Starting phenix.real_space_refine on Thu Mar 14 13:24:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsu_33435/03_2024/7xsu_33435_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsu_33435/03_2024/7xsu_33435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsu_33435/03_2024/7xsu_33435.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsu_33435/03_2024/7xsu_33435.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsu_33435/03_2024/7xsu_33435_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsu_33435/03_2024/7xsu_33435_updated.pdb" } resolution = 3.4 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= 0.005 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 68 5.16 5 C 5929 2.51 5 N 1394 2.21 5 O 1576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 172": "OE1" <-> "OE2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 368": "NH1" <-> "NH2" Residue "A TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 721": "OD1" <-> "OD2" Residue "A PHE 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 738": "OE1" <-> "OE2" Residue "A GLU 745": "OE1" <-> "OE2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 786": "OD1" <-> "OD2" Residue "A PHE 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 896": "NH1" <-> "NH2" Residue "A GLU 904": "OE1" <-> "OE2" Residue "A ASP 908": "OD1" <-> "OD2" Residue "A TYR 1201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1227": "OE1" <-> "OE2" Residue "A GLU 1233": "OE1" <-> "OE2" Residue "A TYR 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1305": "NH1" <-> "NH2" Residue "A ARG 1311": "NH1" <-> "NH2" Residue "A GLU 1320": "OE1" <-> "OE2" Residue "A PHE 1461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1525": "OD1" <-> "OD2" Residue "A PHE 1569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1576": "OE1" <-> "OE2" Residue "A TYR 1588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1628": "NH1" <-> "NH2" Residue "A ARG 1634": "NH1" <-> "NH2" Residue "A ARG 1637": "NH1" <-> "NH2" Residue "A PHE 1696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1731": "OD1" <-> "OD2" Residue "A PHE 1753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1762": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 61": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8969 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8247 Classifications: {'peptide': 1085} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 1058} Chain breaks: 6 Unresolved non-hydrogen bonds: 503 Unresolved non-hydrogen angles: 628 Unresolved non-hydrogen dihedrals: 439 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 7, 'TYR:plan': 8, 'ASN:plan1': 7, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 7, 'GLU:plan': 14, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 324 Chain: "B" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 463 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 62} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 259 Unusual residues: {'6OU': 6, '9Z9': 1, 'BMA': 1, 'NAG': 5} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'6OU:plan-1': 6, '6OU:plan-2': 2, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 5.39, per 1000 atoms: 0.60 Number of scatterers: 8969 At special positions: 0 Unit cell: (135.168, 127.776, 104.544, 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 68 16.00 P 2 15.00 O 1576 8.00 N 1394 7.00 C 5929 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 336 " distance=2.02 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 342 " distance=2.04 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 918 " distance=2.01 Simple disulfide: pdb=" SG CYS A1730 " - pdb=" SG CYS A1744 " distance=2.03 Simple disulfide: pdb=" SG CYS B 12 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 37 " distance=2.03 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 49 " distance=2.04 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: 3.67 Conformation dependent library (CDL) restraints added in 1.6 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 2 sheets defined 68.8% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 132 through 149 removed outlier: 3.713A pdb=" N MET A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 180 removed outlier: 3.557A pdb=" N TYR A 160 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL A 161 " --> pdb=" O TRP A 157 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLU A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR A 164 " --> pdb=" O TYR A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 188 No H-bonds generated for 'chain 'A' and resid 185 through 188' Processing helix chain 'A' and resid 193 through 209 removed outlier: 3.627A pdb=" N ASP A 198 " --> pdb=" O TRP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 233 removed outlier: 3.538A pdb=" N ARG A 223 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL A 224 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'A' and resid 252 through 273 Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 359 through 371 Processing helix chain 'A' and resid 