Starting phenix.real_space_refine on Tue Jul 29 05:18:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qln_53229/07_2025/9qln_53229.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qln_53229/07_2025/9qln_53229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qln_53229/07_2025/9qln_53229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qln_53229/07_2025/9qln_53229.map" model { file = "/net/cci-nas-00/data/ceres_data/9qln_53229/07_2025/9qln_53229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qln_53229/07_2025/9qln_53229.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 46 5.16 5 C 6928 2.51 5 N 1848 2.21 5 O 2001 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 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: 10829 Number of models: 1 Model: "" Number of chains: 2 Chain: "E" Number of atoms: 10823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10823 Classifications: {'peptide': 1340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 82, 'TRANS': 1255} Chain breaks: 6 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' CA': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 7.36, per 1000 atoms: 0.68 Number of scatterers: 10829 At special positions: 0 Unit cell: (82.08, 109.44, 146.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 46 16.00 O 2001 8.00 N 1848 7.00 C 6928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.4 seconds 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2514 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 16 sheets defined 18.5% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'E' and resid 255 through 258 Processing helix chain 'E' and resid 284 through 290 Processing helix chain 'E' and resid 291 through 294 removed outlier: 4.105A pdb=" N ALA E 294 " --> pdb=" O PRO E 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 291 through 294' Processing helix chain 'E' and resid 376 through 381 removed outlier: 3.688A pdb=" N VAL E 381 " --> pdb=" O PHE E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 394 removed outlier: 3.545A pdb=" N ASN E 393 " --> pdb=" O ASP E 390 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU E 394 " --> pdb=" O LYS E 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 390 through 394' Processing helix chain 'E' and resid 558 through 565 Processing helix chain 'E' and resid 566 through 569 Processing helix chain 'E' and resid 650 through 681 removed outlier: 4.497A pdb=" N ALA E 656 " --> pdb=" O HIS E 652 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 703 removed outlier: 3.975A pdb=" N ARG E 703 " --> pdb=" O ILE E 699 " (cutoff:3.500A) Processing helix chain 'E' and resid 716 through 744 removed outlier: 4.138A pdb=" N ALA E 744 " --> pdb=" O MET E 740 " (cutoff:3.500A) Processing helix chain 'E' and resid 750 through 766 removed outlier: 3.563A pdb=" N ASP E 756 " --> pdb=" O ALA E 752 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP E 759 " --> pdb=" O GLU E 755 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU E 766 " --> pdb=" O MET E 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 792 through 796 Processing helix chain 'E' and resid 845 through 852 removed outlier: 3.927A pdb=" N LYS E 848 " --> pdb=" O VAL E 845 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN E 850 " --> pdb=" O LYS E 847 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER E 851 " --> pdb=" O LYS E 848 " (cutoff:3.500A) Processing helix chain 'E' and resid 1086 through 1094 removed outlier: 3.518A pdb=" N ALA E1089 " --> pdb=" O HIS E1086 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE E1091 " --> pdb=" O ALA E1088 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU E1094 " --> pdb=" O ILE E1091 " (cutoff:3.500A) Processing helix chain 'E' and resid 1200 through 1207 removed outlier: 3.637A pdb=" N VAL E1204 " --> pdb=" O GLU E1200 " (cutoff:3.500A) Processing helix chain 'E' and resid 1239 through 1243 Processing helix chain 'E' and resid 1273 through 1277 removed outlier: 3.707A pdb=" N GLY E1276 " --> pdb=" O GLY E1273 " (cutoff:3.500A) Processing helix chain 'E' and resid 1318 through 1322 removed outlier: 4.186A pdb=" N MET E1321 " --> pdb=" O ASN E1318 " (cutoff:3.500A) Processing helix chain 'E' and resid 1381 through 1385 removed outlier: 4.184A pdb=" N GLY E1384 " --> pdb=" O ARG E1381 " (cutoff:3.500A) Processing helix chain 'E' and resid 1452 through 1462 Processing helix chain 'E' and resid 1470 through 1474 Processing helix chain 'E' and resid 1491 through 1495 removed outlier: 3.695A pdb=" N THR E1495 " --> pdb=" O GLU E1492 " (cutoff:3.500A) Processing helix chain 'E' and resid 1641 through 1646 Processing helix chain 'E' and resid 1672 through 1685 Processing helix chain 'E' and resid 1707 through 1712 Processing helix chain 'E' and resid 1722 through 1735 removed outlier: 3.623A pdb=" N HIS E1730 " --> pdb=" O ARG E1726 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 240 through 249 removed outlier: 6.168A pdb=" N PHE E 241 " --> pdb=" O GLU E 207 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLU E 207 " --> pdb=" O PHE E 241 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS E 317 " --> pdb=" O ILE E 206 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY E 208 " --> pdb=" O TYR E 315 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR E 315 " --> pdb=" O GLY E 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 218 through 224 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 227 through 230 current: chain 'E' and resid 275 through 276 Processing sheet with id=AA3, first strand: chain 'E' and resid 499 through 508 removed outlier: 5.150A pdb=" N GLY E 500 " --> pdb=" O