Starting phenix.real_space_refine on Sun Aug 4 07:52:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/08_2024/6pza_20530_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/08_2024/6pza_20530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/08_2024/6pza_20530.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/08_2024/6pza_20530.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/08_2024/6pza_20530_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/08_2024/6pza_20530_neut.cif" } resolution = 3.74 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 ------------------------------------------------------------------------------- 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= 0.004 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 34 5.16 5 Cl 1 4.86 5 C 6209 2.51 5 N 1717 2.21 5 O 1695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 16": "NH1" <-> "NH2" Residue "C TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 258": "NH1" <-> "NH2" Residue "C ARG 285": "NH1" <-> "NH2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C ARG 298": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 598": "NH1" <-> "NH2" Residue "C ARG 702": "NH1" <-> "NH2" Residue "C ARG 837": "NH1" <-> "NH2" Residue "C ARG 1104": "NH1" <-> "NH2" Residue "C ARG 1218": "NH1" <-> "NH2" Residue "C ARG 1300": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9659 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 9501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1422, 9501 Classifications: {'peptide': 1422} Incomplete info: {'truncation_to_alanine': 543} Link IDs: {'CIS': 1, 'PTRANS': 48, 'TRANS': 1372} Chain breaks: 4 Unresolved non-hydrogen bonds: 1768 Unresolved non-hydrogen angles: 2233 Unresolved non-hydrogen dihedrals: 1378 Unresolved non-hydrogen chiralities: 225 Planarities with less than four sites: {'GLN:plan1': 32, 'ASP:plan': 41, 'TYR:plan': 2, 'ASN:plan1': 21, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 44, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 833 Chain: "D" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 94 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 17} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'ATP': 1, 'GBM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.01, per 1000 atoms: 0.62 Number of scatterers: 9659 At special positions: 0 Unit cell: (96.615, 110.295, 140.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 P 3 15.00 O 1695 8.00 N 1717 7.00 C 6209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 26 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.10 Conformation dependent library (CDL) restraints added in 2.1 seconds 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2730 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 8 sheets defined 66.3% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'C' and resid 12 through 16 removed outlier: 3.613A pdb=" N ARG C 16 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 55 removed outlier: 3.885A pdb=" N VAL C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) Proline residue: C 35 - end of helix Proline residue: C 45 - end of helix Processing helix chain 'C' and resid 58 through 63 removed outlier: 3.604A pdb=" N HIS C 61 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N HIS C 62 " --> pdb=" O HIS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 97 Processing helix chain 'C' and resid 108 through 130 removed outlier: 3.599A pdb=" N TYR C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER C 130 " --> pdb=" O ASN C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 135 Processing helix chain 'C' and resid 136 through 160 Processing helix chain 'C' and resid 166 through 194 removed outlier: 3.993A pdb=" N CYS C 170 " --> pdb=" O GLN C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 223 through 230 Processing helix chain 'C' and resid 232 through 238 removed outlier: 4.019A pdb=" N PHE C 236 " --> pdb=" O TRP C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 242 Processing helix chain 'C' and resid 254 through 257 Processing helix chain 'C' and resid 258 through 277 Processing helix chain 'C' and resid 283 through 314 removed outlier: 5.732A pdb=" N ARG