Starting phenix.real_space_refine on Mon Apr 28 10:10:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tmw_26003/04_2025/7tmw_26003_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tmw_26003/04_2025/7tmw_26003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tmw_26003/04_2025/7tmw_26003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tmw_26003/04_2025/7tmw_26003.map" model { file = "/net/cci-nas-00/data/ceres_data/7tmw_26003/04_2025/7tmw_26003_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tmw_26003/04_2025/7tmw_26003_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.936 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 4695 2.51 5 N 1242 2.21 5 O 1334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7320 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 4075 Classifications: {'peptide': 499} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 482} Chain breaks: 7 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2273 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 54 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 2, 'TRANS': 4} Chain: "N" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 918 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 4.97, per 1000 atoms: 0.68 Number of scatterers: 7320 At special positions: 0 Unit cell: (124.02, 95.4, 92.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 1334 8.00 N 1242 7.00 C 4695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 485 " - pdb=" SG CYS R 563 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 159 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 976.5 milliseconds 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1740 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 10 sheets defined 39.6% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'R' and resid 405 through 430 Processing helix chain 'R' and resid 437 through 468 Processing helix chain 'R' and resid 475 through 482 Processing helix chain 'R' and resid 482 through 515 removed outlier: 4.131A pdb=" N GLN R 486 " --> pdb=" O SER R 482 " (cutoff:3.500A) Processing helix chain 'R' and resid 524 through 549 Proline residue: R 546 - end of helix Processing helix chain 'R' and resid 549 through 554 Processing helix chain 'R' and resid 573 through 584 removed outlier: 4.622A pdb=" N TYR R 579 " --> pdb=" O GLY R 575 " (cutoff:3.500A) Processing helix chain 'R' and resid 587 through 608 Processing helix chain 'R' and resid 624 through 653 Proline residue: R 643 - end of helix Processing helix chain 'R' and resid 658 through 668 removed outlier: 3.836A pdb=" N THR R 662 " --> pdb=" O PRO R 658 " (cutoff:3.500A) Processing helix chain 'R' and resid 671 through 681 Proline residue: R 678 - end of helix Processing helix chain 'R' and resid 685 through 699 removed outlier: 3.514A pdb=" N LYS R 689 " --> pdb=" O THR R 685 " (cutoff:3.500A) Processing helix chain 'R' and resid 1008 through 1034 Processing helix chain 'R' and resid 1047 through 1058 removed outlier: 3.636A pdb=" N ILE R1051 " --> pdb=" O GLY R1047 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL R1052 " --> pdb=" O LYS R1048 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE R1057 " --> pdb=" O LYS R1053 " (cutoff:3.500A) Processing helix chain 'R' and resid 1229 through 1233 removed outlier: 3.601A pdb=" N CYS R1232 " --> pdb=" O TRP R1229 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE R1233 " --> pdb=" O ILE R1230 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 1229 through 1233' Processing helix chain 'R' and resid 1247 through 1264 Processing helix chain 'R' and resid 1278 through 1289 Processing helix chain 'R' and resid 1292 through 1297 removed outlier: 3.849A pdb=" N TYR R1296 " --> pdb=" O LYS R1292 " (cutoff:3.500A) Processing helix chain 'R' and resid 1298 through 1303 removed outlier: 3.771A pdb=" N TYR R1303 " --> pdb=" O PHE R1300 " (cutoff:3.500A) Processing helix chain 'R' and resid 1316 through 1336 removed outlier: 3.544A pdb=" N THR R1320 " --> pdb=" O ASP R1316 " (cutoff:3.500A) Processing helix chain 'R' and resid 1355 through 1376 Processing helix chain 'N' and resid 61 through 66 removed outlier: 4.515A pdb=" N GLY N 66 " --> pdb=" O GLY N 62 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 1206 through 1209 removed outlier: 6.476A pdb=" N HIS R1036 " --> pdb=" O HIS R1215 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE R1217 " --> pdb=" O HIS R1036 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU R1038 " --> pdb=" O PHE R1217 