Starting phenix.real_space_refine on Thu Sep 26 04:10:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe3_12860/09_2024/7oe3_12860.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe3_12860/09_2024/7oe3_12860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe3_12860/09_2024/7oe3_12860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe3_12860/09_2024/7oe3_12860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe3_12860/09_2024/7oe3_12860.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oe3_12860/09_2024/7oe3_12860.cif" } resolution = 3.35 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= 0.002 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 Mg 1 5.21 5 S 73 5.16 5 C 7591 2.51 5 N 2012 2.21 5 O 2226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11904 Number of models: 1 Model: "" Number of chains: 2 Chain: "L" Number of atoms: 11902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1478, 11902 Classifications: {'peptide': 1478} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 49, 'TRANS': 1428} Chain breaks: 9 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2599 SG CYS L 321 38.897 106.112 64.399 1.00131.48 S ATOM 2984 SG CYS L 366 38.147 106.803 68.522 1.00142.28 S Time building chain proxies: 6.68, per 1000 atoms: 0.56 Number of scatterers: 11904 At special positions: 0 Unit cell: (125.28, 135.72, 110.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 73 16.00 Mg 1 11.99 O 2226 8.00 N 2012 7.00 C 7591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS L1690 " - pdb=" SG CYS L1790 " distance=2.03 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: 3.01 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L2301 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L 316 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L 364 " pdb="ZN ZN L2301 " - pdb=" SG CYS L 321 " pdb="ZN ZN L2301 " - pdb=" SG CYS L 366 " Number of angles added : 2 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2832 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 10 sheets defined 57.1% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'L' and resid 2 through 15 Processing helix chain 'L' and resid 21 through 32 removed outlier: 4.252A pdb=" N GLN L 25 " --> pdb=" O ARG L 21 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 58 Processing helix chain 'L' and resid 68 through 76 Processing helix chain 'L' and resid 108 through 131 Processing helix chain 'L' and resid 132 through 134 No H-bonds generated for 'chain 'L' and resid 132 through 134' Processing helix chain 'L' and resid 153 through 175 Processing helix chain 'L' and resid 179 through 192 removed outlier: 4.358A pdb=" N MET L 192 " --> pdb=" O GLU L 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 199 through 206 removed outlier: 3.635A pdb=" N LEU L 206 " --> pdb=" O LEU L 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 212 through 222 Processing helix chain 'L' and resid 231 through 251 removed outlier: 4.117A pdb=" N LYS L 235 " --> pdb=" O ALA L 231 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU L 236 " --> pdb=" O HIS L 232 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLN L 237 " --> pdb=" O GLU L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 272 Processing helix chain 'L' and resid 284 through 293 removed outlier: 3.848A pdb=" N LYS L 293 " --> pdb=" O ILE L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 296 through 304 Processing helix chain 'L' and resid 313 through 319 removed outlier: 3.531A pdb=" N HIS L 316 " --> pdb=" O GLU L 313 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE L 318 " --> pdb=" O HIS L 315 " (cutoff:3.500A) Processing helix chain 'L' and resid 321 through 335 removed outlier: 3.746A pdb=" N TYR L 325 " --> pdb=" O CYS L 321 " (cutoff:3.500A) Processing helix chain 'L' and resid 346 through 365 removed outlier: 3.841A pdb=" N ARG L 363 " --> pdb=" O HIS L 359 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS L 364 " --> pdb=" O ASP L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 385 through 403 removed outlier: 3.948A pdb=" N GLU L 403 " --> pdb=" O ARG L 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 435 removed outlier: 4.138A pdb=" N VAL L 435 " --> pdb=" O ALA L 431 " (cutoff:3.500A) Processing helix chain 'L' and resid 439 through 443 removed outlier: 3.812A pdb=" N TYR L 442 " --> pdb=" O VAL L 439 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS L 443 " --> pdb=" O GLU L 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 439 through 443' Processing helix chain 'L' and resid 453 through 458 Processing helix chain 'L' and resid 492 through 507 Processing helix chain 