C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ARG C 298 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 329 through 332 removed outlier: 3.897A pdb=" N HIS C 332 " --> pdb=" O LYS C 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 329 through 332' Processing helix chain 'C' and resid 347 through 352 Processing helix chain 'C' and resid 355 through 398 removed outlier: 3.505A pdb=" N LEU C 368 " --> pdb=" O LEU C 364 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLN C 374 " --> pdb=" O ARG C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 432 removed outlier: 3.510A pdb=" N ILE C 417 " --> pdb=" O THR C 413 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP C 424 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR C 425 " --> pdb=" O VAL C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 456 Proline residue: C 442 - end of helix Processing helix chain 'C' and resid 457 through 468 removed outlier: 3.662A pdb=" N LEU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 504 removed outlier: 3.539A pdb=" N GLN C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU C 494 " --> pdb=" O GLU C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 512 removed outlier: 3.703A pdb=" N TYR C 512 " --> pdb=" O LEU C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 564 removed outlier: 4.277A pdb=" N THR C 525 " --> pdb=" O ARG C 521 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER C 543 " --> pdb=" O TYR C 539 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 544 " --> pdb=" O THR C 540 " (cutoff:3.500A) Proline residue: C 551 - end of helix Processing helix chain 'C' and resid 572 through 615 Proline residue: C 589 - end of helix removed outlier: 3.972A pdb=" N LEU C 592 " --> pdb=" O THR C 588 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 594 " --> pdb=" O LEU C 590 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 595 " --> pdb=" O PHE C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 727 Processing helix chain 'C' and resid 785 through 790 Processing helix chain 'C' and resid 795 through 806 Processing helix chain 'C' and resid 808 through 815 removed outlier: 3.870A pdb=" N LEU C 815 " --> pdb=" O ASP C 811 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 846 removed outlier: 3.698A pdb=" N GLN C 846 " --> pdb=" O ARG C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 879 Processing helix chain 'C' and resid 996 through 1009 removed outlier: 3.602A pdb=" N GLY C1009 " --> pdb=" O LEU C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1009 through 1043 removed outlier: 4.494A pdb=" N LEU C1015 " --> pdb=" O LEU C1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 1061 through 1107 removed outlier: 3.906A pdb=" N LEU C1074 " --> pdb=" O LEU C1070 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU C1087 " --> pdb=" O SER C1083 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1116 removed outlier: 4.033A pdb=" N PHE C1113 " --> pdb=" O PRO C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1117 through 1135 removed outlier: 3.716A pdb=" N ILE C1121 " --> pdb=" O PRO C1117 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASP C1128 " --> pdb=" O ARG C1124 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS C1135 " --> pdb=" O THR C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1135 through 1161 removed outlier: 4.000A pdb=" N LEU C1148 " --> pdb=" O SER C1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 1163 through 1210 removed outlier: 3.744A pdb=" N ALA C1167 " --> pdb=" O VAL C1163 " (cutoff:3.500A) Proline residue: C1170 - end of helix removed outlier: 3.720A pdb=" N ASP C1188 " --> pdb=" O VAL C1184 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C1196 " --> pdb=" O LEU C1192 " (cutoff:3.500A) Proline residue: C1199 - end of helix removed outlier: 3.587A pdb=" N VAL C1208 " --> pdb=" O PHE C1204 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY C1210 " --> pdb=" O GLU C1206 " (cutoff:3.500A) Processing helix chain 'C' and resid 1210 through 1218 removed outlier: 3.769A pdb=" N ILE C1214 " --> pdb=" O GLY C1210 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG C1218 " --> pdb=" O ILE C1214 " (cutoff:3.500A) Processing