LEU E 541 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LEU E 541 " --> pdb=" O GLY E 500 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY E 535 " --> pdb=" O LEU E 506 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLY E 508 " --> pdb=" O TYR E 533 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N TYR E 533 " --> pdb=" O GLY E 508 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG E 536 " --> pdb=" O ALA E 367 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA E 367 " --> pdb=" O ARG E 536 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU E 538 " --> pdb=" O TYR E 365 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL E 358 " --> pdb=" O ILE E 429 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE E 429 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 427 " --> pdb=" O PHE E 360 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ARG E 366 " --> pdb=" O TRP E 421 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TRP E 421 " --> pdb=" O ARG E 366 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 406 through 409 removed outlier: 3.601A pdb=" N THR E 441 " --> pdb=" O GLU E 400 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER E 402 " --> pdb=" O LYS E 439 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY E 455 " --> pdb=" O ILE E 442 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASP E 444 " --> pdb=" O VAL E 453 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL E 453 " --> pdb=" O ASP E 444 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 571 through 584 removed outlier: 8.601A pdb=" N SER E 582 " --> pdb=" O THR E 637 " (cutoff:3.500A) removed outlier: 12.189A pdb=" N THR E 637 " --> pdb=" O SER E 582 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 637 through 648 current: chain 'E' and resid 833 through 842 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 833 through 842 current: chain 'E' and resid 873 through 875 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 873 through 875 current: chain 'E' and resid 1071 through 1082 Processing sheet with id=AA6, first strand: chain 'E' and resid 593 through 599 removed outlier: 6.688A pdb=" N MET E 779 " --> pdb=" O LEU E 786 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 623 through 624 Processing sheet with id=AA8, first strand: chain 'E' and resid 1136 through 1149 removed outlier: 6.591A pdb=" N TYR E1137 " --> pdb=" O GLU E1196 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLU E1196 " --> pdb=" O TYR E1137 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N TYR E1139 " --> pdb=" O GLU E1194 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU E1194 " --> pdb=" O TYR E1139 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLN E1147 " --> pdb=" O TRP E1186 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP E1186 " --> pdb=" O GLN E1147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 1185 through 1198 current: chain 'E' and resid 1258 through 1271 Processing sheet with id=AA9, first strand: chain 'E' and resid 1171 through 1174 removed outlier: 3.521A pdb=" N GLY E1228 " --> pdb=" O LEU E1215 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASP E1217 " --> pdb=" O PHE E1226 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE E1226 " --> pdb=" O ASP E1217 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 1285 through 1287 removed outlier: 3.816A pdb=" N ALA E1287 " --> pdb=" O LEU E1290 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 1356 through 1364 Processing sheet with id=AB3, first strand: chain 'E' and resid 1312 through 1314 removed outlier: 3.818A pdb=" N GLY E1312 " --> pdb=" O LYS E1521 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 1336 through 1339 removed outlier: 3.568A pdb=" N GLU E1336 " --> pdb=" O CYS E1333 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY E1390 " --> pdb=" O VAL E1377 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASP E1379 " --> pdb=" O VAL E1388 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL E1388 " --> pdb=" O ASP E1379 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 1479 through 1480 removed outlier: 6.920A pdb=" N LYS E1479 " --> pdb=" O VAL E1742 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N THR E1744 " --> pdb=" O LYS E1479 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N HIS E1741 " --> pdb=" O VAL E1764 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL E1764 " --> pdb=" O HIS E1741 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU E1760 " --> pdb=" O ARG E1745 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS E1759 " --> pdb=" O GLY E1562 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLY E1562 " --> pdb=" O LYS E1759 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLN E1761 " --> pdb=" O VAL E1560 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE E1559 " --> pdb=" O ARG E1604 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 1585 through 1589 removed outlier: 4.188A pdb=" N ILE E1578 " --> pdb=" O ASP E1589 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASP E1624 " --> pdb=" O LYS E1633 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS E1633 " --> pdb=" O ASP E1624 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 1690 through 1691 303 hydrogen bonds defined for protein. 