Starting phenix.real_space_refine on Wed Sep 17 20:09:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qln_53229/09_2025/9qln_53229.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qln_53229/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9qln_53229/09_2025/9qln_53229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qln_53229/09_2025/9qln_53229.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qln_53229/09_2025/9qln_53229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qln_53229/09_2025/9qln_53229.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.39, per 1000 atoms: 0.22 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: 0.74 Conformation dependent library (CDL) restraints added in 469.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.39 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: 1.89 Time building geometry restraints manager: 0.94 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: 4.880 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.400 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.040 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.016 0.001 ARG E 781 TYR 0.020 0.002 TYR E1139 PHE 0.057 0.002 PHE E 398 TRP 0.054 0.002 TRP E1453 HIS 0.020 0.002 HIS E 460 Details of bonding type rmsd covalent geometry : bond 0.00458 (11092) covalent geometry : angle 1.00246 (15038) hydrogen bonds : bond 0.21473 ( 303) hydrogen bonds : angle 9.06346 ( 810) *********************** 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 : 0.415 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: 0.0914 time to fit residues: 16.6594 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 : 0.341 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.4649 r_free = 0.4649 target = 0.157950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.111536 restraints weight = 26684.909| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 4.33 r_work: 0.3764 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11092 Z= 0.214 Angle : 0.641 11.298 15038 Z= 0.331 Chirality : 0.046 0.181 1630 Planarity : 0.005 0.053 1945 Dihedral : 6.189 48.023 1479 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.45 % Favored : 95.48 % Rotamer: Outliers : 2.34 % Allowed : 13.95 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.23), residues: 1326 helix: -0.37 (0.36), residues: 172 sheet: -0.83 (0.26), residues: 420 loop : -0.68 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 790 TYR 0.017 0.002 TYR E1146 PHE 0.017 0.002 PHE E 398 TRP 0.030 0.002 TRP E1453 HIS 0.008 0.002 HIS E 581 Details of bonding type rmsd covalent geometry : bond 0.00480 (11092) covalent geometry : angle 0.64072 (15038) hydrogen bonds : bond 0.04288 ( 303) hydrogen bonds : angle 6.51110 ( 810) *********************** 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 132 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 257 MET cc_start: 0.6896 (mpp) cc_final: 0.6296 (mmm) REVERT: E 316 MET cc_start: 0.8887 (mmm) cc_final: 0.8610 (mmt) REVERT: E 495 PHE cc_start: 0.6928 (OUTLIER) cc_final: 0.6455 (m-10) REVERT: E 758 LEU cc_start: 0.8656 (tp) cc_final: 0.8448 (tp) REVERT: E 833 GLU cc_start: 0.8148 (tt0) cc_final: 0.7939 (tt0) REVERT: E 1289 ASN cc_start: 0.8809 (t0) cc_final: 0.8516 (p0) REVERT: E 1370 MET cc_start: 0.8608 (tmm) cc_final: 0.8157 (tmm) REVERT: E 1762 MET cc_start: 0.5668 (mtm) cc_final: 0.5346 (mtm) outliers start: 28 outliers final: 14 residues processed: 128 average time/residue: 0.0827 time to fit residues: 16.3503 Evaluate side-chains 112 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 355 LEU 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 695 ILE Chi-restraints excluded: chain E residue 720 THR Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain E residue 1132 ASN 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 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 64 optimal weight: 40.0000 chunk 131 optimal weight: 0.0370 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 16 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 0.3980 chunk 114 optimal weight: 9.