helix chain 'C' and resid 1219 through 1273 removed outlier: 3.927A pdb=" N PHE C1223 " --> pdb=" O TYR C1219 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C1237 " --> pdb=" O SER C1233 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS C1273 " --> pdb=" O SER C1269 " (cutoff:3.500A) Processing helix chain 'C' and resid 1278 through 1292 removed outlier: 3.522A pdb=" N GLY C1282 " --> pdb=" O ALA C1278 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR C1287 " --> pdb=" O LEU C1283 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N MET C1290 " --> pdb=" O THR C1286 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER C1292 " --> pdb=" O ALA C1288 " (cutoff:3.500A) Processing helix chain 'C' and resid 1294 through 1320 removed outlier: 3.806A pdb=" N ALA C1311 " --> pdb=" O ILE C1307 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL C1312 " --> pdb=" O GLN C1308 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE C1315 " --> pdb=" O ALA C1311 " (cutoff:3.500A) Processing helix chain 'C' and resid 1385 through 1392 Processing helix chain 'C' and resid 1414 through 1419 Processing helix chain 'C' and resid 1435 through 1441 Processing helix chain 'C' and resid 1447 through 1458 removed outlier: 3.596A pdb=" N LEU C1451 " --> pdb=" O SER C1447 " (cutoff:3.500A) Processing helix chain 'C' and resid 1460 through 1465 Processing helix chain 'C' and resid 1484 through 1498 removed outlier: 4.140A pdb=" N GLN C1488 " --> pdb=" O GLN C1484 " (cutoff:3.500A) Processing helix chain 'C' and resid 1512 through 1531 Processing helix chain 'C' and resid 1539 through 1543 removed outlier: 3.525A pdb=" N ILE C1543 " --> pdb=" O VAL C1540 " (cutoff:3.500A) Processing helix chain 'C' and resid 1564 through 1570 removed outlier: 4.193A pdb=" N SER C1568 " --> pdb=" O GLU C1564 " (cutoff:3.500A) Processing helix chain 'C' and resid 1571 through 1578 Processing sheet with id=AA1, first strand: chain 'C' and resid 338 through 340 removed outlier: 4.227A pdb=" N THR C 338 " --> pdb=" O PHE C 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AA3, first strand: chain 'C' and resid 852 through 853 removed outlier: 4.264A pdb=" N ILE C 901 " --> pdb=" O MET C 710 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 712 " --> pdb=" O ILE C 901 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ALA C 902 " --> pdb=" O GLN C 909 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 1366 through 1368 removed outlier: 4.391A pdb=" N GLN C1346 " --> pdb=" O ILE C1404 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C1404 " --> pdb=" O GLN C1346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 1352 through 1353 Processing sheet with id=AA6, first strand: chain 'C' and resid 1375 through 1376 Processing sheet with id=AA7, first strand: chain 'C' and resid 1422 through 1424 removed outlier: 6.898A pdb=" N SER C1423 " --> pdb=" O ILE C1504 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 1549 through 1551 698 hydrogen bonds defined for protein. 2052 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: 3.81 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1543 1.31 - 1.43: 2702 1.43 - 1.56: 5567 1.56 - 1.68: 7 1.68 - 1.81: 53 Bond restraints: 9872 Sorted by residual: bond pdb=" O5 GBM C1601 " pdb=" S2 GBM C1601 " ideal model delta sigma weight residual 1.448 1.648 -0.200 2.00e-02 2.50e+03 9.97e+01 bond pdb=" O4 GBM C1601 " pdb=" S2 GBM C1601 " ideal model delta sigma weight residual 1.453 1.647 -0.194 2.00e-02 2.50e+03 9.43e+01 bond pdb=" C4 ATP C1602 " pdb=" C5 ATP C1602 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.26e+01 bond pdb=" C5 ATP C1602 " pdb=" C6 ATP C1602 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.31e+01 bond pdb=" C17 GBM C1601 " pdb=" N8 GBM C1601 " ideal model delta sigma weight residual 1.340 1.443 -0.103 2.00e-02 2.50e+03 2.65e+01 ... (remaining 9867 not shown) Histogram of bond angle deviations from ideal: 98.60 - 106.00: 216 106.00 - 113.41: 5478 113.41 - 120.81: 4781 120.81 - 128.22: 3000 128.22 - 135.62: 101 Bond angle restraints: 13576 Sorted by residual: angle pdb=" PB ATP C1602 " pdb=" O3B ATP C1602 " pdb=" PG ATP C1602 " ideal model delta sigma weight residual 139.87 117.67 