Starting phenix.real_space_refine on Mon Jul 28 04:30:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pza_20530/07_2025/6pza_20530_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pza_20530/07_2025/6pza_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/cci-nas-00/data/ceres_data/6pza_20530/07_2025/6pza_20530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pza_20530/07_2025/6pza_20530.map" model { file = "/net/cci-nas-00/data/ceres_data/6pza_20530/07_2025/6pza_20530_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pza_20530/07_2025/6pza_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. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.65, per 1000 atoms: 0.69 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.6 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: 1.41 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: 3.84 Time building geometry restraints manager: 3.28 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: 0.00 - 4.44: 13477 4.44 - 8.88: 84 8.88 - 13.32: 12 13.32 - 17.76: 1 17.76 - 22.20: 2 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: 0.890 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.150 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.610 ------------------------------------------------------------------------------- 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 9873 Z= 0.366 Angle : 1.063 22.204 13578 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 Details of bonding type rmsd hydrogen bonds : bond 0.22645 ( 698) hydrogen bonds : angle 7.81561 ( 2052) SS BOND : bond 0.01063 ( 1) SS BOND : angle 0.42519 ( 2) covalent geometry : bond 0.00778 ( 9872) covalent geometry : angle 1.06294 (13576) *********************** 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 to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.070 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: 0.2240 time to fit residues: 69.3245 Evaluate side-chains 143 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.134651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.113182 restraints weight = 17724.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.115883 restraints weight = 8323.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.117544 restraints weight = 4850.981| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6020 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9873 Z= 0.165 Angle : 0.700 9.063 13578 Z= 0.363 Chirality : 0.044 0.244 1646 Planarity : 0.006 0.062 1752 Dihedral : 6.886 73.242 1561 Min Nonbonded Distance : 2.564 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: -1.85 (0.21), residues: 1429 helix: -0.13 (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 C1218 Details of bonding type rmsd hydrogen bonds : bond 0.05697 ( 698) hydrogen bonds : angle 4.63443 ( 2052) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.31785 ( 2) covalent geometry : bond 0.00328 ( 9872) covalent geometry : angle 0.70019 (13576) *********************** 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 201 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 263 TYR cc_start: 0.6622 (t80) cc_final: 0.6421 (t80) outliers start: 28 outliers final: 11 residues processed: 190 average time/residue: 0.1999 time to fit residues: 55.6830 Evaluate side-chains 155 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 ************** Weight determination summary: number of chunks: 143 random chunks: chunk 61 optimal weight: 10.0000 chunk 132 optimal weight: 0.0020 chunk 113 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 131 optimal weight: 0.0570 chunk 33 optimal weight: 8.9990 chunk 70 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 overall best weight: 2.3710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 ASN C 105 HIS C 125 HIS C 262 ASN ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1197 GLN C1224 GLN C1245 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.135484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.112302 restraints weight = 18433.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.115097 restraints weight = 8747.