'L' and resid 576 through 580 removed outlier: 3.888A pdb=" N ARG L 579 " --> pdb=" O ASP L 576 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR L 580 " --> pdb=" O PRO L 577 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 576 through 580' Processing helix chain 'L' and resid 586 through 599 removed outlier: 4.128A pdb=" N LEU L 590 " --> pdb=" O SER L 586 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLN L 591 " --> pdb=" O ALA L 587 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR L 592 " --> pdb=" O GLU L 588 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 628 Processing helix chain 'L' and resid 630 through 639 removed outlier: 3.549A pdb=" N GLN L 634 " --> pdb=" O SER L 630 " (cutoff:3.500A) Processing helix chain 'L' and resid 639 through 647 removed outlier: 4.199A pdb=" N PHE L 643 " --> pdb=" O ASN L 639 " (cutoff:3.500A) Processing helix chain 'L' and resid 656 through 661 removed outlier: 3.965A pdb=" N ARG L 661 " --> pdb=" O ASP L 658 " (cutoff:3.500A) Processing helix chain 'L' and resid 666 through 684 removed outlier: 3.704A pdb=" N PHE L 670 " --> pdb=" O THR L 666 " (cutoff:3.500A) Processing helix chain 'L' and resid 691 through 704 removed outlier: 3.897A pdb=" N ARG L 695 " --> pdb=" O MET L 691 " (cutoff:3.500A) Processing helix chain 'L' and resid 705 through 709 removed outlier: 3.703A pdb=" N ILE L 709 " --> pdb=" O CYS L 706 " (cutoff:3.500A) Processing helix chain 'L' and resid 716 through 729 Processing helix chain 'L' and resid 730 through 732 No H-bonds generated for 'chain 'L' and resid 730 through 732' Processing helix chain 'L' and resid 746 through 760 removed outlier: 3.920A pdb=" N ASP L 752 " --> pdb=" O GLU L 748 " (cutoff:3.500A) Processing helix chain 'L' and resid 780 through 794 Processing helix chain 'L' and resid 1088 through 1096 Processing helix chain 'L' and resid 1137 through 1158 removed outlier: 4.103A pdb=" N LEU L1146 " --> pdb=" O MET L1142 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE L1147 " --> pdb=" O PHE L1143 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU L1158 " --> pdb=" O LEU L1154 " (cutoff:3.500A) Processing helix chain 'L' and resid 1167 through 1182 removed outlier: 3.684A pdb=" N ASN L1171 " --> pdb=" O ARG L1167 " (cutoff:3.500A) Processing helix chain 'L' and resid 1194 through 1198 removed outlier: 3.844A pdb=" N MET L1197 " --> pdb=" O TRP L1194 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET L1198 " --> pdb=" O GLY L1195 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1194 through 1198' Processing helix chain 'L' and resid 1199 through 1208 removed outlier: 3.558A pdb=" N PHE L1203 " --> pdb=" O CYS L1199 " (cutoff:3.500A) Processing helix chain 'L' and resid 1216 through 1236 removed outlier: 3.646A pdb=" N HIS L1236 " --> pdb=" O THR L1232 " (cutoff:3.500A) Processing helix chain 'L' and resid 1242 through 1259 removed outlier: 3.928A pdb=" N VAL L1246 " --> pdb=" O PRO L1242 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU L1258 " --> pdb=" O ILE L1254 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY L1259 " --> pdb=" O LYS L1255 " (cutoff:3.500A) Processing helix chain 'L' and resid 1267 through 1276 Processing helix chain 'L' and resid 1298 through 1320 Processing helix chain 'L' and resid 1338 through 1346 removed outlier: 4.008A pdb=" N GLN L1346 " --> pdb=" O THR L1342 " (cutoff:3.500A) Processing helix chain 'L' and resid 1348 through 1366 removed outlier: 3.622A pdb=" N PHE L1352 " --> pdb=" O ASP L1348 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS L1353 " --> pdb=" O PRO L1349 " (cutoff:3.500A) Processing helix chain 'L' and resid 1396 through 1406 removed outlier: 3.863A pdb=" N HIS L1406 " --> pdb=" O ALA L1402 " (cutoff:3.500A) Processing helix chain 'L' and resid 1415 through 1429 removed outlier: 3.781A pdb=" N ALA L1429 " --> pdb=" O ASP L1425 " (cutoff:3.500A) Processing helix chain 'L' and resid 1433 through 1451 removed outlier: 3.950A pdb=" N CYS L1437 " --> pdb=" O PRO L1433 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA L1451 " --> pdb=" O LEU L1447 " (cutoff:3.500A) Processing helix chain 'L' and resid 1466 through 1471 Processing helix chain 'L' and resid 1473 through 1486 removed outlier: 3.627A pdb=" N ARG L1477 " --> pdb=" O ASN L1473 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE L1478 " --> pdb=" O ARG L1474 " (cutoff:3.500A) Processing helix chain 'L' and resid 1489 through 1506 removed outlier: 3.668A pdb=" N ILE L1493 " --> pdb=" O ALA L1489 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET L1496 " --> pdb=" O ARG L1492 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR L1506 " --> pdb=" O ASN L1502 " (cutoff:3.500A) Processing helix chain 'L' and resid 1511 through 1516 Processing helix chain 'L' and resid 1522 through 1532 Processing helix chain 'L' and resid 1578 through 1589 Processing helix chain 'L' and resid 1596 through 1608 removed outlier: 3.790A pdb=" N LEU L1600 " --> pdb=" O ALA L1596 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA L1608 " --> pdb=" O ILE L1604 " (cutoff:3.500A) Processing helix chain 'L' and resid 1612 through 1624 Processing helix chain 'L' and resid 1638 through 1649 removed outlier: 4.098A pdb=" N ILE L1649 " --> pdb=" O LEU L1645 " (cutoff:3.500A) Processing helix chain 'L' and resid 1668 through 1672 Processing helix chain 'L' and resid 1677 through 1679 No H-bonds generated for 'chain 'L' and resid 1677 through 1679' Processing helix chain 'L' and resid 1684 through 1699 Processing helix chain 'L' and resid 1700 through 1705 removed outlier: 3.792A pdb=" N VAL L1703 " --> pdb=" O GLY L1700 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU L1704 " --> pdb=" O ALA L1701 " (cutoff:3.500A) Processing helix chain 'L' and resid 1739 through 1751 removed outlier: 4.340A pdb=" N ILE L1743 " --> pdb=" O GLY L1739 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE L1744 " --> pdb=" O LEU L1740 " (cutoff:3.500A) Processing helix chain 'L' and resid 1751 through 1759 removed outlier: 3.679A pdb=" N LYS L1757 " --> pdb=" O SER L1753 " (cutoff:3.500A) Processing helix chain 'L' and resid 1775 through 1790 removed outlier: 3.751A pdb=" N PHE L1779 " --> pdb=" O PRO L1775 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU L1782 " --> pdb=" O LYS L1778 " (cutoff:3.500A) Processing helix chain 'L' and resid 1795 through 1800 removed outlier: 3.865A pdb=" N VAL L1800 " --> pdb=" O VAL L1796 " (cutoff:3.500A) Processing helix chain 'L' and resid 1812 through 1816 removed outlier: 4.182A pdb=" N ARG L1816 " --> pdb=" O SER L1812 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1812 through 1816' Processing sheet with id=AA1, first strand: chain 'L' and resid 61 through 62 removed outlier: 3.555A pdb=" N GLU L 61 " --> pdb=" O TYR L 91 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU L 98 " --> pdb=" O ILE L 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 103 through 105 removed outlier: 3.545A pdb=" N ARG L 144 " --> pdb=" O PHE L 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 259 through 260 removed outlier: 3.532A pdb=" N TYR L 651 " --> pdb=" O ILE L1376 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE L1376 " --> pdb=" O TYR L 651 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 535 through 540 removed outlier: 3.793A pdb=" N CYS L 571 " --> pdb=" O ILE L 562 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 738 through 739 removed outlier: 7.405A pdb=" N PHE L1119 " --> pdb=" O GLU L1240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 1107 through 1108 removed outlier: 3.928A pdb=" N GLY L1111 " --> pdb=" O SER L1108 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 1381 through 1382 removed outlier: 4.469A pdb=" N VAL L1389 " --> pdb=" O ASP L1392 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP L1392 " --> pdb=" O VAL L1389 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 1653 through 1655 Processing sheet with id=AA9, first strand: chain 'L' and resid 1706 through 1709 removed outlier: 3.871A pdb=" N GLU L1706 " --> pdb=" O THR L1822 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR L1822 " --> pdb=" O GLU L1706 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 1723 through 1726 584 hydrogen bonds defined for protein. 1680 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: 4.40 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3859 1.35 - 1.46: 2730 1.46 - 1.58: 5437 1.58 - 1.70: 0 1.70 - 1.82: 107 Bond restraints: 12133 Sorted by residual: bond pdb=" CA GLY L1128 " pdb=" C GLY L1128 " ideal model delta sigma weight residual 1.530 1.513 0.017 1.04e-02 9.25e+03 2.68e+00 bond pdb=" N GLY L1128 " pdb=" CA GLY L1128 " ideal model delta sigma weight residual 1.464 1.448 0.016 1.12e-02 7.97e+03 2.00e+00 bond pdb=" CA ILE L1241 " pdb=" CB ILE L1241 " ideal model delta sigma weight residual 1.537 1.524 0.013 1.29e-02 6.01e+03 9.71e-01 bond pdb=" CA PRO L 410 " pdb=" C PRO L 410 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.10e-02 2.27e+03 8.55e-01 bond pdb=" C GLN L 610 " pdb=" N LEU L 611 " ideal model delta sigma weight residual 1.332 1.320 0.012 1.40e-02 5.10e+03 7.37e-01 ... (remaining 12128 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 15738 1.17 - 2.35: 527 2.35 - 3.52: 77 3.52 - 4.69: 18 4.69 - 5.86: 