22.20 1.00e+00 1.00e+00 4.93e+02 angle pdb=" PA ATP C1602 " pdb=" O3A ATP C1602 " pdb=" PB ATP C1602 " ideal model delta sigma weight residual 136.83 117.58 19.25 1.00e+00 1.00e+00 3.70e+02 angle pdb=" C5 ATP C1602 " pdb=" C4 ATP C1602 " pdb=" N3 ATP C1602 " ideal model delta sigma weight residual 126.80 119.13 7.67 1.00e+00 1.00e+00 5.88e+01 angle pdb=" C LEU C 571 " pdb=" N SER C 572 " pdb=" CA SER C 572 " ideal model delta sigma weight residual 121.70 134.37 -12.67 1.80e+00 3.09e-01 4.95e+01 angle pdb=" N3 ATP C1602 " pdb=" C4 ATP C1602 " pdb=" N9 ATP C1602 " ideal model delta sigma weight residual 127.04 135.10 -8.06 1.15e+00 7.59e-01 4.93e+01 ... (remaining 13571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 5444 16.79 - 33.58: 219 33.58 - 50.37: 47 50.37 - 67.16: 6 67.16 - 83.95: 5 Dihedral angle restraints: 5721 sinusoidal: 1521 harmonic: 4200 Sorted by residual: dihedral pdb=" CA LYS C 252 " pdb=" C LYS C 252 " pdb=" N LEU C 253 " pdb=" CA LEU C 253 " ideal model delta harmonic sigma weight residual 180.00 132.03 47.97 0 5.00e+00 4.00e-02 9.20e+01 dihedral pdb=" CA ILE C 996 " pdb=" C ILE C 996 " pdb=" N PRO C 997 " pdb=" CA PRO C 997 " ideal model delta harmonic sigma weight residual -180.00 -137.86 -42.14 0 5.00e+00 4.00e-02 7.10e+01 dihedral pdb=" CA LYS C1562 " pdb=" C LYS C1562 " pdb=" N PRO C1563 " pdb=" CA PRO C1563 " ideal model delta harmonic sigma weight residual 180.00 151.85 28.15 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 5718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1144 0.056 - 0.111: 416 0.111 - 0.167: 75 0.167 - 0.222: 7 0.222 - 0.278: 4 Chirality restraints: 1646 Sorted by residual: chirality pdb=" CG LEU C1248 " pdb=" CB LEU C1248 " pdb=" CD1 LEU C1248 " pdb=" CD2 LEU C1248 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA LEU C 175 " pdb=" N LEU C 175 " pdb=" C LEU C 175 " pdb=" CB LEU C 175 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C1' ATP C1602 " pdb=" C2' ATP C1602 " pdb=" N9 ATP C1602 " pdb=" O4' ATP C1602 " both_signs ideal model delta sigma weight residual False 2.41 2.64 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1643 not shown) Planarity restraints: 1752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 420 " -0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C LEU C 420 " 0.058 2.00e-02 2.50e+03 pdb=" O LEU C 420 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL C 421 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET C 441 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO C 442 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 442 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 442 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1037 " 0.023 2.00e-02 2.50e+03 1.62e-02 6.53e+00 pdb=" CG TRP C1037 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP C1037 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP C1037 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C1037 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C1037 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C1037 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1037 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1037 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C1037 " 0.000 2.00e-02 2.50e+03 ... (remaining 1749 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2259 2.78 - 3.31: 9152 3.31 - 3.84: 15453 3.84 - 4.37: 16243 4.37 - 4.90: 28403 Nonbonded interactions: 71510 Sorted by model distance: nonbonded pdb=" OH TYR C 123 " pdb=" O LEU C 135 " model vdw 2.252 3.040 nonbonded pdb=" OD2 ASP C1128 " pdb=" NH1 ARG C1314 " model vdw 2.271 3.120 nonbonded pdb=" O GLU C 791 " pdb=" OH TYR C1219 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR C 338 " pdb=" O PHE C 345 " model vdw 2.291 3.040 nonbonded pdb=" O THR C 789 " pdb=" OG SER C 792 " model vdw 2.308 3.040 ... (remaining 71505 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: 0.670 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 31.710 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5080 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.200 9872 Z= 0.558 Angle : 1.063 22.204 13576 Z= 0.612 Chirality : 0.058 0.278 1646 Planarity : 0.008 