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.116939 restraints weight = 5185.306| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 9873 Z= 0.186 Angle : 0.703 11.946 13578 Z= 0.360 Chirality : 0.046 0.236 1646 Planarity : 0.005 0.061 1752 Dihedral : 6.668 72.444 1561 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.90 % Allowed : 16.71 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: -0.86 (0.22), residues: 1429 helix: 0.68 (0.17), residues: 930 sheet: -3.33 (0.53), residues: 64 loop : -2.91 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 65 HIS 0.010 0.001 HIS C 36 PHE 0.023 0.002 PHE C 314 TYR 0.022 0.002 TYR C 142 ARG 0.006 0.001 ARG C1218 Details of bonding type rmsd hydrogen bonds : bond 0.05148 ( 698) hydrogen bonds : angle 4.02673 ( 2052) SS BOND : bond 0.00211 ( 1) SS BOND : angle 0.33509 ( 2) covalent geometry : bond 0.00400 ( 9872) covalent geometry : angle 0.70282 (13576) *********************** REFINEMENT MACRO_CYCLE 3 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 238 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 162 ILE cc_start: 0.7852 (mm) cc_final: 0.7414 (mm) REVERT: C 264 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7580 (pt0) REVERT: C 1030 ILE cc_start: 0.7752 (tp) cc_final: 0.7181 (pt) outliers start: 34 outliers final: 22 residues processed: 223 average time/residue: 0.1951 time to fit residues: 63.7823 Evaluate side-chains 188 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 397 ASN Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1154 LEU Chi-restraints excluded: chain C residue 1192 LEU Chi-restraints excluded: chain C residue 1242 THR Chi-restraints excluded: chain C residue 1245 ASN Chi-restraints excluded: chain C residue 1253 GLU Chi-restraints excluded: chain C residue 1276 LEU Chi-restraints excluded: chain C residue 1283 LEU Chi-restraints excluded: chain C residue 1293 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 54 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 127 optimal weight: 0.0770 chunk 138 optimal weight: 40.0000 chunk 65 optimal weight: 0.0070 chunk 102 optimal weight: 10.0000 chunk 134 optimal weight: 50.0000 chunk 142 optimal weight: 50.0000 chunk 33 optimal weight: 5.9990 chunk 67 optimal weight: 30.0000 overall best weight: 2.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 HIS ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1203 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.137128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.112553 restraints weight = 18125.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.115355 restraints weight = 8644.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.117264 restraints weight = 5175.255| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.6207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9873 Z= 0.146 Angle : 0.604 8.992 13578 Z= 0.311 Chirality : 0.043 0.389 1646 Planarity : 0.004 0.057 1752 Dihedral : 6.212 69.667 1561 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.19 % Allowed : 20.46 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: -0.13 (0.23), residues: 1429 helix: 1.26 (0.17), residues: 924 sheet: -3.22 (0.54), residues: 64 loop : -2.56 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 232 HIS 0.009 0.001 HIS C 293 PHE 0.024 0.001 PHE C1182 TYR 0.052 0.002 TYR C 142 ARG 0.006 0.001 ARG C 289 Details of bonding type rmsd hydrogen bonds : bond 0.04470 ( 698) hydrogen bonds : angle 3.86161 ( 2052) SS BOND : bond 0.00597 ( 1) SS BOND : angle 0.31648 ( 2) covalent geometry : bond 0.00312 ( 9872) covalent geometry : angle 0.60374 (13576) *********************** REFINEMENT MACRO_CYCLE 4 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 208 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 531 THR cc_start: 0.7463 (OUTLIER) cc_final: 0.7260 (p) REVERT: C 1030 ILE cc_start: 0.7753 (tp) cc_final: 0.7454 (pt) REVERT: C 1230 TYR cc_start: 0.8279 (m-80) cc_final: 0.8043 (m-80) outliers start: 36 outliers final: 20 residues processed: 193 average time/residue: 0.1785 time to fit residues: 51.5277 Evaluate side-chains 182 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1154 LEU Chi-restraints excluded: chain C residue 1165 LEU 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 1253 GLU Chi-restraints excluded: chain C residue 1283 LEU Chi-restraints excluded: chain C residue 1298 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 63 optimal weight: 30.0000 chunk 20 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 135 optimal weight: 50.0000 chunk 87 optimal weight: 9.9990 chunk 128 optimal weight: 40.0000 chunk 66 optimal weight: 40.0000 overall best weight: 11.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 HIS C1098 HIS ** C1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1234 ASN C1301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.124704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.098729 restraints weight = 19473.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.101060 restraints weight = 9989.