375 through 386 Processing helix chain 'A' and resid 388 through 422 removed outlier: 4.082A pdb=" N ILE A 392 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 398 " --> pdb=" O MET A 395 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE A 399 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 400 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY A 401 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER A 402 " --> pdb=" O PHE A 399 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 406 " --> pdb=" O PHE A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 716 removed outlier: 3.580A pdb=" N LYS A 712 " --> pdb=" O LYS A 708 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 Processing helix chain 'A' and resid 744 through 771 Processing helix chain 'A' and resid 777 through 779 No H-bonds generated for 'chain 'A' and resid 777 through 779' Processing helix chain 'A' and resid 781 through 797 Processing helix chain 'A' and resid 808 through 820 removed outlier: 3.935A pdb=" N PHE A 811 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG A 812 " --> pdb=" O ARG A 809 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 814 " --> pdb=" O PHE A 811 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 819 " --> pdb=" O VAL A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 837 removed outlier: 3.659A pdb=" N VAL A 837 " --> pdb=" O ILE A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 868 removed outlier: 4.941A pdb=" N LYS A 864 " --> pdb=" O GLN A 860 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ASN A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 873 No H-bonds generated for 'chain 'A' and resid 870 through 873' Processing helix chain 'A' and resid 887 through 899 Processing helix chain 'A' and resid 902 through 913 removed outlier: 3.891A pdb=" N ASP A 908 " --> pdb=" O GLU A 904 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 912 " --> pdb=" O ASP A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 944 removed outlier: 3.569A pdb=" N LEU A 920 " --> pdb=" O SER A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1205 Processing helix chain 'A' and resid 1207 through 1226 removed outlier: 3.756A pdb=" N LEU A1224 " --> pdb=" O SER A1220 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A1225 " --> pdb=" O SER A1221 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE A1226 " --> pdb=" O GLY A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1270 removed outlier: 3.554A pdb=" N LEU A1240 " --> pdb=" O THR A1236 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N PHE A1265 " --> pdb=" O VAL A1261 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N LYS A1266 " --> pdb=" O ALA A1262 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS A1267 " --> pdb=" O TYR A1263 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A1270 " --> pdb=" O LYS A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1293 Processing helix chain 'A' and resid 1301 through 1318 removed outlier: 3.750A pdb=" N ARG A1308 " --> pdb=" O LEU A1304 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ALA A1309 " --> pdb=" O ARG A1305 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU A1310 " --> pdb=" O THR A1306 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ARG A1311 " --> pdb=" O LEU A1307 " (cutoff:3.500A) Proline residue: A1312 - end of helix removed outlier: 4.250A pdb=" N ALA A1315 " --> pdb=" O ARG A1311 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU A1316 " --> pdb=" O PRO A1312 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG A1318 " --> pdb=" O ARG A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1331 Processing helix chain 'A' and resid 1333 through 1358 removed outlier: 3.597A pdb=" N ASN A1338 " --> pdb=" O PRO A1334 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL A1339 " --> pdb=" O SER A1335 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A1350 " --> pdb=" O PHE A1346 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1389 Processing helix chain 'A' and resid 1407 through 1419 Processing helix chain 'A' and resid 1423 through 1431 Processing helix chain 'A' and resid 1446 through 1459 removed outlier: 3.555A pdb=" N TYR A1449 " --> pdb=" O LEU A1446 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A1457 " --> pdb=" O VAL A1454 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY A1459 " --> pdb=" O ILE A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1481 Processing helix chain 'A' and resid 1518 through 1527 Processing helix chain 'A' and resid 1530 through 1548 removed outlier: 3.664A pdb=" N ILE A1536 " --> pdb=" O PHE A1532 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1579 removed outlier: 3.883A pdb=" N ASN A1560 " --> pdb=" O PRO A1556 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1590 No H-bonds generated for 'chain 'A' and resid 1587 through 1590' Processing helix chain 'A' and resid 1592 through 1609 removed outlier: 3.509A pdb=" N VAL A1599 " --> pdb=" O ILE A1595 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A1609 " --> pdb=" O ILE