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- 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 = 0.4674 r_free = 0.4674 target = 0.159774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.114110 restraints weight = 26782.165| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 4.32 r_work: 0.3824 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11092 Z= 0.109 Angle : 0.564 11.155 15038 Z= 0.285 Chirality : 0.044 0.214 1630 Planarity : 0.004 0.048 1945 Dihedral : 5.299 40.439 1468 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.01 % Allowed : 14.79 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.23), residues: 1326 helix: 0.31 (0.37), residues: 172 sheet: -0.74 (0.26), residues: 413 loop : -0.49 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 703 TYR 0.025 0.001 TYR E 533 PHE 0.015 0.001 PHE E 849 TRP 0.021 0.001 TRP E1453 HIS 0.006 0.001 HIS E1719 Details of bonding type rmsd covalent geometry : bond 0.00245 (11092) covalent geometry : angle 0.56447 (15038) hydrogen bonds : bond 0.03572 ( 303) hydrogen bonds : angle 5.83076 ( 810) *********************** 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 130 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 257 MET cc_start: 0.6901 (mpp) cc_final: 0.6266 (mmm) REVERT: E 277 MET cc_start: 0.7172 (mmm) cc_final: 0.6717 (mmm) REVERT: E 316 MET cc_start: 0.8930 (mmm) cc_final: 0.8602 (mmm) REVERT: E 646 TYR cc_start: 0.6999 (m-10) cc_final: 0.6620 (m-80) REVERT: E 1370 MET cc_start: 0.8488 (tmm) cc_final: 0.7987 (tmm) REVERT: E 1762 MET cc_start: 0.5598 (mtm) cc_final: 0.5286 (mtm) outliers start: 24 outliers final: 11 residues processed: 125 average time/residue: 0.0755 time to fit residues: 14.9126 Evaluate side-chains 108 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 593 ILE Chi-restraints excluded: chain E residue 695 ILE Chi-restraints excluded: chain E residue 697 GLU 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 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 2 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 132 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.4657 r_free = 0.4657 target = 0.158655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.112480 restraints weight = 26917.895| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 4.31 r_work: 0.3788 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11092 Z= 0.137 Angle : 0.571 12.617 15038 Z= 0.288 Chirality : 0.044 0.221 1630 Planarity : 0.004 0.047 1945 Dihedral : 5.159 29.372 1467 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.34 % Allowed : 15.04 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.24), residues: 1326 helix: 0.56 (0.38), residues: 174 sheet: -0.70 (0.26), residues: 420 loop : -0.42 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 536 TYR 0.023 0.001 TYR E 533 PHE 0.013 0.001 PHE E 398 TRP 0.017 0.001 TRP E1453 HIS 0.009 0.001 HIS E1719 Details of bonding type rmsd covalent geometry : bond 0.00312 (11092) covalent geometry : angle 0.57127 (15038) hydrogen bonds : bond 0.03395 ( 303) hydrogen bonds : angle 5.63499 ( 810) *********************** 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 133 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 257 MET cc_start: 0.6900 (mpp) cc_final: 0.6245 (mmm) REVERT: E 277 MET cc_start: 0.7289 (mmm) cc_final: 0.6851 (mmm) REVERT: E 316 MET cc_start: 0.8918 (mmm) cc_final: 0.8591 (mmm) REVERT: E 495 PHE cc_start: 0.6897 (OUTLIER) cc_final: 0.6436 (m-10) REVERT: E 646 TYR cc_start: 0.7133 (m-10) cc_final: 0.6444 (m-80) REVERT: E 694 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8101 (mp) REVERT: E 833 GLU cc_start: 0.8292 (tt0) cc_final: 0.8027 (tt0) REVERT: E 1370 MET cc_start: 0.8484 (tmm) cc_final: 0.7972 (tmm) REVERT: E 1762 MET cc_start: 0.5579 (mtm) cc_final: 0.5277 (mtm) outliers start: 28 outliers final: 15 residues processed: 126 average time/residue: 0.0890 time to fit residues: 17.3226 Evaluate side-chains 116 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 495 PHE Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 577 SER 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 4 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 126 optimal weight: 20.