0.065 1752 Dihedral : 11.133 83.951 2988 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % Twisted General : 0.07 % 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: -4.29 (0.17), residues: 1429 helix: -2.33 (0.12), residues: 915 sheet: -3.78 (0.52), residues: 60 loop : -3.46 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP C1037 HIS 0.012 0.002 HIS C1098 PHE 0.040 0.003 PHE C 432 TYR 0.033 0.003 TYR C 179 ARG 0.014 0.002 ARG C1145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: C 112 MET cc_start: 0.6739 (mtm) cc_final: 0.6412 (mtp) REVERT: C 301 LEU cc_start: 0.6998 (tp) cc_final: 0.6398 (tt) REVERT: C 393 THR cc_start: 0.5310 (m) cc_final: 0.5049 (t) REVERT: C 1163 VAL cc_start: 0.6894 (t) cc_final: 0.6651 (t) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.2206 time to fit residues: 68.2020 Evaluate side-chains 143 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 50.0000 chunk 108 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 50.0000 chunk 57 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 0.0070 chunk 83 optimal weight: 50.0000 chunk 129 optimal weight: 50.0000 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 160 HIS C 219 GLN C 374 GLN C 397 ASN C 707 GLN C 896 HIS ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5540 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9872 Z= 0.212 Angle : 0.698 9.082 13576 Z= 0.362 Chirality : 0.044 0.243 1646 Planarity : 0.006 0.062 1752 Dihedral : 6.890 73.229 1561 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.03 % Allowed : 12.25 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % Twisted General : 0.07 % 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: -1.86 (0.21), residues: 1429 helix: -0.14 (0.16), residues: 924 sheet: -3.56 (0.53), residues: 64 loop : -3.16 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 65 HIS 0.005 0.001 HIS C 867 PHE 0.022 0.002 PHE C 432 TYR 0.032 0.002 TYR C 123 ARG 0.007 0.001 ARG C 826 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 174 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6911 (tm) REVERT: C 263 TYR cc_start: 0.6727 (t80) cc_final: 0.6482 (t80) outliers start: 28 outliers final: 11 residues processed: 191 average time/residue: 0.1857 time to fit residues: 51.8106 Evaluate side-chains 156 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1192 LEU Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1242 THR Chi-restraints excluded: chain C residue 1272 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.7711 > 50: distance: 13 - 79: 29.025 distance: 16 - 76: 22.550 distance: 23 - 63: 29.891 distance: 26 - 60: 26.141 distance: 43 - 45: 28.377 distance: 45 - 46: 16.187 distance: 46 - 47: 19.427 distance: 46 - 49: 23.571 distance: 47 - 48: 17.265 distance: 47 - 50: 10.827 distance: 51 - 52: 7.459 distance: 51 - 54: 19.822 distance: 52 - 53: 15.849 distance: 52 - 55: 32.090 distance: 55 - 56: 12.385 distance: 56 - 57: 14.925 distance: 56 - 59: 16.051 distance: 57 - 58: 5.592 distance: 57 - 60: 16.367 distance: 60 - 61: 19.674 distance: 61 - 62: 17.618 distance: 61 - 64: 10.739 distance: 62 - 63: 23.166 distance: 62 - 65: 5.413 distance: 65 - 66: 14.242 distance: 66 - 67: 21.292 distance: 66 - 69: 6.895 distance: 67 - 68: 23.013 distance: 67 - 76: 17.059 distance: 69 - 70: 25.768 distance: 70 - 71: 3.518 distance: 70 - 72: 9.349 distance: 71 - 73: 7.185 distance: 72 - 74: 14.451 distance: 73 - 75: 8.099 distance: 74 - 75: 8.355 distance: 76 - 77: 10.893 distance: 77 - 78: 28.711 distance: 77 - 80: 33.775 distance: 78 - 79: 53.771 distance: 78 - 81: 7.261 distance: 81 - 82: 21.015 distance: 82 - 83: 12.396 distance: 82 - 85: 21.415 distance: 83 - 84: 20.714 distance: 83 - 86: 11.481 distance: 86 - 87: 8.678 distance: 86 - 92: 30.150 distance: 87 - 88: 18.194 distance: 87 - 90: 25.039 distance: 88 - 89: 9.352 distance: 88 - 93: 39.037 distance: 90 - 91: 19.822 distance: 91 - 92: 17.930 distance: 93 - 94: 17.516 distance: 94 - 95: 17.423 distance: 94 - 97: 5.202 distance: 95 - 96: 13.110 distance: 95 - 98: 8.208 distance: 98 - 99: 19.325 distance: 99 - 100: 9.522 distance: 99 - 102: 13.932 distance: 100 - 101: 6.184 distance: 100 - 103: 9.467 distance: 101 - 117: 16.281