A1605 " (cutoff:3.500A) Processing helix chain 'A' and resid 1611 through 1617 removed outlier: 3.766A pdb=" N GLN A1615 " --> pdb=" O SER A1611 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LYS A1616 " --> pdb=" O ASP A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1638 Processing helix chain 'A' and resid 1644 through 1654 Processing helix chain 'A' and resid 1656 through 1681 removed outlier: 3.685A pdb=" N PHE A1660 " --> pdb=" O LEU A1656 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1711 removed outlier: 3.722A pdb=" N LEU A1704 " --> pdb=" O ALA A1700 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR A1711 " --> pdb=" O PHE A1707 " (cutoff:3.500A) Processing helix chain 'A' and resid 1715 through 1723 Proline residue: A1721 - end of helix Processing helix chain 'A' and resid 1747 through 1776 Processing helix chain 'B' and resid 24 through 30 Processing sheet with id= A, first strand: chain 'A' and resid 280 through 283 Processing sheet with id= B, first strand: chain 'B' and resid 36 through 40 removed outlier: 3.658A pdb=" N HIS B 36 " --> pdb=" O TRP B 48 " (cutoff:3.500A) 539 hydrogen bonds defined for protein. 1425 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: 2.69 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1375 1.30 - 1.43: 2468 1.43 - 1.56: 5200 1.56 - 1.69: 18 1.69 - 1.82: 106 Bond restraints: 9167 Sorted by residual: bond pdb=" C13 9Z9 A3013 " pdb=" C14 9Z9 A3013 " ideal model delta sigma weight residual 1.332 1.670 -0.338 2.00e-02 2.50e+03 2.85e+02 bond pdb=" C07 6OU A3012 " pdb=" C08 6OU A3012 " ideal model delta sigma weight residual 1.524 1.311 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C07 6OU A3011 " pdb=" C08 6OU A3011 " ideal model delta sigma weight residual 1.524 1.312 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C73 9Z9 A3013 " pdb=" O72 9Z9 A3013 " ideal model delta sigma weight residual 1.406 1.568 -0.162 2.00e-02 2.50e+03 6.57e+01 bond pdb=" C04 9Z9 A3013 " pdb=" O72 9Z9 A3013 " ideal model delta sigma weight residual 1.420 1.261 0.159 2.00e-02 2.50e+03 6.35e+01 ... (remaining 9162 not shown) Histogram of bond angle deviations from ideal: 76.18 - 90.71: 1 90.71 - 105.25: 152 105.25 - 119.79: 7876 119.79 - 134.33: 4425 134.33 - 148.87: 2 Bond angle restraints: 12456 Sorted by residual: angle pdb=" N PRO A 349 " pdb=" CA PRO A 349 " pdb=" C PRO A 349 " ideal model delta sigma weight residual 112.47 148.87 -36.40 2.06e+00 2.36e-01 3.12e+02 angle pdb=" N THR A1378 " pdb=" CA THR A1378 " pdb=" C THR A1378 " ideal model delta sigma weight residual 112.93 132.06 -19.13 1.33e+00 5.65e-01 2.07e+02 angle pdb=" N ILE A1379 " pdb=" CA ILE A1379 " pdb=" C ILE A1379 " ideal model delta sigma weight residual 111.90 100.95 10.95 8.10e-01 1.52e+00 1.83e+02 angle pdb=" N ASP A 350 " pdb=" CA ASP A 350 " pdb=" C ASP A 350 " ideal model delta sigma weight residual 112.12 95.77 16.35 1.34e+00 5.57e-01 1.49e+02 angle pdb=" C LEU A1373 " pdb=" N PRO A1374 " pdb=" CA PRO A1374 " ideal model delta sigma weight residual 120.52 132.29 -11.77 9.90e-01 1.02e+00 1.41e+02 ... (remaining 12451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.03: 5264 35.03 - 70.05: 185 70.05 - 105.08: 23 105.08 - 140.11: 18 140.11 - 175.13: 1 Dihedral angle restraints: 5491 sinusoidal: 2158 harmonic: 3333 Sorted by residual: dihedral pdb=" CB CYS A 909 " pdb=" SG CYS A 909 " pdb=" SG CYS A 918 " pdb=" CB CYS A 918 " ideal model delta sinusoidal sigma weight residual -86.00 -170.42 84.42 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS A1730 " pdb=" SG CYS A1730 " pdb=" SG CYS A1744 " pdb=" CB CYS A1744 " ideal model delta sinusoidal sigma weight residual -86.00 -148.90 62.90 1 1.00e+01 1.00e-02 5.23e+01 dihedral pdb=" C PHE A 285 " pdb=" N PHE A 285 " pdb=" CA PHE A 285 " pdb=" CB PHE A 285 " ideal model delta harmonic sigma weight residual -122.60 -105.71 -16.89 0 2.50e+00 1.60e-01 4.56e+01 ... (remaining 5488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.237: 1440 0.237 - 0.474: 46 0.474 - 0.710: 3 0.710 - 0.947: 1 0.947 - 1.184: 1 Chirality restraints: 1491 Sorted by residual: chirality pdb=" CA PRO A 349 " pdb=" N PRO A 349 " pdb=" C PRO A 349 " pdb=" CB PRO A 349 " both_signs ideal model delta sigma weight residual False 2.72 1.53 1.18 2.00e-01 2.50e+01 3.50e+01 chirality pdb=" C02 9Z9 A3013 " pdb=" C03 9Z9 A3013 " pdb=" C06 9Z9 A3013 " pdb=" C10 9Z9 A3013 " both_signs ideal model delta sigma weight residual False 2.92 2.18 0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" CA CYS A1365 " pdb=" N CYS A1365 " pdb=" C CYS A1365 " pdb=" CB CYS A1365 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 1488 not shown) Planarity restraints: 1510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A3003 " 0.324 2.00e-02 2.50e+03 2.82e-01 9.96e+02 pdb=" C7 NAG A3003 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG A3003 " 0.126 2.00e-02 2.50e+03 pdb=" N2 NAG A3003 " -0.505 2.00e-02 2.50e+03 pdb=" O7 NAG A3003 " 0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A3004 " -0.237 2.00e-02 2.50e+03 1.97e-01 