRP 0.017 0.002 TRP A 402 HIS 0.003 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8595) covalent geometry : angle 0.59311 (11844) hydrogen bonds : bond 0.03949 ( 322) hydrogen bonds : angle 4.12910 ( 870) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.269 Fit side-chains REVERT: A 182 GLN cc_start: 0.8154 (pt0) cc_final: 0.7836 (pt0) REVERT: A 281 LYS cc_start: 0.8149 (ttmt) cc_final: 0.7712 (tttt) REVERT: B 203 GLU cc_start: 0.7499 (pp20) cc_final: 0.7239 (pp20) REVERT: B 382 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.7973 (mp) outliers start: 24 outliers final: 19 residues processed: 119 average time/residue: 0.0900 time to fit residues: 15.0703 Evaluate side-chains 115 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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: 59.845 > 50: distance: 34 - 39: 23.213 distance: 39 - 40: 13.824 distance: 40 - 41: 8.402 distance: 40 - 43: 4.395 distance: 41 - 42: 11.790 distance: 41 - 47: 20.857 distance: 43 - 44: 29.287 distance: 47 - 48: 19.704 distance: 48 - 49: 19.437 distance: 48 - 51: 33.990 distance: 49 - 50: 20.722 distance: 49 - 54: 17.741 distance: 51 - 52: 6.254 distance: 51 - 53: 29.553 distance: 54 - 55: 13.250 distance: 54 - 60: 19.001 distance: 55 - 56: 9.600 distance: 55 - 58: 32.495 distance: 56 - 57: 9.442 distance: 56 - 61: 26.972 distance: 58 - 59: 7.874 distance: 59 - 60: 27.699 distance: 61 - 62: 20.377 distance: 62 - 63: 18.980 distance: 62 - 65: 23.396 distance: 63 - 64: 25.435 distance: 63 - 66: 17.613 distance: 66 - 67: 5.900 distance: 67 - 68: 32.142 distance: 67 - 70: 12.337 distance: 68 - 77: 20.929 distance: 70 - 71: 4.000 distance: 71 - 72: 8.544 distance: 72 - 74: 3.330 distance: 73 - 75: 6.994 distance: 74 - 76: 4.240 distance: 75 - 76: 6.987 distance: 77 - 78: 22.437 distance: 78 - 79: 18.193 distance: 78 - 81: 15.933 distance: 79 - 80: 16.685 distance: 79 - 82: 15.833 distance: 82 - 83: 17.827 distance: 83 - 84: 14.349 distance: 83 - 86: 17.000 distance: 84 - 88: 26.299 distance: 86 - 87: 21.839 distance: 88 - 89: 5.414 distance: 89 - 90: 18.495 distance: 89 - 92: 21.745 distance: 90 - 91: 22.736 distance: 93 - 94: 13.669 distance: 94 - 95: 18.231 distance: 94 - 97: 20.080 distance: 95 - 96: 21.719 distance: 95 - 101: 28.279 distance: 97 - 98: 24.978 distance: 98 - 99: 7.988 distance: 98 - 100: 19.785 distance: 101 - 102: 15.316 distance: 102 - 103: 11.203 distance: 102 - 105: 7.959 distance: 103 - 104: 12.076 distance: 103 - 108: 21.881 distance: 105 - 106: 33.368 distance: 105 - 107: 21.764