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.102678 restraints weight = 6380.645| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 1.0001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.153 9873 Z= 0.466 Angle : 0.994 11.044 13578 Z= 0.521 Chirality : 0.058 0.235 1646 Planarity : 0.006 0.058 1752 Dihedral : 7.948 71.917 1561 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 9.94 % Allowed : 17.29 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: -1.58 (0.21), residues: 1429 helix: 0.05 (0.16), residues: 926 sheet: -3.78 (0.58), residues: 52 loop : -3.01 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP C 65 HIS 0.008 0.002 HIS C 401 PHE 0.035 0.004 PHE C 577 TYR 0.035 0.004 TYR C1254 ARG 0.010 0.002 ARG C1183 Details of bonding type rmsd hydrogen bonds : bond 0.06672 ( 698) hydrogen bonds : angle 5.15551 ( 2052) SS BOND : bond 0.00683 ( 1) SS BOND : angle 2.53646 ( 2) covalent geometry : bond 0.01039 ( 9872) covalent geometry : angle 0.99359 (13576) *********************** REFINEMENT MACRO_CYCLE 5 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 247 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 178 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 74 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7523 (tpt-90) REVERT: C 156 LYS cc_start: 0.9336 (tppt) cc_final: 0.9136 (mmmt) REVERT: C 158 TYR cc_start: 0.7477 (t80) cc_final: 0.6988 (t80) REVERT: C 167 LEU cc_start: 0.8754 (tp) cc_final: 0.8288 (tp) REVERT: C 289 ARG cc_start: 0.8651 (ttm110) cc_final: 0.8451 (mtt90) REVERT: C 314 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7567 (m-10) REVERT: C 387 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8252 (tp) REVERT: C 444 GLN cc_start: 0.8012 (tp-100) cc_final: 0.7685 (tt0) REVERT: C 483 GLN cc_start: 0.8606 (tt0) cc_final: 0.8165 (tm-30) REVERT: C 528 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7453 (mtpt) REVERT: C 574 SER cc_start: 0.8099 (p) cc_final: 0.7847 (p) REVERT: C 1025 MET cc_start: 0.8181 (tpp) cc_final: 0.7926 (mmp) REVERT: C 1030 ILE cc_start: 0.8667 (tp) cc_final: 0.8465 (mt) REVERT: C 1091 LEU cc_start: 0.8715 (tp) cc_final: 0.8350 (tt) REVERT: C 1194 ASP cc_start: 0.7948 (t0) cc_final: 0.7694 (t0) outliers start: 69 outliers final: 44 residues processed: 227 average time/residue: 0.2102 time to fit residues: 68.1014 Evaluate side-chains 189 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 141 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 1026 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1096 ARG Chi-restraints excluded: chain C residue 1158 SER Chi-restraints excluded: chain C residue 1160 VAL Chi-restraints excluded: chain C residue 1165 LEU Chi-restraints excluded: chain C residue 1173 VAL Chi-restraints excluded: chain C residue 1212 THR Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1231 THR Chi-restraints excluded: chain C residue 1242 THR Chi-restraints excluded: chain C residue 1250 VAL Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1266 THR Chi-restraints excluded: chain C residue 1272 LEU Chi-restraints excluded: chain C residue 1291 VAL Chi-restraints excluded: chain C residue 1298 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 108 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 33 optimal weight: 0.0050 chunk 10 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 82 optimal weight: 30.0000 chunk 76 optimal weight: 10.0000 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 HIS ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 ASN ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.132636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.106950 restraints weight = 18546.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.109650 restraints weight = 9099.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.111489 restraints weight = 5593.941| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 1.0155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9873 Z= 0.142 Angle : 0.662 9.319 13578 Z= 0.335 Chirality : 0.044 0.335 1646 Planarity : 0.005 0.060 1752 Dihedral : 6.802 68.959 1561 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.90 % Allowed : 27.81 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: -0.40 (0.23), residues: 1429 helix: 0.99 (0.17), residues: 927 sheet: -3.47 (0.56), residues: 65 loop : -2.52 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 899 HIS 0.009 0.001 HIS C 293 PHE 0.030 0.001 PHE C1164 TYR 0.048 0.002 TYR C 142 ARG 0.008 0.001 ARG C 370 Details of bonding type rmsd hydrogen bonds : bond 0.04787 ( 698) hydrogen bonds : angle 4.15664 ( 2052) SS BOND : bond 0.00157 ( 1) SS BOND : angle 0.70027 ( 2) covalent geometry : bond 0.00288 ( 9872) covalent geometry : angle 0.66170 (13576) *********************** REFINEMENT MACRO_CYCLE 6 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 217 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 32 ASN cc_start: 0.8327 (m-40) cc_final: 0.7718 (m-40) REVERT: C 54 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6561 (mp10) REVERT: C 80 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8071 (tp) REVERT: C 158 TYR cc_start: 0.7231 (t80) cc_final: 0.6681 (t80) REVERT: C 176 VAL cc_start: 0.9142 (OUTLIER) cc_final: 0.8917 (p) REVERT: C 483 GLN cc_start: 0.8481 (tt0) cc_final: 0.8085 (tm-30) REVERT: C 574 SER cc_start: 0.7612 (p) cc_final: 