4.87e+02 pdb=" C7 NAG A3004 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG A3004 " -0.165 2.00e-02 2.50e+03 pdb=" N2 NAG A3004 " 0.327 2.00e-02 2.50e+03 pdb=" O7 NAG A3004 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A3001 " 0.239 2.00e-02 2.50e+03 1.97e-01 4.84e+02 pdb=" C7 NAG A3001 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG A3001 " 0.169 2.00e-02 2.50e+03 pdb=" N2 NAG A3001 " -0.322 2.00e-02 2.50e+03 pdb=" O7 NAG A3001 " -0.020 2.00e-02 2.50e+03 ... (remaining 1507 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 4 2.13 - 2.82: 3030 2.82 - 3.52: 13290 3.52 - 4.21: 19045 4.21 - 4.90: 35029 Nonbonded interactions: 70398 Sorted by model distance: nonbonded pdb=" OD1 ASN A1445 " pdb=" CE MET A1448 " model vdw 1.440 3.460 nonbonded pdb=" CG ASN A1445 " pdb=" CE MET A1448 " model vdw 1.598 3.690 nonbonded pdb=" ND2 ASN A1445 " pdb=" CE MET A1448 " model vdw 1.748 3.540 nonbonded pdb=" O3 NAG A3001 " pdb=" O6 NAG A3001 " model vdw 1.809 2.440 nonbonded pdb=" N PHE A 285 " pdb=" O PHE A 285 " model vdw 2.255 2.496 ... (remaining 70393 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.680 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: 3.900 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.440 Find NCS groups from input model: 0.220 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 : 0.011 0.338 9167 Z= 0.744 Angle : 1.611 36.397 12456 Z= 1.013 Chirality : 0.106 1.184 1491 Planarity : 0.013 0.282 1510 Dihedral : 19.266 175.133 3314 Min Nonbonded Distance : 1.440 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.46 % Favored : 94.10 % Rotamer: Outliers : 5.06 % Allowed : 18.09 % Favored : 76.85 % Cbeta Deviations : 0.83 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 1.66 (0.25), residues: 1136 helix: 2.38 (0.18), residues: 731 sheet: -0.35 (2.23), residues: 12 loop : -1.44 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1715 HIS 0.008 0.002 HIS A 279 PHE 0.020 0.002 PHE A 887 TYR 0.025 0.002 TYR A 379 ARG 0.004 0.001 ARG A 881 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 243 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.5939 (tpp) cc_final: 0.5328 (tmm) REVERT: A 137 LEU cc_start: 0.8841 (tt) cc_final: 0.8600 (tp) REVERT: A 249 LYS cc_start: 0.6300 (mptt) cc_final: 0.6004 (tttp) REVERT: A 260 PHE cc_start: 0.8580 (t80) cc_final: 0.8278 (t80) REVERT: A 351 HIS cc_start: 0.7222 (OUTLIER) cc_final: 0.6090 (t-90) REVERT: A 379 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.8035 (t80) REVERT: A 778 PHE cc_start: 0.5588 (t80) cc_final: 0.4781 (t80) REVERT: A 835 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8471 (t0) REVERT: A 1197 ARG cc_start: 0.7806 (ttp80) cc_final: 0.7480 (ttm-80) REVERT: A 1202 ARG cc_start: 0.7576 (ttm170) cc_final: 0.7356 (mtp-110) REVERT: A 1209 PHE cc_start: 0.8539 (t80) cc_final: 0.8145 (t80) REVERT: A 1233 GLU cc_start: 0.6449 (tt0) cc_final: 0.6204 (tt0) REVERT: A 1302 LYS cc_start: 0.7936 (pttt) cc_final: 0.7734 (mptt) REVERT: A 1424 MET cc_start: 0.7862 (mmp) cc_final: 0.7588 (mmm) REVERT: A 1538 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7324 (t80) REVERT: A 1581 MET cc_start: 0.4007 (ppp) cc_final: 0.3189 (tpp) REVERT: A 1619 PHE cc_start: 0.6115 (OUTLIER) cc_final: 0.5788 (p90) REVERT: A 1664 LEU cc_start: 0.7984 (tp) cc_final: 0.7748 (mt) REVERT: A 1762 PHE cc_start: 0.8989 (t80) cc_final: 0.8611 (t80) outliers start: 45 outliers final: 19 residues processed: 276 average time/residue: 0.1763 time to fit residues: 69.4004 Evaluate side-chains 213 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 189 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 835 ASN Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 1345 ILE Chi-restraints excluded: chain A residue 1402 VAL Chi-restraints excluded: chain A residue 1404 PHE Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1474 ASN Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1538 PHE Chi-restraints excluded: chain A residue 1619 PHE Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain B residue 29 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN A 827 ASN A 865 ASN A 889 HIS A1271 ASN A1441 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9167 Z= 0.223 Angle : 0.670 8.430 12456 Z= 0.344 Chirality : 0.040 0.278 1491 Planarity : 0.005 0.050 1510 Dihedral : 13.291 147.269 1582 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.99 % Favored : 96.92 % Rotamer: Outliers : 4.16 % Allowed : 20.67 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 0.96 (0.25), residues: 1136 helix: 1.68 (0.18), residues: 750 sheet: -0.38 (2.01), residues: 12 loop : -1.54 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1715 HIS 0.002 0.001 HIS A 131 PHE 0.019 0.001 PHE A1215 TYR 0.020 0.001 TYR A 379 ARG 0.005 0.001 ARG A1305 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 218 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 HIS cc_start: 0.8352 (t-90) cc_final: 0.7967 (t-90) REVERT: A 136 MET cc_start: 0.6029 (tpp) cc_final: 0.5432 (tmm) REVERT: A 137 LEU cc_start: 0.8698 (tt) cc_final: 