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 581 HIS E1748 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.155717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.108319 restraints weight = 26610.741| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 4.31 r_work: 0.3704 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11092 Z= 0.215 Angle : 0.629 11.642 15038 Z= 0.317 Chirality : 0.046 0.230 1630 Planarity : 0.005 0.050 1945 Dihedral : 5.341 29.004 1467 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.43 % Allowed : 15.04 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.24), residues: 1326 helix: 0.56 (0.38), residues: 172 sheet: -0.72 (0.27), residues: 404 loop : -0.43 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 739 TYR 0.019 0.002 TYR E 533 PHE 0.021 0.002 PHE E 398 TRP 0.016 0.001 TRP E1453 HIS 0.007 0.001 HIS E1719 Details of bonding type rmsd covalent geometry : bond 0.00493 (11092) covalent geometry : angle 0.62927 (15038) hydrogen bonds : bond 0.03744 ( 303) hydrogen bonds : angle 5.79533 ( 810) *********************** 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 152 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 246 PHE cc_start: 0.8439 (m-10) cc_final: 0.8230 (m-80) REVERT: E 257 MET cc_start: 0.6949 (mpp) cc_final: 0.6532 (mpp) REVERT: E 277 MET cc_start: 0.7334 (mmm) cc_final: 0.6895 (mmm) REVERT: E 316 MET cc_start: 0.8866 (mmm) cc_final: 0.8531 (mmm) REVERT: E 495 PHE cc_start: 0.7058 (OUTLIER) cc_final: 0.6661 (m-10) REVERT: E 546 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6388 (mp0) REVERT: E 694 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8138 (mp) REVERT: E 833 GLU cc_start: 0.8341 (tt0) cc_final: 0.8092 (tt0) REVERT: E 1177 ILE cc_start: 0.6896 (OUTLIER) cc_final: 0.6584 (mt) REVERT: E 1370 MET cc_start: 0.8422 (tmm) cc_final: 0.7921 (tmm) REVERT: E 1558 TYR cc_start: 0.7794 (m-80) cc_final: 0.7562 (m-80) REVERT: E 1762 MET cc_start: 0.5765 (mtm) cc_final: 0.5481 (mtm) outliers start: 41 outliers final: 23 residues processed: 144 average time/residue: 0.0816 time to fit residues: 18.0521 Evaluate side-chains 128 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 263 ILE Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 366 ARG Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 452 ASP Chi-restraints excluded: chain E residue 495 PHE Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain E residue 577 SER Chi-restraints excluded: chain E residue 588 ASP Chi-restraints excluded: chain E residue 593 ILE 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 1177 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 58 optimal weight: 0.5980 chunk 97 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 104 optimal weight: 20.0000 chunk 84 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 372 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.158239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.112049 restraints weight = 26784.561| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 4.25 r_work: 0.3780 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11092 Z= 0.115 Angle : 0.577 11.357 15038 Z= 0.288 Chirality : 0.044 0.230 1630 Planarity : 0.004 0.041 1945 Dihedral : 5.092 30.633 1467 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.26 % Allowed : 16.62 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.24), residues: 1326 helix: 0.71 (0.39), residues: 174 sheet: -0.62 (0.26), residues: 416 loop : -0.36 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 653 TYR 0.021 0.001 TYR E 533 PHE 0.014 0.001 PHE E 849 TRP 0.015 0.001 TRP E1453 HIS 0.008 0.001 HIS E1719 Details of bonding type rmsd covalent geometry : bond 0.00260 (11092) covalent geometry : angle 0.57722 (15038) hydrogen bonds : bond 0.03238 ( 303) hydrogen bonds : angle 5.39765 ( 810) *********************** 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 135 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 257 MET cc_start: 0.7007 (mpp) cc_final: 0.6573 (mpp) REVERT: E 277 MET cc_start: 0.7398 (mmm) cc_final: 0.6950 (mmm) REVERT: E 316 MET cc_start: 0.8958 (mmm) cc_final: 0.8622 (mmm) REVERT: E 373 MET cc_start: 0.7204 (mmm) cc_final: 0.6967 (mmm) REVERT: E 459 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8397 (tt) REVERT: E 495 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.6498 (m-10) REVERT: E 694 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8165 (mp) REVERT: E 833 GLU cc_start: 0.8235 (tt0) cc_final: 0.7907 (tt0) REVERT: E 1344 LYS cc_start: 0.8577 (pptt) cc_final: 0.8324 (pptt) REVERT: E 1370 MET cc_start: 0.8332 (tmm) cc_final: 0.7843 (tmm) REVERT: E 1762 