810 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: 4.08 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3502 1.34 - 1.46: 2483 1.46 - 1.58: 5034 1.58 - 1.70: 1 1.70 - 1.82: 72 Bond restraints: 11092 Sorted by residual: bond pdb=" C LEU E 349 " pdb=" N PRO E 350 " ideal model delta sigma weight residual 1.332 1.363 -0.031 1.12e-02 7.97e+03 7.68e+00 bond pdb=" CB ASN E 267 " pdb=" CG ASN E 267 " ideal model delta sigma weight residual 1.516 1.574 -0.058 2.50e-02 1.60e+03 5.47e+00 bond pdb=" CB LYS E1619 " pdb=" CG LYS E1619 " ideal model delta sigma weight residual 1.520 1.586 -0.066 3.00e-02 1.11e+03 4.89e+00 bond pdb=" CA ARG E1396 " pdb=" CB ARG E1396 " ideal model delta sigma weight residual 1.524 1.552 -0.027 1.30e-02 5.92e+03 4.40e+00 bond pdb=" CB PHE E1319 " pdb=" CG PHE E1319 " ideal model delta sigma weight residual 1.502 1.550 -0.048 2.30e-02 1.89e+03 4.32e+00 ... (remaining 11087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 14922 4.18 - 8.36: 89 8.36 - 12.54: 26 12.54 - 16.72: 0 16.72 - 20.90: 1 Bond angle restraints: 15038 Sorted by residual: angle pdb=" CA LEU E 563 " pdb=" CB LEU E 563 " pdb=" CG LEU E 563 " ideal model delta sigma weight residual 116.30 137.20 -20.90 3.50e+00 8.16e-02 3.57e+01 angle pdb=" N VAL E 589 " pdb=" CA VAL E 589 " pdb=" C VAL E 589 " ideal model delta sigma weight residual 113.71 108.46 5.25 9.50e-01 1.11e+00 3.05e+01 angle pdb=" C HIS E1464 " pdb=" N GLU E1465 " pdb=" CA GLU E1465 " ideal model delta sigma weight residual 121.54 131.85 -10.31 1.91e+00 2.74e-01 2.91e+01 angle pdb=" CA LYS E1619 " pdb=" CB LYS E1619 " pdb=" CG LYS E1619 " ideal model delta sigma weight residual 114.10 124.65 -10.55 2.00e+00 2.50e-01 2.78e+01 angle pdb=" CA LYS E1502 " pdb=" CB LYS E1502 " pdb=" CG LYS E1502 " ideal model delta sigma weight residual 114.10 124.51 -10.41 2.00e+00 2.50e-01 2.71e+01 ... (remaining 15033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5936 17.98 - 35.96: 586 35.96 - 53.94: 132 53.94 - 71.91: 19 71.91 - 89.89: 13 Dihedral angle restraints: 6686 sinusoidal: 2787 harmonic: 3899 Sorted by residual: dihedral pdb=" CA ASN E 303 " pdb=" C ASN E 303 " pdb=" N ASP E 304 " pdb=" CA ASP E 304 " ideal model delta harmonic sigma weight residual 180.00 154.06 25.94 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA THR E 548 " pdb=" C THR E 548 " pdb=" N PRO E 549 " pdb=" CA PRO E 549 " ideal model delta harmonic sigma weight residual -180.00 -155.69 -24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA CYS E1467 " pdb=" C CYS E1467 " pdb=" N GLY E1468 " pdb=" CA GLY E1468 " ideal model delta harmonic sigma weight residual -180.00 -156.64 -23.36 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 6683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 1606 0.150 - 0.300: 21 0.300 - 0.450: 1 0.450 - 0.600: 1 0.600 - 0.750: 1 Chirality restraints: 1630 Sorted by residual: chirality pdb=" CB VAL E 845 " pdb=" CA VAL E 845 " pdb=" CG1 VAL E 845 " pdb=" CG2 VAL E 845 " both_signs ideal model delta sigma weight residual False -2.63 -1.88 -0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" CG LEU E1732 " pdb=" CB LEU E1732 " pdb=" CD1 LEU E1732 " pdb=" CD2 LEU E1732 " both_signs ideal model delta sigma weight residual False -2.59 -2.03 -0.56 2.00e-01 2.50e+01 7.90e+00 chirality pdb=" CG LEU E1271 " pdb=" CB LEU E1271 " pdb=" CD1 LEU E1271 " pdb=" CD2 LEU E1271 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 1627 not shown) Planarity restraints: 1945 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E1453 " -0.035 2.00e-02 2.50e+03 2.16e-02 1.16e+01 pdb=" CG TRP E1453 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP E1453 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP E1453 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP E1453 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E1453 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E1453 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP E1453 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP E1453 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E1453 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 398 " 0.019 2.00e-02 2.50e+03 2.49e-02 1.09e+01 pdb=" CG PHE E 398 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE E 398 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE E 398 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE E 398 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE E 398 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE E 398 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 702 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.35e+00 pdb=" C THR E 702 " -0.053 2.00e-02 2.50e+03 pdb=" O THR E 702 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG E 703 " 0.018 2.00e-02 2.50e+03 ... (remaining 1942 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 3459 2.87 - 3.38: 9740 3.38 - 3.88: 18214 3.88 - 4.39: 20061 4.39 - 4.90: 34244 Nonbonded interactions: 85718 Sorted by model distance: nonbonded pdb=" O TYR E1625 " pdb="CA CA E2005 " model vdw 2.362 2.510 nonbonded pdb=" OD2 ASP E1626 " pdb="CA CA E2006 " model vdw 2.363 2.510 nonbonded pdb=" OD2 ASP E1575 " pdb="CA CA E2005 " model vdw 2.367 2.510 nonbonded pdb=" OD1 ASP E1624 " pdb="CA CA E2005 " model vdw 2.371 2.510 nonbonded pdb=" O GLN E1568 " pdb="CA CA E2006 " model vdw 2.372 2.510 ... (remaining 85713 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 20.