0.8415 (tp) REVERT: A 260 PHE cc_start: 0.8655 (t80) cc_final: 0.8348 (t80) REVERT: A 341 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7277 (tpt-90) REVERT: A 415 MET cc_start: 0.4799 (mmm) cc_final: 0.4444 (mmm) REVERT: A 1197 ARG cc_start: 0.7768 (ttp80) cc_final: 0.7291 (ttm-80) REVERT: A 1201 TYR cc_start: 0.8573 (t80) cc_final: 0.8231 (t80) REVERT: A 1202 ARG cc_start: 0.7510 (ttm170) cc_final: 0.7293 (mtp-110) REVERT: A 1209 PHE cc_start: 0.8483 (t80) cc_final: 0.8172 (t80) REVERT: A 1216 MET cc_start: 0.8920 (mmm) cc_final: 0.8594 (tpt) REVERT: A 1233 GLU cc_start: 0.6639 (tt0) cc_final: 0.6250 (tt0) REVERT: A 1275 TRP cc_start: 0.8798 (m100) cc_final: 0.8490 (m100) REVERT: A 1323 ARG cc_start: 0.7131 (ttp80) cc_final: 0.6907 (ttp80) REVERT: A 1406 ASN cc_start: 0.7286 (m110) cc_final: 0.7062 (m-40) REVERT: A 1448 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7410 (mpp) REVERT: A 1538 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.7442 (t80) REVERT: A 1547 MET cc_start: 0.6299 (mtm) cc_final: 0.5973 (mtm) REVERT: A 1562 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8333 (mm) REVERT: A 1664 LEU cc_start: 0.7950 (tp) cc_final: 0.7663 (tp) outliers start: 37 outliers final: 16 residues processed: 247 average time/residue: 0.1808 time to fit residues: 63.6254 Evaluate side-chains 210 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 190 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1448 MET Chi-restraints excluded: chain A residue 1538 PHE Chi-restraints excluded: chain A residue 1540 ILE Chi-restraints excluded: chain A residue 1562 LEU Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1662 ILE Chi-restraints excluded: chain B residue 3 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 9167 Z= 0.219 Angle : 0.592 9.821 12456 Z= 0.308 Chirality : 0.037 0.172 1491 Planarity : 0.004 0.045 1510 Dihedral : 10.185 140.284 1553 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 5.28 % Allowed : 22.02 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 0.61 (0.25), residues: 1136 helix: 1.35 (0.19), residues: 754 sheet: -0.78 (1.89), residues: 12 loop : -1.55 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1715 HIS 0.002 0.001 HIS B 66 PHE 0.017 0.001 PHE A 778 TYR 0.018 0.001 TYR A 379 ARG 0.006 0.000 ARG A1634 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 205 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 HIS cc_start: 0.8430 (t-90) cc_final: 0.8180 (t-90) REVERT: A 136 MET cc_start: 0.6459 (tpp) cc_final: 0.5741 (tmm) REVERT: A 137 LEU cc_start: 0.8623 (tt) cc_final: 0.8337 (tp) REVERT: A 260 PHE cc_start: 0.8665 (t80) cc_final: 0.8378 (t80) REVERT: A 415 MET cc_start: 0.4901 (mmm) cc_final: 0.4550 (mmm) REVERT: A 904 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: A 1197 ARG cc_start: 0.7705 (ttp80) cc_final: 0.7221 (ttm-80) REVERT: A 1209 PHE cc_start: 0.8592 (t80) cc_final: 0.8279 (t80) REVERT: A 1263 TYR cc_start: 0.7593 (m-80) cc_final: 0.7233 (m-80) REVERT: A 1275 TRP cc_start: 0.8783 (m100) cc_final: 0.8458 (m100) REVERT: A 1302 LYS cc_start: 0.8038 (mptt) cc_final: 0.7198 (ttpp) REVERT: A 1406 ASN cc_start: 0.7363 (m110) cc_final: 0.7143 (m-40) REVERT: A 1448 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7573 (mpp) REVERT: A 1562 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8302 (mm) REVERT: A 1653 MET cc_start: 0.6647 (mmt) cc_final: 0.6318 (mmm) outliers start: 47 outliers final: 25 residues processed: 242 average time/residue: 0.1709 time to fit residues: 59.9227 Evaluate side-chains 219 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 191 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1351 SER Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1448 MET Chi-restraints excluded: chain A residue 1562 LEU Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1662 ILE Chi-restraints excluded: chain A residue 1674 SER Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 52 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 104 optimal weight: 0.0970 chunk 110 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9167 Z= 0.200 Angle : 0.564 8.355 12456 Z= 0.293 Chirality : 0.037 0.177 1491 Planarity : 0.003 0.041 1510 Dihedral : 9.345 135.193 1551 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.51 % Rotamer: Outliers : 5.84 % Allowed : 21.91 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 0.49 (0.25), residues: 1136 helix: 1.21 (0.19), residues: 761 sheet: -1.05 (1.79), residues: 12 loop : -1.52 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1715 HIS 0.001 0.000 HIS A 739 PHE 0.028 0.001 PHE A 778 TYR 0.018 0.001 TYR A 379 ARG 0.003 0.000 ARG A1634 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 199 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 HIS cc_start: 0.8411 (t-90) cc_final: 0.8144 (t-90) REVERT: A 136 MET cc_start: 0.6487 (tpp) cc_final: 0.5762 (tmm) REVERT: A 137 LEU cc_start: 0.8627 (tt) cc_final: 0.8334 (tp) REVERT: A 260 PHE cc_start: 0.8580 (t80) cc_final: 0.8317 (t80) REVERT: A 415 MET cc_start: 0.5154 (mmm) cc_final: 