0.7250 (p) REVERT: C 577 PHE cc_start: 0.8050 (m-80) cc_final: 0.7799 (m-80) REVERT: C 1025 MET cc_start: 0.7987 (tpp) cc_final: 0.7754 (mmp) REVERT: C 1038 THR cc_start: 0.8064 (t) cc_final: 0.7777 (t) REVERT: C 1091 LEU cc_start: 0.8707 (tp) cc_final: 0.8232 (tt) outliers start: 34 outliers final: 20 residues processed: 201 average time/residue: 0.1836 time to fit residues: 55.0464 Evaluate side-chains 176 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 546 MET Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain C residue 1158 SER Chi-restraints excluded: chain C residue 1242 THR Chi-restraints excluded: chain C residue 1283 LEU Chi-restraints excluded: chain C residue 1315 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 20 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 chunk 5 optimal weight: 30.0000 chunk 127 optimal weight: 30.0000 chunk 97 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 136 optimal weight: 30.0000 chunk 58 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 HIS ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 HIS C 491 HIS C 547 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.130047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.104256 restraints weight = 19038.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.106872 restraints weight = 9461.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.108638 restraints weight = 5810.479| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 1.0313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9873 Z= 0.161 Angle : 0.648 9.443 13578 Z= 0.331 Chirality : 0.045 0.297 1646 Planarity : 0.005 0.058 1752 Dihedral : 6.646 67.583 1561 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 5.91 % Allowed : 29.54 % Favored : 64.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: -0.00 (0.23), residues: 1429 helix: 1.29 (0.17), residues: 924 sheet: -3.47 (0.63), residues: 51 loop : -2.37 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C1297 HIS 0.021 0.002 HIS C 293 PHE 0.037 0.002 PHE C 41 TYR 0.041 0.002 TYR C 142 ARG 0.015 0.001 ARG C 289 Details of bonding type rmsd hydrogen bonds : bond 0.04599 ( 698) hydrogen bonds : angle 4.00700 ( 2052) SS BOND : bond 0.00440 ( 1) SS BOND : angle 0.91475 ( 2) covalent geometry : bond 0.00358 ( 9872) covalent geometry : angle 0.64828 (13576) *********************** REFINEMENT MACRO_CYCLE 7 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 198 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 32 ASN cc_start: 0.8375 (m-40) cc_final: 0.7798 (m-40) REVERT: C 54 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.6571 (mp10) REVERT: C 80 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8197 (tp) REVERT: C 158 TYR cc_start: 0.7250 (t80) cc_final: 0.6695 (t80) REVERT: C 387 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8026 (tt) REVERT: C 483 GLN cc_start: 0.8373 (tt0) cc_final: 0.8133 (tm-30) REVERT: C 574 SER cc_start: 0.7762 (p) cc_final: 0.7447 (p) REVERT: C 1025 MET cc_start: 0.8030 (tpp) cc_final: 0.7772 (mmp) REVERT: C 1091 LEU cc_start: 0.8771 (tp) cc_final: 0.8303 (tt) REVERT: C 1230 TYR cc_start: 0.8826 (m-80) cc_final: 0.8626 (m-80) outliers start: 41 outliers final: 29 residues processed: 181 average time/residue: 0.1903 time to fit residues: 50.4759 Evaluate side-chains 179 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 1096 ARG Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain C residue 1158 SER Chi-restraints excluded: chain C residue 1165 LEU Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1242 THR Chi-restraints excluded: chain C residue 1272 LEU Chi-restraints excluded: chain C residue 1283 LEU Chi-restraints excluded: chain C residue 1315 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 50 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 141 optimal weight: 50.0000 chunk 12 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 73 optimal weight: 0.0000 chunk 140 optimal weight: 40.0000 chunk 66 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 HIS ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.132094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.106459 restraints weight = 19046.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.109113 restraints weight = 9367.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.110893 restraints weight = 5783.276| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 1.0435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9873 Z= 0.134 Angle : 0.623 9.330 13578 Z= 0.317 Chirality : 0.043 0.288 1646 Planarity : 0.005 0.058 1752 Dihedral : 6.441 65.616 1561 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.76 % Allowed : 31.12 % Favored : 64.