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 28.230 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 11092 Z= 0.222 Angle : 1.002 20.901 15038 Z= 0.533 Chirality : 0.060 0.750 1630 Planarity : 0.007 0.064 1945 Dihedral : 15.290 89.894 4172 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.45 % Favored : 95.48 % Rotamer: Outliers : 1.34 % Allowed : 13.12 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.22), residues: 1326 helix: -2.02 (0.30), residues: 178 sheet: -0.80 (0.26), residues: 410 loop : -1.05 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP E1453 HIS 0.020 0.002 HIS E 460 PHE 0.057 0.002 PHE E 398 TYR 0.020 0.002 TYR E1139 ARG 0.016 0.001 ARG E 781 Details of bonding type rmsd hydrogen bonds : bond 0.21473 ( 303) hydrogen bonds : angle 9.06346 ( 810) covalent geometry : bond 0.00458 (11092) covalent geometry : angle 1.00246 (15038) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 257 MET cc_start: 0.6805 (mpp) cc_final: 0.6586 (mpp) REVERT: E 316 MET cc_start: 0.8720 (mmm) cc_final: 0.8466 (mmt) REVERT: E 1254 MET cc_start: 0.8404 (tmm) cc_final: 0.8080 (mpp) REVERT: E 1762 MET cc_start: 0.5312 (mtm) cc_final: 0.4959 (mtm) outliers start: 16 outliers final: 11 residues processed: 122 average time/residue: 0.2324 time to fit residues: 43.2146 Evaluate side-chains 118 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 720 THR Chi-restraints excluded: chain E residue 870 MET Chi-restraints excluded: chain E residue 1083 SER Chi-restraints excluded: chain E residue 1158 SER Chi-restraints excluded: chain E residue 1233 SER Chi-restraints excluded: chain E residue 1300 VAL Chi-restraints excluded: chain E residue 1625 TYR Chi-restraints excluded: chain E residue 1732 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 54 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.161147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.116781 restraints weight = 26563.161| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 4.26 r_work: 0.3861 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11092 Z= 0.122 Angle : 0.586 12.293 15038 Z= 0.301 Chirality : 0.045 0.189 1630 Planarity : 0.005 0.052 1945 Dihedral : 6.021 48.385 1479 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.17 % Allowed : 14.45 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.23), residues: 1326 helix: -0.52 (0.35), residues: 174 sheet: -0.73 (0.26), residues: 426 loop : -0.69 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E1453 HIS 0.006 0.001 HIS E 460 PHE 0.017 0.001 PHE E1778 TYR 0.016 0.001 TYR E 533 ARG 0.002 0.000 ARG E 781 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 303) hydrogen bonds : angle 6.46720 ( 810) covalent geometry : bond 0.00269 (11092) covalent geometry : angle 0.58640 (15038) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 257 MET cc_start: 0.6801 (mpp) cc_final: 0.6177 (mmm) REVERT: E 316 MET cc_start: 0.8929 (mmm) cc_final: 0.8488 (mmm) REVERT: E 1289 ASN cc_start: 0.8721 (t0) cc_final: 0.8462 (p0) REVERT: E 1370 MET cc_start: 0.8558 (tmm) cc_final: 0.8080 (tmm) REVERT: E 1762 MET cc_start: 0.5591 (mtm) cc_final: 0.5269 (mtm) outliers start: 14 outliers final: 7 residues processed: 118 average time/residue: 0.1919 time to fit residues: 35.0620 Evaluate side-chains 106 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 720 THR Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1167 CYS Chi-restraints excluded: chain E residue 1300 VAL Chi-restraints excluded: chain E residue 1611 TYR Chi-restraints excluded: chain E residue 1732 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 122 optimal weight: 0.3980 chunk 62 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 128 optimal weight: 20.0000 chunk 89 optimal weight: 0.0050 chunk 77 optimal weight: 0.6980 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.160940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.115754 restraints weight = 26947.323| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 4.31 r_work: 0.3848 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11092 Z= 0.109 Angle : 0.552 11.175 15038 Z= 0.278 Chirality : 0.044 0.214 1630 Planarity : 0.004 0.049 1945 Dihedral : 5.167 41.199 1468 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.76 % Allowed : 13.87 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.23), residues: 1326 helix: 0.34 (0.37), residues: 172 sheet: -0.61 (0.26), residues: 415 loop : -0.46 (0.24), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E1453 HIS 0.006 0.001 HIS E 460 PHE 0.015 0.001 PHE E 849 TYR 0.017 0.001 TYR E1558 ARG 0.003 0.000 ARG E 781 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 303) hydrogen bonds : angle 5.71616 ( 810) covalent geometry : bond 0.00245 (11092) covalent geometry : angle 0.55239 (15038) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 257 MET cc_start: 0.6875 (mpp) cc_final: 0.6242 (mmm) REVERT: E 277 MET cc_start: 0.7114 (mmm) cc_final: 0.6683 (mmm) REVERT: E 316 MET cc_start: 0.8910 (mmm) cc_final: 0.8472 (mmm) REVERT: E 373 MET cc_start: 0.7050 (mmm) cc_final: 0.6785 (mmm) REVERT: E 495 PHE cc_start: 0.6813 (OUTLIER) cc_final: 0.6366 (m-10) REVERT: E 1370 MET cc_start: 0.8546 (tmm) cc_final: 0.8046 (tmm) REVERT: E 1762 MET cc_start: 0.5547 (mtm) cc_final: 0.5242 (mtm) outliers start: 33 outliers final: 12 residues processed: 135 average time/residue: 0.3019 time to fit residues: 63.8968 Evaluate side-chains 116 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 495 PHE Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1132 ASN Chi-restraints excluded: chain E residue 1158 SER Chi-restraints excluded: chain E residue 1167 CYS Chi-restraints excluded: chain E residue 1242 MET Chi-restraints excluded: chain E residue 1300 VAL Chi-restraints excluded: chain E residue 1557 ILE Chi-restraints excluded: chain E residue 1605 MET Chi-restraints excluded: chain E residue 1611 TYR Chi-restraints excluded: chain E residue 1732 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 121 optimal weight: 30.0000 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E1289 ASN ** E1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.158337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.112248 restraints weight = 