12 Bond angle restraints: 16372 Sorted by residual: angle pdb=" N VAL L1677 " pdb=" CA VAL L1677 " pdb=" C VAL L1677 " ideal model delta sigma weight residual 113.53 109.57 3.96 9.80e-01 1.04e+00 1.63e+01 angle pdb=" N ILE L1759 " pdb=" CA ILE L1759 " pdb=" C ILE L1759 " ideal model delta sigma weight residual 112.96 108.97 3.99 1.00e+00 1.00e+00 1.59e+01 angle pdb=" N ILE L1289 " pdb=" CA ILE L1289 " pdb=" C ILE L1289 " ideal model delta sigma weight residual 113.53 109.70 3.83 9.80e-01 1.04e+00 1.53e+01 angle pdb=" N ASP L1542 " pdb=" CA ASP L1542 " pdb=" C ASP L1542 " ideal model delta sigma weight residual 113.18 108.55 4.63 1.33e+00 5.65e-01 1.21e+01 angle pdb=" C LEU L1509 " pdb=" N HIS L1510 " pdb=" CA HIS L1510 " ideal model delta sigma weight residual 121.54 126.50 -4.96 1.91e+00 2.74e-01 6.75e+00 ... (remaining 16367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 6472 17.70 - 35.40: 737 35.40 - 53.10: 143 53.10 - 70.79: 30 70.79 - 88.49: 11 Dihedral angle restraints: 7393 sinusoidal: 3040 harmonic: 4353 Sorted by residual: dihedral pdb=" CB CYS L1690 " pdb=" SG CYS L1690 " pdb=" SG CYS L1790 " pdb=" CB CYS L1790 " ideal model delta sinusoidal sigma weight residual -86.00 -51.81 -34.19 1 1.00e+01 1.00e-02 1.66e+01 dihedral pdb=" CA VAL L 275 " pdb=" C VAL L 275 " pdb=" N ASP L 276 " pdb=" CA ASP L 276 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA SER L1329 " pdb=" C SER L1329 " pdb=" N SER L1330 " pdb=" CA SER L1330 " ideal model delta harmonic sigma weight residual 180.00 160.54 19.46 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 7390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1276 0.033 - 0.066: 426 0.066 - 0.099: 104 0.099 - 0.132: 44 0.132 - 0.165: 4 Chirality restraints: 1854 Sorted by residual: chirality pdb=" CB ILE L 138 " pdb=" CA ILE L 138 " pdb=" CG1 ILE L 138 " pdb=" CG2 ILE L 138 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CA ILE L1376 " pdb=" N ILE L1376 " pdb=" C ILE L1376 " pdb=" CB ILE L1376 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA VAL L1389 " pdb=" N VAL L1389 " pdb=" C VAL L1389 " pdb=" CB VAL L1389 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 1851 not shown) Planarity restraints: 2075 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE L 479 " 0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO L 480 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO L 480 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 480 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE L 152 " 0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO L 153 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO L 153 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 153 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY L1195 " 0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO L1196 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO L1196 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO L1196 " 0.018 5.00e-02 4.00e+02 ... (remaining 2072 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 606 2.72 - 3.27: 12080 3.27 - 3.81: 17878 3.81 - 4.36: 20595 4.36 - 4.90: 36138 Nonbonded interactions: 87297 Sorted by model distance: nonbonded pdb=" OD1 ASP L1190 " pdb="MG MG L2302 " model vdw 2.179 2.170 nonbonded pdb=" OD2 ASP L1332 " pdb="MG MG L2302 " model vdw 2.196 2.170 nonbonded pdb=" OD1 ASN L 204 " pdb=" OH TYR L1226 " model vdw 2.204 3.040 nonbonded pdb=" O VAL L1703 " pdb=" NH1 ARG L1821 " model vdw 2.239 3.120 nonbonded pdb=" OD1 ASP L 208 " pdb=" OH TYR L1107 " model vdw 2.244 3.040 ... (remaining 87292 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.070 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 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 : 0.003 0.034 12133 Z= 0.168 Angle : 0.519 5.865 16372 Z= 0.309 Chirality : 0.038 0.165 1854 Planarity : 0.003 0.032 2075 Dihedral : 15.393 88.493 4558 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 3.39 % Allowed : 17.93 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.02 (0.20), residues: 1458 helix: 0.07 (0.18), residues: 769 sheet: -1.04 (0.48), residues: 100 loop : -3.43 (0.21), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 155 HIS 0.002 0.001 HIS L 652 PHE 0.009 0.001 PHE L 165 TYR 0.008 0.001 TYR L 574 ARG 0.002 0.000 ARG L1480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 84 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 155 TRP cc_start: 0.8235 (p-90) cc_final: 0.7973 (p-90) REVERT: L 185 ARG cc_start: 0.9337 (mtt-85) cc_final: 0.9032 (mmt90) REVERT: L 1601 SER cc_start: 0.8640 (t) cc_final: 0.8111 (p) outliers start: 46 outliers final: 24 residues processed: 129 