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: 0.34 (0.23), residues: 1429 helix: 1.57 (0.17), residues: 924 sheet: -3.40 (0.63), residues: 51 loop : -2.25 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 232 HIS 0.009 0.001 HIS C 125 PHE 0.033 0.001 PHE C 41 TYR 0.035 0.002 TYR C 142 ARG 0.011 0.001 ARG C 289 Details of bonding type rmsd hydrogen bonds : bond 0.04322 ( 698) hydrogen bonds : angle 3.83395 ( 2052) SS BOND : bond 0.00318 ( 1) SS BOND : angle 0.71803 ( 2) covalent geometry : bond 0.00288 ( 9872) covalent geometry : angle 0.62337 (13576) *********************** REFINEMENT MACRO_CYCLE 8 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 188 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 32 ASN cc_start: 0.8238 (m-40) cc_final: 0.7638 (m-40) REVERT: C 54 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.6535 (mp10) REVERT: C 80 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8089 (tp) REVERT: C 158 TYR cc_start: 0.7232 (t80) cc_final: 0.6674 (t80) REVERT: C 257 MET cc_start: 0.8668 (mpp) cc_final: 0.8316 (mtt) REVERT: C 483 GLN cc_start: 0.8350 (tt0) cc_final: 0.8122 (tm-30) REVERT: C 574 SER cc_start: 0.7622 (p) cc_final: 0.7225 (p) REVERT: C 1025 MET cc_start: 0.7971 (tpp) cc_final: 0.7717 (mmp) REVERT: C 1091 LEU cc_start: 0.8779 (tp) cc_final: 0.8335 (tt) REVERT: C 1230 TYR cc_start: 0.8810 (m-80) cc_final: 0.8593 (m-80) outliers start: 33 outliers final: 27 residues processed: 175 average time/residue: 0.1850 time to fit residues: 47.7343 Evaluate side-chains 176 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 491 HIS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 1096 ARG Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain C residue 1165 LEU Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1242 THR Chi-restraints excluded: chain C residue 1315 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 97 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 126 optimal weight: 50.0000 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 124 optimal weight: 50.0000 chunk 82 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 HIS ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 HIS ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.130221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.104778 restraints weight = 18950.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.107307 restraints weight = 9559.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.108975 restraints weight = 5972.946| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 1.0537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9873 Z= 0.150 Angle : 0.625 9.250 13578 Z= 0.319 Chirality : 0.044 0.260 1646 Planarity : 0.005 0.058 1752 Dihedral : 6.396 67.102 1561 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.33 % Allowed : 30.69 % Favored : 63.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: 0.43 (0.23), residues: 1429 helix: 1.62 (0.17), residues: 930 sheet: -3.43 (0.64), residues: 51 loop : -2.23 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 232 HIS 0.011 0.001 HIS C 125 PHE 0.035 0.001 PHE C 41 TYR 0.033 0.002 TYR C 845 ARG 0.008 0.001 ARG C 289 Details of bonding type rmsd hydrogen bonds : bond 0.04325 ( 698) hydrogen bonds : angle 3.81937 ( 2052) SS BOND : bond 0.00409 ( 1) SS BOND : angle 0.78099 ( 2) covalent geometry : bond 0.00332 ( 9872) covalent geometry : angle 0.62477 (13576) *********************** REFINEMENT MACRO_CYCLE 9 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 185 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 32 ASN cc_start: 0.8288 (m-40) cc_final: 0.7715 (m-40) REVERT: C 54 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6514 (mp10) REVERT: C 80 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8149 (tp) REVERT: C 158 TYR cc_start: 0.7272 (t80) cc_final: 0.6700 (t80) REVERT: C 257 MET cc_start: 0.8724 (mpp) cc_final: 0.8319 (mtt) REVERT: C 483 GLN cc_start: 0.8373 (tt0) cc_final: 0.8146 (tm-30) REVERT: C 574 SER cc_start: 0.7706 (p) cc_final: 0.7298 (p) REVERT: C 1025 MET cc_start: 0.8012 (tpp) cc_final: 0.7743 (mmp) REVERT: C 1091 LEU cc_start: 0.8797 (tp) cc_final: 0.8365 (tt) REVERT: C 1230 TYR cc_start: 0.8799 (m-80) cc_final: 0.8595 (m-80) outliers start: 37 outliers final: 29 residues processed: 169 average time/residue: 0.1851 time to fit residues: 46.3579 Evaluate side-chains 176 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 491 HIS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 1018 PHE Chi-restraints excluded: chain C residue 1096 ARG Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain C residue 1158 SER Chi-restraints excluded: chain C residue 1165 LEU Chi-restraints excluded: chain C residue 1201 VAL Chi-restraints excluded: chain C residue 1242 THR Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1315 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.0030 chunk 139 optimal weight: 20.0000 chunk 15 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 93 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 5 optimal weight: 30.0000 chunk 76 optimal weight: 10.0000 overall best weight: 1.