MET cc_start: 0.5641 (mtm) cc_final: 0.5356 (mtm) outliers start: 27 outliers final: 19 residues processed: 128 average time/residue: 0.0857 time to fit residues: 16.9069 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 : 0.417 ------------------------------------------------------------------------------- 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 357 TRP Chi-restraints excluded: chain E residue 366 ARG Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 495 PHE Chi-restraints excluded: chain E residue 544 PHE Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 577 SER Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 694 LEU 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 127 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 45 optimal weight: 0.1980 chunk 70 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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** E1643 ASN E1757 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.157262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.110892 restraints weight = 26584.689| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 4.20 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: 0.7429 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11092 Z= 0.150 Angle : 0.591 12.090 15038 Z= 0.297 Chirality : 0.045 0.272 1630 Planarity : 0.004 0.042 1945 Dihedral : 5.096 29.640 1467 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.76 % Allowed : 16.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.24), residues: 1326 helix: 0.69 (0.39), residues: 174 sheet: -0.57 (0.27), residues: 413 loop : -0.32 (0.24), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 536 TYR 0.019 0.001 TYR E 533 PHE 0.013 0.001 PHE E 398 TRP 0.014 0.001 TRP E1453 HIS 0.009 0.001 HIS E1719 Details of bonding type rmsd covalent geometry : bond 0.00345 (11092) covalent geometry : angle 0.59071 (15038) hydrogen bonds : bond 0.03396 ( 303) hydrogen bonds : angle 5.42246 ( 810) *********************** 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 133 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 257 MET cc_start: 0.6993 (mpp) cc_final: 0.6568 (mpp) REVERT: E 277 MET cc_start: 0.7457 (mmm) cc_final: 0.7026 (mmm) REVERT: E 316 MET cc_start: 0.8943 (mmm) cc_final: 0.8609 (mmm) REVERT: E 373 MET cc_start: 0.7278 (mmm) cc_final: 0.7059 (mmm) REVERT: E 495 PHE cc_start: 0.6941 (OUTLIER) cc_final: 0.6530 (m-10) REVERT: E 694 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8118 (mp) REVERT: E 833 GLU cc_start: 0.8261 (tt0) cc_final: 0.7967 (tt0) REVERT: E 1197 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7701 (mt) REVERT: E 1370 MET cc_start: 0.8301 (tmm) cc_final: 0.7813 (tmm) REVERT: E 1762 MET cc_start: 0.5739 (mtm) cc_final: 0.5460 (mtm) outliers start: 33 outliers final: 24 residues processed: 126 average time/residue: 0.0922 time to fit residues: 17.6021 Evaluate side-chains 125 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 357 TRP Chi-restraints excluded: chain E residue 366 ARG Chi-restraints excluded: chain E residue 452 ASP Chi-restraints excluded: chain E residue 495 PHE Chi-restraints excluded: chain E residue 544 PHE Chi-restraints excluded: chain E residue 577 SER Chi-restraints excluded: chain E residue 588 ASP 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 720 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 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 1731 ILE 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 100 optimal weight: 10.0000 chunk 127 optimal weight: 0.0000 chunk 60 optimal weight: 0.0970 chunk 15 optimal weight: 9.9990 chunk 103 optimal weight: 30.0000 chunk 131 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- 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 E1487 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.153941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.108314 restraints weight = 26603.644| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 4.65 r_work: 0.3644 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 11092 Z= 0.249 Angle : 0.685 12.730 15038 Z= 0.345 Chirality : 0.047 0.242 1630 Planarity : 0.005 0.043 1945 Dihedral : 5.520 29.264 1467 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.92 % Allowed : 16.