average time/residue: 0.2300 time to fit residues: 44.3530 Evaluate side-chains 82 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 58 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 306 ILE Chi-restraints excluded: chain L residue 318 ILE Chi-restraints excluded: chain L residue 498 SER Chi-restraints excluded: chain L residue 680 VAL Chi-restraints excluded: chain L residue 687 ASP Chi-restraints excluded: chain L residue 702 ILE Chi-restraints excluded: chain L residue 723 CYS Chi-restraints excluded: chain L residue 746 THR Chi-restraints excluded: chain L residue 1110 THR Chi-restraints excluded: chain L residue 1175 SER Chi-restraints excluded: chain L residue 1188 SER Chi-restraints excluded: chain L residue 1189 MET Chi-restraints excluded: chain L residue 1229 THR Chi-restraints excluded: chain L residue 1277 PHE Chi-restraints excluded: chain L residue 1318 CYS Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1375 VAL Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1506 THR Chi-restraints excluded: chain L residue 1509 LEU Chi-restraints excluded: chain L residue 1629 VAL Chi-restraints excluded: chain L residue 1712 VAL Chi-restraints excluded: chain L residue 1743 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 0.4980 chunk 111 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 56 ASN ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN L 125 GLN ** L 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 ASN L 213 HIS L 547 GLN L 610 GLN L 694 ASN L1095 ASN L1298 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12133 Z= 0.209 Angle : 0.548 9.026 16372 Z= 0.283 Chirality : 0.039 0.159 1854 Planarity : 0.004 0.046 2075 Dihedral : 5.591 57.119 1630 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.88 % Allowed : 18.30 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.75 (0.22), residues: 1458 helix: 1.28 (0.19), residues: 776 sheet: -0.66 (0.47), residues: 110 loop : -3.16 (0.22), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 155 HIS 0.004 0.001 HIS L1758 PHE 0.013 0.001 PHE L1151 TYR 0.009 0.001 TYR L 704 ARG 0.005 0.000 ARG L1821 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 69 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 146 SER cc_start: 0.8539 (m) cc_final: 0.8320 (t) REVERT: L 155 TRP cc_start: 0.8276 (p-90) cc_final: 0.7965 (p-90) REVERT: L 185 ARG cc_start: 0.9328 (mtt-85) cc_final: 0.8999 (mmt90) REVERT: L 345 LEU cc_start: 0.8829 (mp) cc_final: 0.8275 (tt) REVERT: L 1601 SER cc_start: 0.8593 (t) cc_final: 0.8212 (p) outliers start: 39 outliers final: 22 residues processed: 105 average time/residue: 0.2211 time to fit residues: 35.7443 Evaluate side-chains 84 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 179 GLU Chi-restraints excluded: chain L residue 306 ILE Chi-restraints excluded: chain L residue 318 ILE Chi-restraints excluded: chain L residue 498 SER Chi-restraints excluded: chain L residue 507 SER Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 541 LEU Chi-restraints excluded: chain L residue 649 SER Chi-restraints excluded: chain L residue 746 THR Chi-restraints excluded: chain L residue 1277 PHE Chi-restraints excluded: chain L residue 1318 CYS Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1393 GLU Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1434 VAL Chi-restraints excluded: chain L residue 1497 LEU Chi-restraints excluded: chain L residue 1559 VAL Chi-restraints excluded: chain L residue 1618 VAL Chi-restraints excluded: chain L residue 1629 VAL Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1710 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 133 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12133 Z= 0.184 Angle : 0.513 7.132 16372 Z= 0.264 Chirality : 0.039 0.157 1854 Planarity : 0.003 0.044 2075 Dihedral : 5.316 59.981 1610 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.73 % Allowed : 19.34 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.22), residues: 1458 helix: 1.72 (0.19), residues: 777 sheet: -0.48 (0.47), residues: 110 loop : -3.03 (0.22), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 155 HIS 0.003 0.001 HIS L1758 PHE 0.019 0.001 PHE L 178 TYR 0.008 0.001 TYR L1107 ARG 0.004 0.000 ARG L1821 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 66 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 155 TRP cc_start: 0.8342 (p-90) cc_final: 0.8047 (p-90) REVERT: L 164 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9067 (mm) REVERT: L 185 ARG cc_start: 0.9317 (mtt-85) cc_final: 0.9006 (mmt90) REVERT: L 192 MET cc_start: 0.8514 (ttt) cc_final: 0.8112 (tmm) REVERT: L 345 LEU cc_start: 0.8795 (mp) cc_final: 