26607.526| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 4.26 r_work: 0.3771 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11092 Z= 0.160 Angle : 0.587 11.828 15038 Z= 0.296 Chirality : 0.045 0.230 1630 Planarity : 0.004 0.048 1945 Dihedral : 5.169 34.854 1467 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.34 % Allowed : 14.62 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.24), residues: 1326 helix: 0.50 (0.38), residues: 175 sheet: -0.61 (0.26), residues: 417 loop : -0.40 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E1453 HIS 0.007 0.001 HIS E 460 PHE 0.015 0.001 PHE E 398 TYR 0.015 0.001 TYR E1146 ARG 0.004 0.000 ARG E 703 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 303) hydrogen bonds : angle 5.57007 ( 810) covalent geometry : bond 0.00368 (11092) covalent geometry : angle 0.58714 (15038) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 257 MET cc_start: 0.6916 (mpp) cc_final: 0.6273 (mmm) REVERT: E 277 MET cc_start: 0.7295 (mmm) cc_final: 0.6861 (mmm) REVERT: E 316 MET cc_start: 0.8882 (mmm) cc_final: 0.8533 (mmm) REVERT: E 495 PHE cc_start: 0.6930 (OUTLIER) cc_final: 0.6484 (m-10) REVERT: E 646 TYR cc_start: 0.7071 (m-10) cc_final: 0.6599 (m-80) REVERT: E 694 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8025 (mp) REVERT: E 758 LEU cc_start: 0.8683 (tp) cc_final: 0.8482 (tp) REVERT: E 1370 MET cc_start: 0.8501 (tmm) cc_final: 0.7993 (tmm) REVERT: E 1762 MET cc_start: 0.5550 (mtm) cc_final: 0.5254 (mtm) outliers start: 28 outliers final: 16 residues processed: 125 average time/residue: 0.2048 time to fit residues: 39.2914 Evaluate side-chains 117 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain E residue 288 TYR Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 495 PHE Chi-restraints excluded: chain E residue 593 ILE Chi-restraints excluded: chain E residue 694 LEU Chi-restraints excluded: chain E residue 800 THR Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1132 ASN Chi-restraints excluded: chain E residue 1158 SER Chi-restraints excluded: chain E residue 1167 CYS Chi-restraints excluded: chain E residue 1300 VAL Chi-restraints excluded: chain E residue 1557 ILE Chi-restraints excluded: chain E residue 1605 MET Chi-restraints excluded: chain E residue 1611 TYR Chi-restraints excluded: chain E residue 1732 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 44 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 125 optimal weight: 0.0050 chunk 80 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 18 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 133 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 126 optimal weight: 8.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E1643 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.160238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.114718 restraints weight = 26608.961| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 4.31 r_work: 0.3828 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11092 Z= 0.099 Angle : 0.548 12.696 15038 Z= 0.274 Chirality : 0.044 0.230 1630 Planarity : 0.004 0.040 1945 Dihedral : 4.931 36.114 1467 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.60 % Favored : 95.32 % Rotamer: Outliers : 2.26 % Allowed : 15.20 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.24), residues: 1326 helix: 0.75 (0.38), residues: 173 sheet: -0.50 (0.26), residues: 413 loop : -0.32 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E1453 HIS 0.008 0.001 HIS E1719 PHE 0.017 0.001 PHE E1683 TYR 0.024 0.001 TYR E 533 ARG 0.002 0.000 ARG E 536 Details of bonding type rmsd hydrogen bonds : bond 0.03056 ( 303) hydrogen bonds : angle 5.31763 ( 810) covalent geometry : bond 0.00223 (11092) covalent geometry : angle 0.54815 (15038) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 257 MET cc_start: 0.6891 (mpp) cc_final: 0.6478 (mpp) REVERT: E 277 MET cc_start: 0.7301 (mmm) cc_final: 0.6869 (mmm) REVERT: E 316 MET cc_start: 0.8941 (mmm) cc_final: 0.8613 (mmm) REVERT: E 373 MET cc_start: 0.7095 (mmm) cc_final: 0.6834 (mmm) REVERT: E 495 PHE cc_start: 0.6804 (OUTLIER) cc_final: 0.6373 (m-10) REVERT: E 646 TYR cc_start: 0.6924 (m-10) cc_final: 0.6512 (m-80) REVERT: E 694 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7994 (mp) REVERT: E 833 GLU cc_start: 0.8272 (tt0) cc_final: 0.7986 (tt0) REVERT: E 1370 MET cc_start: 0.8385 (tmm) cc_final: 0.7877 (tmm) REVERT: E 1762 MET cc_start: 0.5647 (mtm) cc_final: 0.5351 (mtm) outliers start: 27 outliers final: 18 residues processed: 130 average time/residue: 0.1953 time to fit residues: 39.1018 Evaluate side-chains 121 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 495 PHE Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 593 ILE Chi-restraints excluded: chain E residue 619 TYR Chi-restraints excluded: chain E residue 694 LEU Chi-restraints excluded: chain E residue 800 THR Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1132 ASN Chi-restraints excluded: chain E residue 1158 SER Chi-restraints excluded: chain E residue 1167 CYS Chi-restraints excluded: chain E residue 1300 VAL Chi-restraints excluded: chain E residue 1557 ILE Chi-restraints excluded: chain E residue 1605 MET Chi-restraints excluded: chain E residue 1611 TYR Chi-restraints excluded: chain E residue 1664 VAL Chi-restraints excluded: chain E residue 1732 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 114 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 79 optimal weight: 0.1980 chunk 125 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 581 HIS ** E1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1748 HIS E1757 