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.24), residues: 1326 helix: 0.25 (0.38), residues: 180 sheet: -0.64 (0.27), residues: 384 loop : -0.47 (0.24), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 334 TYR 0.017 0.002 TYR E 533 PHE 0.024 0.002 PHE E 398 TRP 0.015 0.002 TRP E1453 HIS 0.009 0.001 HIS E1719 Details of bonding type rmsd covalent geometry : bond 0.00570 (11092) covalent geometry : angle 0.68548 (15038) hydrogen bonds : bond 0.03955 ( 303) hydrogen bonds : angle 5.79609 ( 810) *********************** 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 135 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 257 MET cc_start: 0.6978 (mpp) cc_final: 0.6576 (mpp) REVERT: E 277 MET cc_start: 0.7477 (mmm) cc_final: 0.7020 (mmm) REVERT: E 316 MET cc_start: 0.8948 (mmm) cc_final: 0.8621 (mmm) REVERT: E 495 PHE cc_start: 0.7100 (OUTLIER) cc_final: 0.6751 (m-10) REVERT: E 1370 MET cc_start: 0.8368 (tmm) cc_final: 0.7887 (tmm) REVERT: E 1558 TYR cc_start: 0.7322 (m-80) cc_final: 0.6852 (m-80) REVERT: E 1762 MET cc_start: 0.5980 (mtm) cc_final: 0.5699 (mtm) outliers start: 35 outliers final: 27 residues processed: 127 average time/residue: 0.0889 time to fit residues: 17.2854 Evaluate side-chains 125 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 263 ILE Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 357 TRP Chi-restraints excluded: chain E residue 366 ARG Chi-restraints excluded: chain E residue 452 ASP Chi-restraints excluded: chain E residue 495 PHE Chi-restraints excluded: chain E residue 577 SER Chi-restraints excluded: chain E residue 588 ASP Chi-restraints excluded: chain E residue 619 TYR Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 695 ILE Chi-restraints excluded: chain E residue 697 GLU Chi-restraints excluded: chain E residue 720 THR Chi-restraints excluded: chain E residue 1086 HIS 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 1731 ILE 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 25 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 69 optimal weight: 30.0000 chunk 129 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 460 HIS ** E 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 825 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.156498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.109691 restraints weight = 26761.137| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 4.26 r_work: 0.3732 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11092 Z= 0.141 Angle : 0.626 12.172 15038 Z= 0.312 Chirality : 0.046 0.272 1630 Planarity : 0.004 0.040 1945 Dihedral : 5.293 29.573 1467 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.26 % Allowed : 17.46 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.24), residues: 1326 helix: 0.23 (0.38), residues: 180 sheet: -0.55 (0.27), residues: 400 loop : -0.40 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 536 TYR 0.021 0.001 TYR E 533 PHE 0.012 0.001 PHE E 849 TRP 0.016 0.001 TRP E1453 HIS 0.009 0.001 HIS E1719 Details of bonding type rmsd covalent geometry : bond 0.00323 (11092) covalent geometry : angle 0.62644 (15038) hydrogen bonds : bond 0.03474 ( 303) hydrogen bonds : angle 5.56724 ( 810) *********************** 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 132 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 257 MET cc_start: 0.7019 (mpp) cc_final: 0.6593 (mpp) REVERT: E 277 MET cc_start: 0.7521 (mmm) cc_final: 0.7063 (mmm) REVERT: E 316 MET cc_start: 0.8919 (mmm) cc_final: 0.8581 (mmm) REVERT: E 495 PHE cc_start: 0.7034 (OUTLIER) cc_final: 0.6688 (m-10) REVERT: E 833 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7962 (tt0) REVERT: E 1370 MET cc_start: 0.8307 (tmm) cc_final: 0.7798 (tmm) REVERT: E 1558 TYR cc_start: 0.7291 (m-80) cc_final: 0.6623 (m-80) REVERT: E 1762 MET cc_start: 0.5843 (mtm) cc_final: 0.5553 (mtm) outliers start: 27 outliers final: 24 residues processed: 126 average time/residue: 0.0912 time to fit residues: 17.5011 Evaluate side-chains 123 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 263 ILE Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 357 TRP Chi-restraints excluded: chain E residue 366 ARG Chi-restraints excluded: chain E residue 452 ASP Chi-restraints excluded: chain E residue 495 PHE Chi-restraints excluded: chain E residue 577 SER Chi-restraints excluded: chain E residue 588 ASP Chi-restraints