0.8176 (tt) REVERT: L 352 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9391 (mp) REVERT: L 1393 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7769 (mm-30) outliers start: 37 outliers final: 21 residues processed: 99 average time/residue: 0.2113 time to fit residues: 32.4096 Evaluate side-chains 85 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 61 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain L residue 179 GLU Chi-restraints excluded: chain L residue 306 ILE Chi-restraints excluded: chain L residue 318 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 498 SER Chi-restraints excluded: chain L residue 507 SER Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 541 LEU Chi-restraints excluded: chain L residue 649 SER Chi-restraints excluded: chain L residue 746 THR Chi-restraints excluded: chain L residue 1277 PHE Chi-restraints excluded: chain L residue 1292 MET Chi-restraints excluded: chain L residue 1318 CYS Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1393 GLU Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1462 CYS Chi-restraints excluded: chain L residue 1497 LEU Chi-restraints excluded: chain L residue 1559 VAL Chi-restraints excluded: chain L residue 1629 VAL Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1710 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 142 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12133 Z= 0.150 Angle : 0.505 9.724 16372 Z= 0.256 Chirality : 0.038 0.151 1854 Planarity : 0.003 0.040 2075 Dihedral : 5.200 59.162 1610 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.66 % Allowed : 19.56 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.04 (0.23), residues: 1458 helix: 1.91 (0.19), residues: 777 sheet: -0.35 (0.48), residues: 110 loop : -2.91 (0.23), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 155 HIS 0.002 0.001 HIS L1510 PHE 0.015 0.001 PHE L 178 TYR 0.008 0.001 TYR L1107 ARG 0.004 0.000 ARG L1804 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 63 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 155 TRP cc_start: 0.8373 (p-90) cc_final: 0.8082 (p-90) REVERT: L 164 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9075 (mm) REVERT: L 185 ARG cc_start: 0.9313 (mtt-85) cc_final: 0.9015 (mmt90) REVERT: L 192 MET cc_start: 0.8515 (ttt) cc_final: 0.8075 (tmm) REVERT: L 345 LEU cc_start: 0.8794 (mp) cc_final: 0.8166 (tt) REVERT: L 352 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9373 (mp) REVERT: L 1393 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7689 (mm-30) outliers start: 36 outliers final: 23 residues processed: 96 average time/residue: 0.2006 time to fit residues: 30.1880 Evaluate side-chains 86 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 60 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 164 LEU Chi-restraints excluded: chain L residue 179 GLU Chi-restraints excluded: chain L residue 306 ILE Chi-restraints excluded: chain L residue 318 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 498 SER Chi-restraints excluded: chain L residue 507 SER Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 541 LEU Chi-restraints excluded: chain L residue 649 SER Chi-restraints excluded: chain L residue 746 THR Chi-restraints excluded: chain L residue 795 SER Chi-restraints excluded: chain L residue 1238 MET Chi-restraints excluded: chain L residue 1277 PHE Chi-restraints excluded: chain L residue 1318 CYS Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1375 VAL Chi-restraints excluded: chain L residue 1393 GLU Chi-restraints excluded: chain L residue 1462 CYS Chi-restraints excluded: chain L residue 1479 MET Chi-restraints excluded: chain L residue 1497 LEU Chi-restraints excluded: chain L residue 1629 VAL Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1710 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 0.1980 chunk 121 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 25 GLN ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1179 ASN L1298 HIS L1819 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12133 Z= 0.117 Angle : 0.486 8.337 16372 Z= 0.247 Chirality : 0.038 0.163 1854 Planarity : 0.003 0.037 2075 Dihedral : 4.940 59.986 1608 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.51 % Allowed : 20.44 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.23), residues: 1458 helix: 2.02 (0.19), residues: 778 sheet: -0.34 (0.48), residues: 112 loop : -2.81 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 155 HIS 0.002 0.000 HIS L1798 PHE 0.017 0.001 PHE L 178 TYR 0.008 0.001 TYR L 574 ARG 0.005 0.000 ARG L1804 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 68 time to evaluate : 1.335 