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.156332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.109173 restraints weight = 26745.211| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 4.30 r_work: 0.3723 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11092 Z= 0.200 Angle : 0.621 11.288 15038 Z= 0.312 Chirality : 0.046 0.208 1630 Planarity : 0.004 0.043 1945 Dihedral : 5.247 37.511 1467 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.05 % Favored : 94.87 % Rotamer: Outliers : 2.59 % Allowed : 15.96 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.24), residues: 1326 helix: 0.71 (0.38), residues: 173 sheet: -0.58 (0.26), residues: 416 loop : -0.37 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E1453 HIS 0.007 0.001 HIS E1719 PHE 0.022 0.002 PHE E 398 TYR 0.020 0.002 TYR E 533 ARG 0.003 0.000 ARG E1298 Details of bonding type rmsd hydrogen bonds : bond 0.03571 ( 303) hydrogen bonds : angle 5.53174 ( 810) covalent geometry : bond 0.00460 (11092) covalent geometry : angle 0.62145 (15038) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 257 MET cc_start: 0.6989 (mpp) cc_final: 0.6555 (mpp) REVERT: E 277 MET cc_start: 0.7400 (mmm) cc_final: 0.6965 (mmm) REVERT: E 316 MET cc_start: 0.8866 (mmm) cc_final: 0.8527 (mmm) REVERT: E 495 PHE cc_start: 0.7001 (OUTLIER) cc_final: 0.6611 (m-10) REVERT: E 694 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8015 (mp) REVERT: E 863 MET cc_start: 0.2204 (ppp) cc_final: 0.1988 (ppp) REVERT: E 1344 LYS cc_start: 0.8541 (pptt) cc_final: 0.8258 (pptt) REVERT: E 1558 TYR cc_start: 0.7043 (m-80) cc_final: 0.6682 (m-80) REVERT: E 1762 MET cc_start: 0.5662 (mtm) cc_final: 0.5371 (mtm) outliers start: 31 outliers final: 22 residues processed: 133 average time/residue: 0.2089 time to fit residues: 41.7641 Evaluate side-chains 125 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 366 ARG Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 452 ASP Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 495 PHE Chi-restraints excluded: chain E residue 588 ASP Chi-restraints excluded: chain E residue 593 ILE Chi-restraints excluded: chain E residue 676 SER Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 694 LEU Chi-restraints excluded: chain E residue 695 ILE Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1132 ASN Chi-restraints excluded: chain E residue 1158 SER Chi-restraints excluded: chain E residue 1167 CYS Chi-restraints excluded: chain E residue 1300 VAL Chi-restraints excluded: chain E residue 1557 ILE Chi-restraints excluded: chain E residue 1605 MET Chi-restraints excluded: chain E residue 1611 TYR Chi-restraints excluded: chain E residue 1664 VAL Chi-restraints excluded: chain E residue 1732 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 96 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 32 optimal weight: 0.0020 chunk 38 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 6 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 7 optimal weight: 0.1980 chunk 43 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 372 GLN E 460 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.159685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.113769 restraints weight = 26976.571| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 4.30 r_work: 0.3807 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11092 Z= 0.102 Angle : 0.575 11.627 15038 Z= 0.288 Chirality : 0.044 0.227 1630 Planarity : 0.004 0.040 1945 Dihedral : 4.947 35.276 1467 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.22 % Favored : 95.70 % Rotamer: Outliers : 1.92 % Allowed : 17.21 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.24), residues: 1326 helix: 0.76 (0.39), residues: 174 sheet: -0.43 (0.26), residues: 416 loop : -0.29 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E1763 HIS 0.007 0.001 HIS E1719 PHE 0.012 0.001 PHE E 849 TYR 0.022 0.001 TYR E 533 ARG 0.003 0.000 ARG E 536 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 303) hydrogen bonds : angle 5.21497 ( 810) covalent geometry : bond 0.00227 (11092) covalent geometry : angle 0.57533 (15038) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 257 MET cc_start: 0.6979 (mpp) cc_final: 0.6544 (mpp) REVERT: E 277 MET cc_start: 0.7366 (mmm) cc_final: 0.6928 (mmm) REVERT: E 316 MET cc_start: 0.8969 (mmm) cc_final: 0.8635 (mmm) REVERT: E 373 MET cc_start: 0.7213 (mmm) cc_final: 0.6979 (mmm) REVERT: E 495 PHE cc_start: 0.6859 (OUTLIER) cc_final: 0.6465 (m-10) REVERT: E 646 TYR cc_start: 0.6906 (m-10) cc_final: 0.6415 (m-80) REVERT: E 694 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8031 (mp) REVERT: E 701 ASP cc_start: 0.8067 (t70) cc_final: 0.7797 (t0) REVERT: E 833 GLU cc_start: 0.8250 (tt0) cc_final: 0.7818 (tm-30) REVERT: E 1344 LYS cc_start: 0.8576 (pptt) cc_final: 0.8321 (pptt) REVERT: E 1370 MET cc_start: 0.8443 (tmm) cc_final: 0.7756 (tmm) REVERT: E 1558 TYR cc_start: 0.7078 (m-80) cc_final: 0.6767 (m-80) REVERT: E 1762 MET cc_start: 0.5590 (mtm) cc_final: 0.5325 (mtm) outliers start: 23 outliers final: 18 residues processed: 125 average time/residue: 0.2076 time to fit residues: 39.2647 Evaluate side-chains 121 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 366 ARG Chi-restraints excluded: chain E residue 495 PHE Chi-restraints excluded: chain E residue 642 THR Chi-restraints excluded: chain E residue 676 SER Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 694 LEU Chi-restraints excluded: chain E residue 800 THR Chi-restraints excluded: chain E residue 1132 ASN Chi-restraints excluded: chain E residue 1158 SER Chi-restraints excluded: chain E residue 1167 CYS Chi-restraints excluded: chain E residue 1300 VAL Chi-restraints excluded: chain E