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N ALA R1238 " --> pdb=" O THR R1035 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG R1037 " --> pdb=" O ALA R1238 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ILE R1240 " --> pdb=" O ARG R1037 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU R1039 " --> pdb=" O ILE R1240 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL R1242 " --> pdb=" O LEU R1039 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU R1041 " --> pdb=" O VAL R1242 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ASP R1244 " --> pdb=" O LEU R1041 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE R1239 " --> pdb=" O ILE R1273 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N PHE R1275 " --> pdb=" O ILE R1239 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE R1241 " --> pdb=" O PHE R1275 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASN R1277 " --> pdb=" O PHE R1241 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL R1243 " --> pdb=" O ASN R1277 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL R1272 " --> pdb=" O TYR R1345 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N HIS R1347 " --> pdb=" O VAL R1272 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU R1274 " --> pdb=" O HIS R1347 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 61 removed outlier: 3.719A pdb=" N ARG B 59 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 68 through 72 removed outlier: 7.010A pdb=" N ALA B 83 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET B 71 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL B 81 " --> pdb=" O MET B 71 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS B 88 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS B 101 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP B 93 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LYS B 99 " --> pdb=" O ASP B 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 115 removed outlier: 5.687A pdb=" N ASN B 135 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N VAL B 145 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 158 through 161 removed outlier: 3.660A pdb=" N CYS B 158 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP B 180 " --> pdb=" O GLN B 186 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLN B 186 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 197 through 202 Processing sheet with id=AA7, first strand: chain 'B' and resid 239 through 244 Processing sheet with id=AA8, first strand: chain 'B' and resid 283 through 288 removed outlier: 3.981A pdb=" N SER B 285 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASP B 308 " --> pdb=" O ARG B 314 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ARG B 314 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.700A pdb=" N THR N 69 " --> pdb=" O GLN N 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.611A pdb=" N GLU N 46 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1065 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: 2.93 Time building geometry restraints manager: 2.15 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: 2341 1.34 - 1.46: 1885 1.46 - 1.59: 3188 1.59 - 1.71: 0 1.71 - 1.83: 67 Bond restraints: 7481 Sorted by residual: bond pdb=" CG GLU R1329 " pdb=" CD GLU R1329 " ideal model delta sigma weight residual 1.516 1.470 0.046 2.50e-02 1.60e+03 3.43e+00 bond pdb=" C ILE R 642 " pdb=" N PRO R 643 " ideal model delta sigma weight residual 1.336 1.349 -0.013 1.23e-02 6.61e+03 1.18e+00 bond pdb=" CG PRO R 671 " pdb=" CD PRO R 671 " ideal model delta sigma weight residual 1.503 1.469 0.034 3.40e-02 8.65e+02 1.00e+00 bond pdb=" CB GLU R1329 " pdb=" CG GLU R1329 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.58e-01 bond pdb=" N GLU R1329 " pdb=" CA GLU R1329 " ideal model delta sigma weight residual 1.459 1.471 -0.012 1.28e-02 6.10e+03 8.79e-01 ... (remaining 7476 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 9923 2.04 - 4.09: 178 4.09 - 6.13: 30 6.13 - 8.17: 5 8.17 - 10.21: 3 Bond angle restraints: 10139 Sorted by residual: angle pdb=" N GLU R1329 " pdb=" CA GLU R1329 " pdb=" CB GLU R1329 " ideal model delta sigma weight residual 110.28 116.39 -6.11 1.55e+00 4.16e-01 1.56e+01 angle pdb=" CB ARG R1327 " pdb=" CG ARG R1327 " pdb=" CD ARG R1327 " ideal model delta sigma weight residual 111.30 119.93 -8.63 2.30e+00 1.89e-01 1.41e+01 angle pdb=" N VAL B 100 " pdb=" CA VAL B 100 " pdb=" C VAL B 100 " ideal model delta sigma weight residual 113.53 110.20 3.33 9.80e-01 1.04e+00 1.15e+01 angle pdb=" CA