0.4821 (mmm) REVERT: A 1197 ARG cc_start: 0.7701 (ttp80) cc_final: 0.7244 (ttm110) REVERT: A 1209 PHE cc_start: 0.8586 (t80) cc_final: 0.8292 (t80) REVERT: A 1263 TYR cc_start: 0.7618 (m-80) cc_final: 0.7373 (m-80) REVERT: A 1302 LYS cc_start: 0.8008 (mptt) cc_final: 0.7130 (tttm) REVERT: A 1406 ASN cc_start: 0.7426 (m110) cc_final: 0.7219 (m-40) REVERT: A 1538 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7492 (t80) REVERT: A 1562 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8333 (mm) REVERT: A 1653 MET cc_start: 0.6631 (mmt) cc_final: 0.6198 (mmm) REVERT: B 3 ASP cc_start: 0.4770 (OUTLIER) cc_final: 0.4499 (t70) outliers start: 52 outliers final: 33 residues processed: 232 average time/residue: 0.1666 time to fit residues: 56.5992 Evaluate side-chains 231 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 195 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1424 MET Chi-restraints excluded: chain A residue 1538 PHE Chi-restraints excluded: chain A residue 1562 LEU Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1662 ILE Chi-restraints excluded: chain A residue 1674 SER Chi-restraints excluded: chain A residue 1777 PHE Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 52 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 0.0670 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 0.0870 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1767 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9167 Z= 0.159 Angle : 0.529 8.212 12456 Z= 0.274 Chirality : 0.035 0.177 1491 Planarity : 0.003 0.038 1510 Dihedral : 8.910 129.949 1551 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.60 % Rotamer: Outliers : 5.06 % Allowed : 23.15 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 0.57 (0.25), residues: 1136 helix: 1.25 (0.19), residues: 761 sheet: -1.07 (1.87), residues: 12 loop : -1.44 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1715 HIS 0.003 0.000 HIS A 883 PHE 0.028 0.001 PHE A 778 TYR 0.014 0.001 TYR A 379 ARG 0.006 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 211 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 HIS cc_start: 0.8394 (t-90) cc_final: 0.8120 (t-90) REVERT: A 136 MET cc_start: 0.6575 (tpp) cc_final: 0.5837 (tmm) REVERT: A 137 LEU cc_start: 0.8601 (tt) cc_final: 0.8313 (tp) REVERT: A 260 PHE cc_start: 0.8590 (t80) cc_final: 0.8342 (t80) REVERT: A 415 MET cc_start: 0.5087 (mmm) cc_final: 0.4816 (mmm) REVERT: A 860 GLN cc_start: 0.7243 (mm-40) cc_final: 0.6991 (mm-40) REVERT: A 904 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: A 1197 ARG cc_start: 0.7665 (ttp80) cc_final: 0.7238 (ttm-80) REVERT: A 1209 PHE cc_start: 0.8580 (t80) cc_final: 0.8287 (t80) REVERT: A 1263 TYR cc_start: 0.7676 (m-80) cc_final: 0.7437 (m-10) REVERT: A 1275 TRP cc_start: 0.8808 (m100) cc_final: 0.8492 (m100) REVERT: A 1298 MET cc_start: 0.3033 (ptm) cc_final: 0.2750 (ptt) REVERT: A 1302 LYS cc_start: 0.7984 (mptt) cc_final: 0.7077 (tttm) REVERT: A 1406 ASN cc_start: 0.7379 (m110) cc_final: 0.7160 (m-40) REVERT: A 1562 LEU cc_start: 0.8518 (mm) cc_final: 0.8300 (mm) REVERT: A 1653 MET cc_start: 0.6499 (mmt) cc_final: 0.6056 (mmm) REVERT: B 3 ASP cc_start: 0.5046 (OUTLIER) cc_final: 0.4808 (t70) outliers start: 45 outliers final: 28 residues processed: 237 average time/residue: 0.1729 time to fit residues: 59.6808 Evaluate side-chains 227 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 197 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1242 GLU Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1662 ILE Chi-restraints excluded: chain B residue 3 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 20.0000 chunk 36 optimal weight: 0.4980 chunk 57 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9167 Z= 0.159 Angle : 0.529 7.565 12456 Z= 0.273 Chirality : 0.035 0.208 1491 Planarity : 0.003 0.037 1510 Dihedral : 8.611 123.180 1550 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 4.94 % Allowed : 23.82 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 0.33 (0.25), residues: 1136 helix: 1.12 (0.19), residues: 782 sheet: -1.19 (1.83), residues: 12 loop : -1.85 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1715 HIS 0.003 0.000 HIS A 883 PHE 0.029 0.001 PHE A 778 TYR 0.018 0.001 TYR A1201 ARG 0.006 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 210 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 HIS cc_start: 0.8365 (t-90) cc_final: 0.8103 (t-90) REVERT: A 136 MET cc_start: 0.6576 (tpp) cc_final: 0.5828 (tmm) REVERT: A 137 LEU cc_start: 0.8700 (tt) cc_final: 0.8404 (tp) REVERT: A 260 PHE cc_start: 0.8592 (t80) cc_final: 0.8357 (t80) REVERT: A 415 MET cc_start: 0.4882 (mmm) cc_final: 0.4650 (mmm) REVERT: A 904 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: A 1194 TRP cc_start: 0.7009 (m100) cc_final: 0.6759 (m-10) REVERT: A 1209 PHE cc_start: 0.8580 (t80) cc_final: 0.8282 (t80) REVERT: A 1263 TYR cc_start: 0.7647 (m-80) cc_final: 0.7411 (m-10) REVERT: A 1275 TRP cc_start: 0.8833 (m100) cc_final: 0.8488 (m100) REVERT: A 1298 MET cc_start: 0.3051 (ptm) cc_final: 0.2842 (ptt) REVERT: A 1302 LYS cc_start: 0.8037 (mptt) cc_final: 0.7086 (tttm) REVERT: A 1406 ASN cc_start: 0.7396 (m110) cc_final: 0.7171 (m-40) REVERT: A 1562 LEU cc_start: 0.8492 (mm) cc_final: 0.8282 (mm) REVERT: A 1649 LEU cc_start: 0.7924 (mt) cc_final: 0.7285 (pp) REVERT: A 1653 MET cc_start: 0.6455 (mmt) cc_final: 0.6001 (mmm) REVERT: A 1654 MET cc_start: 0.7141 (ttp) cc_final: 0.6791 (ttt) REVERT: A 1664 LEU cc_start: 0.7979 (tp) cc_final: 0.7731 (tp) REVERT: A 1693 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7860 (ttp) REVERT: B 3 ASP cc_start: 0.5226 (OUTLIER) cc_final: 0.5007 (t70) outliers start: 44 outliers final: 30 residues processed: 240 average time/residue: 0.1718 time to fit residues: 59.8239 Evaluate side-chains 235 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 202 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1242 GLU Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1351 SER Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1662 ILE Chi-restraints excluded: chain A residue 1693 MET Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 52 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 chunk 68 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 67 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 HIS A1356 ASN A1441 GLN ** A1680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9167 Z= 0.190 Angle : 0.555 8.225 12456 Z= 0.287 Chirality : 0.035 0.211 1491 Planarity : 0.003 0.036 1510 Dihedral : 8.446 115.890 1548 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.51 % Rotamer: Outliers : 5.17 % Allowed : 23.93 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 0.29 (0.25), residues: 1136 helix: 1.09 (0.19), residues: 780 sheet: -1.37 (1.80), residues: 12 loop : -1.85 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 375 HIS 0.003 0.000 HIS A 883 PHE 0.030 0.001 PHE A 778 TYR 0.018 0.001 TYR A 379 ARG 0.006 0.001 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 205 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 HIS cc_start: 0.8392 (t-90) cc_final: 0.8101 (t-90) REVERT: A 136 MET cc_start: 0.6583 (tpp) cc_final: 0.5835 (tmm) REVERT: A 137 LEU cc_start: 0.8714 (tt) cc_final: 0.8422 (tp) REVERT: A 260 PHE cc_start: 0.8591 (t80) cc_final: 0.8354 (t80) REVERT: A 415 MET cc_start: 0.4913 (mmm) cc_final: 0.4670 (mmm) REVERT: A 901 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7058 (mt-10) REVERT: A 904 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: A 1275 TRP cc_start: 0.8841 (m100) cc_final: 0.8570 (m100) REVERT: A 1302 LYS cc_start: 0.8040 (mptt) cc_final: 0.7267 (tttp) REVERT: A 1538 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.7416 (t80) REVERT: A 1562 LEU cc_start: 0.8457 (mm) cc_final: 0.8252 (mm) REVERT: A 1649 LEU cc_start: 0.7927 (mt) cc_final: 0.7331 (pp) REVERT: A 1654 MET cc_start: 0.7145 (ttp) cc_final: 0.6900 (ttt) REVERT: A 1661 ASN cc_start: 0.7252 (t0) cc_final: 0.7023 (t0) REVERT: A 1664 LEU cc_start: 0.7975 (tp) cc_final: 0.7711 (tp) outliers start: 46 outliers final: 36 residues processed: 238 average time/residue: 0.1682 time to fit residues: 58.8260 Evaluate side-chains 236 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 197 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1242 GLU Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1351 SER Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1424 MET Chi-restraints excluded: chain A residue 1538 PHE Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1662 ILE Chi-restraints excluded: chain B residue 52 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9167 Z= 0.213 Angle : 0.560 8.675 12456 Z= 0.290 Chirality : 0.037 0.213 1491 Planarity : 0.003 0.039 1510 Dihedral : 8.426 115.736 1548 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.60 % Rotamer: Outliers : 5.39 % Allowed : 24.49 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 0.20 (0.25), residues: 1136 helix: 1.01 (0.19), residues: 780 sheet: -1.57 (1.71), residues: 12 loop : -1.81 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 375 HIS 0.002 0.000 HIS A 739 PHE 0.025 0.001 PHE A1215 TYR 0.022 0.002 TYR A 379 ARG 0.004 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 203 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 HIS cc_start: 0.8397 (t-90) cc_final: 0.8099 (t-90) REVERT: A 136 MET cc_start: 0.6557 (tpp) cc_final: 0.5823 (tmm) REVERT: A 137 LEU cc_start: 0.8719 (tt) cc_final: 0.8418 (tp) REVERT: A 260 PHE cc_start: 0.8593 (t80) cc_final: 0.8355 (t80) REVERT: A 749 MET cc_start: 0.9161 (tmm) cc_final: 0.8933 (tmm) REVERT: A 901 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7091 (mt-10) REVERT: A 904 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: A 1275 TRP cc_start: 0.8849 (m100) cc_final: 0.8587 (m100) REVERT: A 1302 LYS cc_start: 0.8110 (mptt) cc_final: 0.7302 (tttp) REVERT: A 1538 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7416 (t80) REVERT: A 1562 LEU cc_start: 0.8469 (mm) cc_final: 0.8267 (mm) REVERT: A 1649 LEU cc_start: 0.7941 (mt) cc_final: 0.7342 (pp) REVERT: A 1664 LEU cc_start: 0.7955 (tp) cc_final: 0.7752 (tp) REVERT: A 1693 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7942 (ttp) outliers start: 48 outliers final: 37 residues processed: 237 average time/residue: 0.1771 time to fit residues: 61.2846 Evaluate side-chains 238 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 197 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1242 GLU Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1351 SER Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1538 PHE Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1662 ILE Chi-restraints excluded: chain A residue 1693 MET Chi-restraints excluded: chain A residue 1772 ILE Chi-restraints excluded: chain B residue 52 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 105 optimal weight: 0.0060 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 0.0770 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 92 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.4154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1356 ASN ** A1680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9167 Z= 0.157 Angle : 0.538 8.883 12456 Z= 0.278 Chirality : 0.035 0.215 1491 Planarity : 0.003 0.038 1510 Dihedral : 8.015 113.542 1548 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.77 % Rotamer: Outliers : 4.83 % Allowed : 25.28 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 0.30 (0.26), residues: 1136 helix: 1.04 (0.19), residues: 788 sheet: -1.68 (1.63), residues: 12 loop : -1.71 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 375 HIS 0.002 0.000 HIS A 883 PHE 0.030 0.001 PHE A 778 TYR 0.017 0.001 TYR A1201 ARG 0.004 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 211 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 HIS cc_start: 0.8381 (t-90) cc_final: 0.8100 (t-90) REVERT: A 136 MET cc_start: 0.6689 (tpp) cc_final: 0.5943 (tmm) REVERT: A 137 LEU cc_start: 0.8707 (tt) cc_final: 0.8422 (tp) REVERT: A 238 LYS cc_start: 0.7895 (mtpt) cc_final: 0.7161 (mtmm) REVERT: A 260 PHE cc_start: 0.8558 (t80) cc_final: 0.8322 (t80) REVERT: A 749 MET cc_start: 0.9131 (tmm) cc_final: 0.8888 (tmm) REVERT: A 901 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6905 (mt-10) REVERT: A 904 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: A 1263 TYR cc_start: 0.7699 (m-80) cc_final: 0.7323 (m-80) REVERT: A 1275 TRP cc_start: 0.8848 (m100) cc_final: 0.8579 (m100) REVERT: A 1302 LYS cc_start: 0.8069 (mptt) cc_final: 0.7289 (tttp) REVERT: A 1448 MET cc_start: 0.8264 (mmt) cc_final: 0.7490 (mmm) REVERT: A 1538 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.7406 (t80) REVERT: A 1562 LEU cc_start: 0.8493 (mm) cc_final: 0.8280 (mm) REVERT: A 1649 LEU cc_start: 0.7725 (mt) cc_final: 0.7275 (pp) REVERT: A 1664 LEU cc_start: 0.7863 (tp) cc_final: 0.7656 (tp) REVERT: A 1693 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7778 (ttp) outliers start: 43 outliers final: 34 residues processed: 241 average time/residue: 0.1726 time to fit residues: 60.3618 Evaluate side-chains 231 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 193 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1242 GLU Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1351 SER Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1424 MET Chi-restraints excluded: chain A residue 1538 PHE Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1662 ILE Chi-restraints excluded: chain A residue 1693 MET Chi-restraints excluded: chain A residue 1772 ILE Chi-restraints excluded: chain B residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 54.4786 > 50: distance: 19 - 25: 7.073 distance: 26 - 27: 5.200 distance: 26 - 29: 8.283 distance: 27 - 28: 11.782 distance: 27 - 30: 15.569 distance: 30 - 31: 5.125 distance: 31 - 32: 4.822 distance: 31 - 34: 5.568 distance: 32 - 33: 4.663 distance: 32 - 37: 7.773 distance: 34 - 35: 14.478 distance: 34 - 36: 8.693 distance: 37 - 38: 5.523 distance: 38 - 39: 18.826 distance: 38 - 41: 17.931 distance: 39 - 40: 14.172 distance: 39 - 42: 13.909 distance: 42 - 43: 37.539 distance: 43 - 44: 24.188 distance: 44 - 45: 23.959 distance: 44 - 46: 17.690 distance: 46 - 47: 6.960 distance: 47 - 48: 17.679 distance: 47 - 50: 3.652 distance: 48 - 49: 19.183 distance: 48 - 54: 6.280 distance: 50 - 51: 9.016 distance: 51 - 52: 8.451 distance: 51 - 53: 3.086 distance: 54 - 55: 17.060 distance: 55 - 56: 11.172 distance: 55 - 58: 22.041 distance: 56 - 57: 18.151 distance: 56 - 62: 6.840 distance: 58 - 59: 22.876 distance: 59 - 60: 10.084 distance: 59 - 61: 7.026 distance: 62 - 63: 6.026 distance: 62 - 68: 9.326 distance: 63 - 64: 7.346 distance: 63 - 66: 4.327 distance: 64 - 65: 23.068 distance: 64 - 69: 26.145 distance: 66 - 67: 18.915 distance: 67 - 68: 8.071 distance: 69 - 70: 12.677 distance: 70 - 71: 14.697 distance: 70 - 73: 14.655 distance: 71 - 72: 10.640 distance: 71 - 74: 16.020 distance: 74 - 75: 10.642 distance: 75 - 76: 11.931 distance: 76 - 77: 18.231 distance: 76 - 79: 23.905 distance: 79 - 80: 19.832 distance: 80 - 81: 3.739 distance: 80 - 83: 6.188 distance: 81 - 82: 14.986 distance: 81 - 84: 15.034