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 HIS C 293 HIS ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.131317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.106005 restraints weight = 19008.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.108635 restraints weight = 9546.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.110355 restraints weight = 5907.522| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 1.0614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9873 Z= 0.131 Angle : 0.621 9.346 13578 Z= 0.314 Chirality : 0.043 0.258 1646 Planarity : 0.005 0.058 1752 Dihedral : 6.323 67.883 1561 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 5.04 % Allowed : 30.69 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: 0.59 (0.23), residues: 1429 helix: 1.76 (0.17), residues: 931 sheet: -3.41 (0.65), residues: 51 loop : -2.20 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 232 HIS 0.022 0.001 HIS C 125 PHE 0.034 0.001 PHE C 41 TYR 0.035 0.002 TYR C 845 ARG 0.011 0.001 ARG C 289 Details of bonding type rmsd hydrogen bonds : bond 0.04195 ( 698) hydrogen bonds : angle 3.75531 ( 2052) SS BOND : bond 0.00311 ( 1) SS BOND : angle 0.65613 ( 2) covalent geometry : bond 0.00280 ( 9872) covalent geometry : angle 0.62062 (13576) ********************** REFINEMENT MACRO_CYCLE 10 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 185 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 32 ASN cc_start: 0.8214 (m-40) cc_final: 0.7633 (m-40) REVERT: C 54 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.6640 (mp10) REVERT: C 80 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8093 (tp) REVERT: C 158 TYR cc_start: 0.7240 (t80) cc_final: 0.6668 (t80) REVERT: C 176 VAL cc_start: 0.9172 (OUTLIER) cc_final: 0.8970 (p) REVERT: C 257 MET cc_start: 0.8663 (mpp) cc_final: 0.8434 (mtt) REVERT: C 483 GLN cc_start: 0.8353 (tt0) cc_final: 0.8148 (tm-30) REVERT: C 574 SER cc_start: 0.7534 (p) cc_final: 0.7140 (p) REVERT: C 1025 MET cc_start: 0.7988 (tpp) cc_final: 0.7717 (mmp) REVERT: C 1091 LEU cc_start: 0.8800 (tp) cc_final: 0.8379 (tt) REVERT: C 1230 TYR cc_start: 0.8771 (m-80) cc_final: 0.8547 (m-80) outliers start: 35 outliers final: 31 residues processed: 171 average time/residue: 0.1971 time to fit residues: 49.8624 Evaluate side-chains 179 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 491 HIS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 1018 PHE Chi-restraints excluded: chain C residue 1096 ARG Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain C residue 1158 SER Chi-restraints excluded: chain C residue 1163 VAL Chi-restraints excluded: chain C residue 1165 LEU Chi-restraints excluded: chain C residue 1201 VAL Chi-restraints excluded: chain C residue 1242 THR Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1272 LEU Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain C residue 1315 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 121 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 116 optimal weight: 30.0000 chunk 13 optimal weight: 7.9990 chunk 127 optimal weight: 40.0000 chunk 16 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 chunk 118 optimal weight: 20.0000 overall best weight: 4.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 HIS C 293 HIS C 491 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.128325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.102743 restraints weight = 19088.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.105302 restraints weight = 9592.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.106994 restraints weight = 5992.592| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 1.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9873 Z= 0.208 Angle : 0.667 9.192 13578 Z= 0.342 Chirality : 0.045 0.231 1646 Planarity : 0.005 0.057 1752 Dihedral : 6.444 69.882 1561 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 5.91 % Allowed : 29.68 % Favored : 64.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: 0.38 (0.23), residues: 1429 helix: 1.60 (0.17), residues: 938 sheet: -3.52 (0.63), residues: 51 loop : -2.34 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 232 HIS 0.014 0.002 HIS C 125 PHE 0.034 0.002 PHE C 41 TYR 0.031 0.002 TYR C 142 ARG 0.009 0.001 ARG C 289 Details of bonding type rmsd hydrogen bonds : bond 0.04453 ( 698) hydrogen bonds : angle 3.88882 ( 2052) SS BOND : bond 0.00538 ( 1) SS BOND : angle 0.93898 ( 2) covalent geometry : bond 0.00469 ( 9872) covalent geometry : angle 0.66663 (13576) =============================================================================== Job complete usr+sys time: 3922.24 seconds wall clock time: 70 minutes 18.16 seconds (4218.16 seconds total)