excluded: chain E residue 697 GLU Chi-restraints excluded: chain E residue 720 THR 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 1731 ILE 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 34 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 84 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 109 optimal weight: 0.0270 chunk 25 optimal weight: 0.8980 chunk 89 optimal weight: 0.2980 chunk 93 optimal weight: 20.0000 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 825 ASN 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 = 0.158277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.112089 restraints weight = 26652.001| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 4.26 r_work: 0.3781 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11092 Z= 0.113 Angle : 0.628 12.379 15038 Z= 0.313 Chirality : 0.045 0.276 1630 Planarity : 0.004 0.043 1945 Dihedral : 5.032 30.823 1467 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.13 % Favored : 94.80 % Rotamer: Outliers : 1.84 % Allowed : 18.13 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.24), residues: 1326 helix: 0.29 (0.38), residues: 180 sheet: -0.42 (0.27), residues: 409 loop : -0.30 (0.25), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 536 TYR 0.024 0.001 TYR E1593 PHE 0.009 0.001 PHE E 849 TRP 0.016 0.001 TRP E1453 HIS 0.008 0.001 HIS E1719 Details of bonding type rmsd covalent geometry : bond 0.00253 (11092) covalent geometry : angle 0.62839 (15038) hydrogen bonds : bond 0.03224 ( 303) hydrogen bonds : angle 5.35594 ( 810) ********************** 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 131 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 257 MET cc_start: 0.7043 (mpp) cc_final: 0.6618 (mpp) REVERT: E 277 MET cc_start: 0.7490 (mmm) cc_final: 0.7042 (mmm) REVERT: E 316 MET cc_start: 0.8943 (mmm) cc_final: 0.8592 (mmm) REVERT: E 495 PHE cc_start: 0.6958 (OUTLIER) cc_final: 0.6605 (m-10) REVERT: E 833 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7894 (tt0) REVERT: E 1370 MET cc_start: 0.8186 (tmm) cc_final: 0.7791 (tmm) REVERT: E 1558 TYR cc_start: 0.7326 (m-80) cc_final: 0.6810 (m-80) REVERT: E 1561 ARG cc_start: 0.7867 (ptt180) cc_final: 0.7584 (ptt90) REVERT: E 1762 MET cc_start: 0.5834 (mtm) cc_final: 0.5559 (mtm) outliers start: 22 outliers final: 19 residues processed: 124 average time/residue: 0.0939 time to fit residues: 17.4523 Evaluate side-chains 122 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 322 VAL Chi-restraints excluded: chain E residue 357 TRP Chi-restraints excluded: chain E residue 366 ARG Chi-restraints excluded: chain E residue 495 PHE Chi-restraints excluded: chain E residue 544 PHE Chi-restraints excluded: chain E residue 697 GLU Chi-restraints excluded: chain E residue 800 THR Chi-restraints excluded: chain E residue 825 ASN 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 1731 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 8 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 chunk 133 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 70 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 594 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.158250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.112097 restraints weight = 26910.993| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 4.21 r_work: 0.3779 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.185 11092 Z= 0.192 Angle : 0.886 59.199 15038 Z= 0.509 Chirality : 0.049 0.771 1630 Planarity : 0.004 0.044 1945 Dihedral : 4.983 30.743 1465 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.13 % Favored : 94.80 % Rotamer: Outliers : 1.84 % Allowed : 18.46 % Favored : 79.70 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.24), residues: 1326 helix: 0.29 (0.38), residues: 180 sheet: -0.41 (0.27), residues: 409 loop : -0.31 (0.25), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 202 TYR 0.022 0.001 TYR E1593 PHE 0.009 0.001 PHE E1683 TRP 0.023 0.001 TRP E1250 HIS 0.007 0.001 HIS E1719 Details of bonding type rmsd covalent geometry : bond 0.00365 (11092) covalent geometry : angle 0.88602 (15038) hydrogen bonds : bond 0.03226 ( 303) hydrogen bonds : angle 5.35284 ( 810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3710.77 seconds wall clock time: 64 minutes 5.16 seconds (3845.16 seconds total)