residue 1557 ILE Chi-restraints excluded: chain E residue 1605 MET Chi-restraints excluded: chain E residue 1611 TYR Chi-restraints excluded: chain E residue 1664 VAL Chi-restraints excluded: chain E residue 1732 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 53 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 69 optimal weight: 30.0000 chunk 120 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 129 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.157372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.110599 restraints weight = 26509.754| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 4.28 r_work: 0.3741 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11092 Z= 0.161 Angle : 0.610 12.025 15038 Z= 0.305 Chirality : 0.045 0.263 1630 Planarity : 0.004 0.042 1945 Dihedral : 5.024 33.939 1467 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.90 % Favored : 95.02 % Rotamer: Outliers : 2.34 % Allowed : 16.96 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.24), residues: 1326 helix: 0.74 (0.39), residues: 173 sheet: -0.45 (0.26), residues: 418 loop : -0.28 (0.25), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 357 HIS 0.008 0.001 HIS E1719 PHE 0.015 0.001 PHE E 398 TYR 0.019 0.001 TYR E 533 ARG 0.003 0.000 ARG E 726 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 303) hydrogen bonds : angle 5.32385 ( 810) covalent geometry : bond 0.00369 (11092) covalent geometry : angle 0.61012 (15038) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 257 MET cc_start: 0.7001 (mpp) cc_final: 0.6571 (mpp) REVERT: E 277 MET cc_start: 0.7456 (mmm) cc_final: 0.7036 (mmm) REVERT: E 316 MET cc_start: 0.8922 (mmm) cc_final: 0.8584 (mmm) REVERT: E 373 MET cc_start: 0.7334 (mmm) cc_final: 0.7123 (mmm) REVERT: E 495 PHE cc_start: 0.6907 (OUTLIER) cc_final: 0.6541 (m-10) REVERT: E 694 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8029 (mp) REVERT: E 708 LEU cc_start: 0.8772 (tp) cc_final: 0.8497 (tt) REVERT: E 833 GLU cc_start: 0.8263 (tt0) cc_final: 0.7799 (tm-30) REVERT: E 863 MET cc_start: 0.1965 (ppp) cc_final: 0.1750 (ppp) REVERT: E 1197 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7678 (mt) REVERT: E 1344 LYS cc_start: 0.8585 (pptt) cc_final: 0.8323 (pptt) REVERT: E 1370 MET cc_start: 0.8468 (tmm) cc_final: 0.7777 (tmm) REVERT: E 1558 TYR cc_start: 0.7267 (m-80) cc_final: 0.6879 (m-80) REVERT: E 1762 MET cc_start: 0.5688 (mtm) cc_final: 0.5393 (mtm) outliers start: 28 outliers final: 19 residues processed: 121 average time/residue: 0.2139 time to fit residues: 40.1340 Evaluate side-chains 122 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 366 ARG Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 495 PHE Chi-restraints excluded: chain E residue 676 SER Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 694 LEU Chi-restraints excluded: chain E residue 697 GLU Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1132 ASN Chi-restraints excluded: chain E residue 1158 SER Chi-restraints excluded: chain E residue 1167 CYS Chi-restraints excluded: chain E residue 1197 ILE Chi-restraints excluded: chain E residue 1300 VAL Chi-restraints excluded: chain E residue 1557 ILE Chi-restraints excluded: chain E residue 1605 MET Chi-restraints excluded: chain E residue 1611 TYR Chi-restraints excluded: chain E residue 1664 VAL Chi-restraints excluded: chain E residue 1732 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 115 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 69 optimal weight: 30.0000 chunk 31 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1568 GLN ** E1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.156605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.109403 restraints weight = 26971.371| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 4.31 r_work: 0.3724 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11092 Z= 0.175 Angle : 0.613 12.063 15038 Z= 0.308 Chirality : 0.046 0.263 1630 Planarity : 0.004 0.041 1945 Dihedral : 5.118 34.637 1467 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.81 % Favored : 94.12 % Rotamer: Outliers : 2.17 % Allowed : 17.21 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.24), residues: 1326 helix: 0.77 (0.39), residues: 172 sheet: -0.48 (0.27), residues: 407 loop : -0.31 (0.24), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 357 HIS 0.008 0.001 HIS E1719 PHE 0.015 0.001 PHE E 398 TYR 0.019 0.001 TYR E 533 ARG 0.003 0.000 ARG E 334 Details of bonding type rmsd hydrogen bonds : bond 0.03391 ( 303) hydrogen bonds : angle 5.33166 ( 810) covalent geometry : bond 0.00401 (11092) covalent geometry : angle 0.61257 (15038) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 257 MET cc_start: 0.7072 (mpp) cc_final: 0.6649 (mpp) REVERT: E 277 MET cc_start: 0.7476 (mmm) cc_final: 0.7035 (mmm) REVERT: E 316 MET cc_start: 0.8960 (mmm) cc_final: 0.8629 (mmm) REVERT: E 373 MET cc_start: 0.7366 (mmm) cc_final: 0.7162 (mmm) REVERT: E 495 PHE cc_start: 0.6964 (OUTLIER) cc_final: 0.6650 (m-10) REVERT: E 663 MET cc_start: 0.7250 (mmm) cc_final: 0.7001 (mmm) REVERT: E 694 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8045 (mp) REVERT: E 708 LEU cc_start: 0.8786 (tp) cc_final: 0.8433 (tt) REVERT: E 833 GLU cc_start: 0.8288 (tt0) cc_final: 0.7856 (tm-30) REVERT: E 863 MET cc_start: 0.1995 (ppp) cc_final: 0.1776 (ppp) REVERT: E 1254 MET cc_start: 0.8308 (tmm) cc_final: 0.7858 (mmm) REVERT: E 1370 MET cc_start: 0.8490 (tmm) cc_final: 0.7800 (tmm) REVERT: E 1558 TYR cc_start: 0.7329 (m-80) cc_final: 0.6876 (m-80) REVERT: E 1762 MET cc_start: 0.5825 (mtm) cc_final: 0.5555 (mtm) outliers start: 26 outliers final: 20 residues processed: 120 average