Fit side-chains revert: symmetry clash REVERT: L 155 TRP cc_start: 0.8357 (p-90) cc_final: 0.8100 (p-90) REVERT: L 185 ARG cc_start: 0.9311 (mtt-85) cc_final: 0.9015 (mmt90) REVERT: L 192 MET cc_start: 0.8442 (ttt) cc_final: 0.7951 (tmm) REVERT: L 345 LEU cc_start: 0.8743 (mp) cc_final: 0.8395 (mt) REVERT: L 352 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9297 (mp) REVERT: L 432 LEU cc_start: 0.9517 (tp) cc_final: 0.9307 (tt) REVERT: L 1393 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7671 (mm-30) outliers start: 34 outliers final: 20 residues processed: 100 average time/residue: 0.2180 time to fit residues: 33.5884 Evaluate side-chains 84 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 306 ILE Chi-restraints excluded: chain L residue 318 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 498 SER Chi-restraints excluded: chain L residue 507 SER Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 541 LEU Chi-restraints excluded: chain L residue 746 THR Chi-restraints excluded: chain L residue 795 SER Chi-restraints excluded: chain L residue 1109 SER Chi-restraints excluded: chain L residue 1277 PHE Chi-restraints excluded: chain L residue 1318 CYS Chi-restraints excluded: chain L residue 1375 VAL Chi-restraints excluded: chain L residue 1393 GLU Chi-restraints excluded: chain L residue 1397 LEU Chi-restraints excluded: chain L residue 1462 CYS Chi-restraints excluded: chain L residue 1479 MET Chi-restraints excluded: chain L residue 1497 LEU Chi-restraints excluded: chain L residue 1629 VAL Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1710 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12133 Z= 0.157 Angle : 0.520 8.940 16372 Z= 0.259 Chirality : 0.038 0.186 1854 Planarity : 0.003 0.036 2075 Dihedral : 4.813 55.321 1605 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.73 % Allowed : 20.30 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.23), residues: 1458 helix: 2.09 (0.19), residues: 778 sheet: -0.21 (0.48), residues: 110 loop : -2.76 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 155 HIS 0.002 0.001 HIS L1406 PHE 0.016 0.001 PHE L 178 TYR 0.009 0.001 TYR L1107 ARG 0.005 0.000 ARG L1804 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 65 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 155 TRP cc_start: 0.8372 (p-90) cc_final: 0.8110 (p-90) REVERT: L 182 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.8662 (mm-30) REVERT: L 185 ARG cc_start: 0.9304 (mtt-85) cc_final: 0.9016 (mmt90) REVERT: L 192 MET cc_start: 0.8481 (ttt) cc_final: 0.8120 (tmm) REVERT: L 345 LEU cc_start: 0.8762 (mp) cc_final: 0.8472 (mt) REVERT: L 432 LEU cc_start: 0.9531 (tp) cc_final: 0.9312 (tt) REVERT: L 1393 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7679 (mm-30) REVERT: L 1804 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7853 (ptm-80) outliers start: 37 outliers final: 25 residues processed: 99 average time/residue: 0.2149 time to fit residues: 33.0564 Evaluate side-chains 90 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 63 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 36 ARG Chi-restraints excluded: chain L residue 168 LEU Chi-restraints excluded: chain L residue 182 GLU Chi-restraints excluded: chain L residue 306 ILE Chi-restraints excluded: chain L residue 318 ILE Chi-restraints excluded: chain L residue 498 SER Chi-restraints excluded: chain L residue 507 SER Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 541 LEU Chi-restraints excluded: chain L residue 612 CYS Chi-restraints excluded: chain L residue 687 ASP Chi-restraints excluded: chain L residue 746 THR Chi-restraints excluded: chain L residue 795 SER Chi-restraints excluded: chain L residue 1109 SER Chi-restraints excluded: chain L residue 1277 PHE Chi-restraints excluded: chain L residue 1375 VAL Chi-restraints excluded: chain L residue 1393 GLU Chi-restraints excluded: chain L residue 1397 LEU Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1462 CYS Chi-restraints excluded: chain L residue 1509 LEU Chi-restraints excluded: chain L residue 1629 VAL Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1710 VAL Chi-restraints excluded: chain L residue 1783 CYS Chi-restraints excluded: chain L residue 1798 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 103 optimal weight: 0.0050 chunk 80 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12133 Z= 0.201 Angle : 0.535 8.657 16372 Z= 0.270 Chirality : 0.039 0.158 1854 Planarity : 0.003 0.036 2075 Dihedral : 4.802 58.699 1604 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 2.51 % Allowed : 20.59 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.18 (0.23), residues: 