PRO R 546 " pdb=" N PRO R 546 " pdb=" CD PRO R 546 " ideal model delta sigma weight residual 112.00 107.34 4.66 1.40e+00 5.10e-01 1.11e+01 angle pdb=" CG ARG B 324 " pdb=" CD ARG B 324 " pdb=" NE ARG B 324 " ideal model delta sigma weight residual 112.00 118.76 -6.76 2.20e+00 2.07e-01 9.44e+00 ... (remaining 10134 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 3968 17.20 - 34.40: 359 34.40 - 51.60: 60 51.60 - 68.79: 5 68.79 - 85.99: 6 Dihedral angle restraints: 4398 sinusoidal: 1705 harmonic: 2693 Sorted by residual: dihedral pdb=" CB CYS R 485 " pdb=" SG CYS R 485 " pdb=" SG CYS R 563 " pdb=" CB CYS R 563 " ideal model delta sinusoidal sigma weight residual -86.00 -120.04 34.04 1 1.00e+01 1.00e-02 1.64e+01 dihedral pdb=" CA MET R1055 " pdb=" C MET R1055 " pdb=" N ARG R1056 " pdb=" CA ARG R1056 " ideal model delta harmonic sigma weight residual 180.00 161.93 18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA TRP B 92 " pdb=" C TRP B 92 " pdb=" N ASP B 93 " pdb=" CA ASP B 93 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 4395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 808 0.044 - 0.087: 237 0.087 - 0.131: 89 0.131 - 0.175: 9 0.175 - 0.219: 4 Chirality restraints: 1147 Sorted by residual: chirality pdb=" CA VAL N 37 " pdb=" N VAL N 37 " pdb=" C VAL N 37 " pdb=" CB VAL N 37 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL N 37 " pdb=" CA VAL N 37 " pdb=" CG1 VAL N 37 " pdb=" CG2 VAL N 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.49e-01 chirality pdb=" CG LEU B 346 " pdb=" CB LEU B 346 " pdb=" CD1 LEU B 346 " pdb=" CD2 LEU B 346 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.69e-01 ... (remaining 1144 not shown) Planarity restraints: 1277 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 664 " -0.026 2.00e-02 2.50e+03 2.83e-02 2.01e+01 pdb=" CG TRP R 664 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP R 664 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP R 664 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 664 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 664 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 664 " -0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 664 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 664 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP R 664 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 545 " 0.075 5.00e-02 4.00e+02 1.11e-01 1.98e+01 pdb=" N PRO R 546 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO R 546 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO R 546 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 109 " 0.023 2.00e-02 2.50e+03 2.08e-02 1.08e+01 pdb=" CG TRP B 109 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP B 109 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 109 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 109 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 109 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 109 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 109 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 109 " 0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP B 109 " -0.001 2.00e-02 2.50e+03 ... (remaining 1274 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 450 2.73 - 3.28: 7442 3.28 - 3.82: 12428 3.82 - 4.36: 14502 4.36 - 4.90: 25054 Nonbonded interactions: 59876 Sorted by model distance: nonbonded pdb=" OG SER B 84 " pdb=" OD1 ASP B 86 " model vdw 2.193 3.040 nonbonded pdb=" O VAL R 542 " pdb=" OH TYR R 579 " model vdw 2.250 3.040 nonbonded pdb=" OG SER B 237 " pdb=" O PRO N 100 " model vdw 2.255 3.040 nonbonded pdb=" O ALA R 543 " pdb=" OH TYR R 557 " model vdw 2.262 3.040 nonbonded pdb=" O ILE B 133 " pdb=" OG SER B 146 " model vdw 2.266 3.040 ... (remaining 59871 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: 1.910 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.330 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7485 Z= 0.157 Angle : 0.702 10.213 10147 Z= 0.382 Chirality : 0.048 0.219 1147 Planarity : 0.006 0.111 1277 Dihedral : 13.225 85.993 2646 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.27), residues: 906 helix: 1.33 (0.29), residues: 326 sheet: -0.69 (0.34), residues: 210 loop : -1.22 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.003 TRP R 664 HIS 0.003 0.001 HIS R1342 PHE 0.037 0.002 PHE R1325 TYR 0.016 0.002 TYR N 32 ARG 0.009 0.001 ARG B 160 Details of bonding type rmsd hydrogen bonds : bond 0.11046 ( 369) hydrogen bonds : angle 5.60595 ( 1065) SS BOND : bond 0.00601 ( 4) SS