time/residue: 0.1911 time to fit residues: 35.2297 Evaluate side-chains 121 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 366 ARG Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 495 PHE Chi-restraints excluded: chain E residue 676 SER Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 694 LEU Chi-restraints excluded: chain E residue 697 GLU Chi-restraints excluded: chain E residue 800 THR Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1132 ASN Chi-restraints excluded: chain E residue 1158 SER Chi-restraints excluded: chain E residue 1167 CYS Chi-restraints excluded: chain E residue 1300 VAL Chi-restraints excluded: chain E residue 1557 ILE Chi-restraints excluded: chain E residue 1605 MET Chi-restraints excluded: chain E residue 1611 TYR Chi-restraints excluded: chain E residue 1664 VAL Chi-restraints excluded: chain E residue 1732 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 26 optimal weight: 0.2980 chunk 63 optimal weight: 5.9990 chunk 69 optimal weight: 30.0000 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 36 optimal weight: 0.0870 chunk 129 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 132 optimal weight: 6.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.158770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.112880 restraints weight = 26525.790| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 4.27 r_work: 0.3781 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11092 Z= 0.108 Angle : 0.585 13.503 15038 Z= 0.291 Chirality : 0.045 0.301 1630 Planarity : 0.004 0.040 1945 Dihedral : 4.846 31.149 1467 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.30 % Favored : 95.63 % Rotamer: Outliers : 1.67 % Allowed : 17.46 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1326 helix: 0.83 (0.40), residues: 174 sheet: -0.36 (0.27), residues: 418 loop : -0.23 (0.25), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 357 HIS 0.007 0.001 HIS E1719 PHE 0.009 0.001 PHE E1352 TYR 0.021 0.001 TYR E 533 ARG 0.003 0.000 ARG E 536 Details of bonding type rmsd hydrogen bonds : bond 0.03130 ( 303) hydrogen bonds : angle 5.10528 ( 810) covalent geometry : bond 0.00245 (11092) covalent geometry : angle 0.58540 (15038) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 246 PHE cc_start: 0.8605 (m-80) cc_final: 0.8349 (m-80) REVERT: E 257 MET cc_start: 0.7017 (mpp) cc_final: 0.6600 (mpp) REVERT: E 277 MET cc_start: 0.7478 (mmm) cc_final: 0.7040 (mmm) REVERT: E 316 MET cc_start: 0.8995 (mmm) cc_final: 0.8655 (mmm) REVERT: E 373 MET cc_start: 0.7228 (mmm) cc_final: 0.7002 (mmm) REVERT: E 459 LEU cc_start: 0.8643 (tt) cc_final: 0.8439 (tp) REVERT: E 495 PHE cc_start: 0.6954 (OUTLIER) cc_final: 0.6624 (m-10) REVERT: E 694 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8006 (mp) REVERT: E 701 ASP cc_start: 0.7956 (p0) cc_final: 0.7514 (p0) REVERT: E 708 LEU cc_start: 0.8842 (tp) cc_final: 0.8478 (tt) REVERT: E 833 GLU cc_start: 0.8252 (tt0) cc_final: 0.7818 (tm-30) REVERT: E 1370 MET cc_start: 0.8407 (tmm) cc_final: 0.7720 (tmm) REVERT: E 1558 TYR cc_start: 0.7352 (m-80) cc_final: 0.6939 (m-80) REVERT: E 1762 MET cc_start: 0.5866 (mtm) cc_final: 0.5592 (mtm) outliers start: 20 outliers final: 17 residues processed: 120 average time/residue: 0.2086 time to fit residues: 38.0510 Evaluate side-chains 121 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 212 SER Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 366 ARG Chi-restraints excluded: chain E residue 495 PHE Chi-restraints excluded: chain E residue 588 ASP Chi-restraints excluded: chain E residue 676 SER Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 694 LEU Chi-restraints excluded: chain E residue 800 THR Chi-restraints excluded: chain E residue 1132 ASN Chi-restraints excluded: chain E residue 1158 SER Chi-restraints excluded: chain E residue 1167 CYS Chi-restraints excluded: chain E residue 1300 VAL Chi-restraints excluded: chain E residue 1557 ILE Chi-restraints excluded: chain E residue 1605 MET Chi-restraints excluded: chain E residue 1611 TYR Chi-restraints excluded: chain E residue 1664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 48 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 64 optimal weight: 40.0000 chunk 4 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 88 optimal weight: 0.3980 chunk 71 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 15 optimal weight: 0.0770 overall best weight: 3.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS E1086 HIS ** E1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.153756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.107906 restraints weight = 26484.900| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 4.59 r_work: 0.3648 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 11092 Z= 0.287 Angle : 0.713 12.891 15038 Z= 0.359 Chirality : 0.049 0.258 1630 Planarity : 0.005 0.048 1945 Dihedral : 5.304 24.047 1465 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.49 % Favored : 93.44 % Rotamer: Outliers : 1.84 % Allowed : 17.79 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.24), residues: 1326 helix: 0.46 (0.38), residues: 178 sheet: -0.58 (0.27), residues: 402 loop : -0.46 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 357 HIS 0.010 0.001 HIS E1719 PHE 0.028 0.002 PHE E 398 TYR 0.022 0.002 TYR E1593 ARG 0.007 0.001 ARG E1561 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 303) hydrogen bonds : angle 5.64168 ( 810) covalent geometry : bond 0.00657 (11092) covalent geometry : angle 0.71311 (15038) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7451.06 seconds wall clock time: 129 minutes 13.53 seconds (7753.53 seconds total)