BOND : angle 1.51565 ( 8) covalent geometry : bond 0.00337 ( 7481) covalent geometry : angle 0.70120 (10139) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: R 447 LEU cc_start: 0.7776 (tp) cc_final: 0.7549 (tp) REVERT: R 467 LYS cc_start: 0.7077 (tptm) cc_final: 0.6724 (mttt) REVERT: R 1019 LYS cc_start: 0.7276 (mtpp) cc_final: 0.7022 (mtpp) REVERT: R 1299 GLU cc_start: 0.7579 (mp0) cc_final: 0.7346 (mp0) REVERT: B 323 ASN cc_start: 0.7941 (m-40) cc_final: 0.7732 (m-40) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.3063 time to fit residues: 62.8833 Evaluate side-chains 149 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 423 ASN R1249 ASN B 305 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.164226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.149040 restraints weight = 11068.950| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 2.51 r_work: 0.4022 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 7485 Z= 0.229 Angle : 0.649 8.705 10147 Z= 0.347 Chirality : 0.046 0.173 1147 Planarity : 0.005 0.077 1277 Dihedral : 4.843 21.127 1003 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.27 % Allowed : 11.17 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.27), residues: 906 helix: 1.11 (0.28), residues: 346 sheet: -0.81 (0.34), residues: 209 loop : -1.13 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP R 664 HIS 0.005 0.001 HIS R1342 PHE 0.025 0.002 PHE B 209 TYR 0.019 0.002 TYR N 94 ARG 0.009 0.001 ARG R1327 Details of bonding type rmsd hydrogen bonds : bond 0.04872 ( 369) hydrogen bonds : angle 5.08394 ( 1065) SS BOND : bond 0.00982 ( 4) SS BOND : angle 1.95661 ( 8) covalent geometry : bond 0.00511 ( 7481) covalent geometry : angle 0.64687 (10139) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 447 LEU cc_start: 0.8147 (tp) cc_final: 0.7902 (tp) REVERT: R 1019 LYS cc_start: 0.7454 (mtpp) cc_final: 0.7185 (mtpp) REVERT: R 1242 VAL cc_start: 0.7865 (p) cc_final: 0.7659 (t) REVERT: B 242 ILE cc_start: 0.8178 (tt) cc_final: 0.7640 (tp) REVERT: B 272 MET cc_start: 0.6669 (tpp) cc_final: 0.6396 (tpp) REVERT: B 323 ASN cc_start: 0.8118 (m-40) cc_final: 0.7717 (m-40) outliers start: 10 outliers final: 4 residues processed: 154 average time/residue: 0.4033 time to fit residues: 79.7707 Evaluate side-chains 146 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 529 ILE Chi-restraints excluded: chain R residue 1219 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain N residue 30 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.5445 > 50: distance: 27 - 116: 14.464 distance: 36 - 96: 33.584 distance: 49 - 56: 28.610 distance: 56 - 57: 11.913 distance: 57 - 58: 10.956 distance: 58 - 59: 11.436 distance: 58 - 61: 19.230 distance: 61 - 62: 11.097 distance: 61 - 67: 9.946 distance: 62 - 63: 7.467 distance: 62 - 65: 10.334 distance: 63 - 64: 4.735 distance: 63 - 68: 3.090 distance: 65 - 66: 7.365 distance: 66 - 67: 9.195 distance: 68 - 69: 8.870 distance: 69 - 70: 9.596 distance: 70 - 71: 3.110 distance: 73 - 74: 9.676 distance: 73 - 76: 12.165 distance: 74 - 75: 3.918 distance: 74 - 81: 5.314 distance: 76 - 77: 5.899 distance: 77 - 78: 21.135 distance: 78 - 79: 20.364 distance: 79 - 80: 37.885 distance: 81 - 82: 5.350 distance: 82 - 83: 12.020 distance: 83 - 84: 8.076 distance: 83 - 85: 5.137 distance: 85 - 86: 10.147 distance: 86 - 87: 4.694 distance: 86 - 89: 5.584 distance: 87 - 88: 9.711 distance: 87 - 93: 6.822 distance: 89 - 90: 12.301 distance: 90 - 91: 28.767 distance: 90 - 92: 18.786 distance: 93 - 94: 4.859 distance: 94 - 95: 12.533 distance: 94 - 97: 23.565 distance: 95 - 96: 17.468 distance: 95 - 102: 13.351 distance: 97 - 98: 8.397 distance: 98 - 99: 27.221 distance: 99 - 100: 6.031 distance: 99 - 101: 8.153 distance: 102 - 103: 12.147 distance: 103 - 104: 13.242 distance: 103 - 106: 22.583 distance: 104 - 105: 13.221 distance: 104 - 116: 21.586 distance: 106 - 107: 20.039 distance: 107 - 108: 5.901 distance: 107 - 109: 10.144 distance: 108 - 110: 4.109 distance: 109 - 111: 3.595 distance: 109 - 112: 11.114 distance: 110 - 111: 5.375 distance: 111 - 113: 7.549 distance: 112 - 114: 10.124 distance: 113 - 115: 12.501 distance: 114 - 115: 3.526 distance: 116 - 117: 23.178 distance: 117 - 118: 12.870 distance: 117 - 120: 21.478 distance: 118 - 119: 30.513 distance: 118 - 123: 13.296 distance: 120 - 121: 15.261 distance: 120 - 122: 11.089 distance: 123 - 124: 10.404 distance: 124 - 125: 7.528 distance: 124 - 127: 11.142 distance: 125 - 126: 9.541 distance: 125 - 129: 12.038 distance: 127 - 128: 6.512