1458 helix: 2.05 (0.19), residues: 778 sheet: -0.25 (0.48), residues: 110 loop : -2.76 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 155 HIS 0.003 0.001 HIS L1359 PHE 0.022 0.001 PHE L1592 TYR 0.009 0.001 TYR L1107 ARG 0.003 0.000 ARG L1821 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 62 time to evaluate : 1.287 Fit side-chains revert: symmetry clash REVERT: L 155 TRP cc_start: 0.8380 (p-90) cc_final: 0.8096 (p-90) REVERT: L 185 ARG cc_start: 0.9301 (mtt-85) cc_final: 0.9032 (mmt90) REVERT: L 192 MET cc_start: 0.8465 (ttt) cc_final: 0.8114 (tmm) REVERT: L 345 LEU cc_start: 0.8889 (mp) cc_final: 0.8521 (mt) REVERT: L 1393 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7668 (mm-30) REVERT: L 1496 MET cc_start: 0.9015 (tmm) cc_final: 0.8612 (tmm) REVERT: L 1804 ARG cc_start: 0.8087 (ttp80) cc_final: 0.7868 (ptm-80) outliers start: 34 outliers final: 25 residues processed: 94 average time/residue: 0.2124 time to fit residues: 30.8517 Evaluate side-chains 87 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 61 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 306 ILE Chi-restraints excluded: chain L residue 318 ILE Chi-restraints excluded: chain L residue 498 SER Chi-restraints excluded: chain L residue 507 SER Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 541 LEU Chi-restraints excluded: chain L residue 612 CYS Chi-restraints excluded: chain L residue 687 ASP Chi-restraints excluded: chain L residue 746 THR Chi-restraints excluded: chain L residue 795 SER Chi-restraints excluded: chain L residue 1109 SER Chi-restraints excluded: chain L residue 1277 PHE Chi-restraints excluded: chain L residue 1292 MET Chi-restraints excluded: chain L residue 1318 CYS Chi-restraints excluded: chain L residue 1375 VAL Chi-restraints excluded: chain L residue 1393 GLU Chi-restraints excluded: chain L residue 1397 LEU Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1462 CYS Chi-restraints excluded: chain L residue 1509 LEU Chi-restraints excluded: chain L residue 1629 VAL Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1710 VAL Chi-restraints excluded: chain L residue 1783 CYS Chi-restraints excluded: chain L residue 1798 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12133 Z= 0.175 Angle : 0.547 8.739 16372 Z= 0.270 Chirality : 0.039 0.168 1854 Planarity : 0.003 0.037 2075 Dihedral : 4.740 57.904 1604 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.44 % Allowed : 20.89 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.18 (0.23), residues: 1458 helix: 2.04 (0.19), residues: 776 sheet: -0.26 (0.48), residues: 110 loop : -2.71 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 155 HIS 0.003 0.001 HIS L1510 PHE 0.015 0.001 PHE L 178 TYR 0.008 0.001 TYR L1107 ARG 0.004 0.000 ARG L 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 63 time to evaluate : 1.415 Fit side-chains revert: symmetry clash REVERT: L 40 MET cc_start: 0.8905 (mpp) cc_final: 0.8666 (pmm) REVERT: L 155 TRP cc_start: 0.8441 (p-90) cc_final: 0.8160 (p-90) REVERT: L 182 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.8599 (mm-30) REVERT: L 185 ARG cc_start: 0.9292 (mtt-85) cc_final: 0.9037 (mmt90) REVERT: L 192 MET cc_start: 0.8426 (ttt) cc_final: 0.8082 (tmm) REVERT: L 345 LEU cc_start: 0.8853 (mp) cc_final: 0.8487 (mt) REVERT: L 1393 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7693 (mm-30) REVERT: L 1496 MET cc_start: 0.8991 (tmm) cc_final: 0.8595 (tmm) REVERT: L 1804 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7885 (ptm-80) outliers start: 33 outliers final: 28 residues processed: 95 average time/residue: 0.2096 time to fit residues: 31.0719 Evaluate side-chains 92 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 62 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 168 LEU Chi-restraints excluded: chain L residue 182 GLU Chi-restraints excluded: chain L residue 306 ILE Chi-restraints excluded: chain L residue 318 ILE Chi-restraints excluded: chain L residue 498 SER Chi-restraints excluded: chain L residue 507 SER Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 541 LEU Chi-restraints excluded: chain L residue 687 ASP Chi-restraints excluded: chain L residue 746 THR Chi-restraints excluded: chain L residue 795 SER Chi-restraints excluded: chain L residue 1109 SER Chi-restraints excluded: chain L residue 1277 PHE Chi-restraints excluded: chain L residue 1292 MET Chi-restraints excluded: chain L residue 1318 CYS Chi-restraints excluded: chain L residue 1375 VAL Chi-restraints excluded: chain L residue 1393 GLU Chi-restraints excluded: chain L residue 1397 LEU Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1424 ILE Chi-restraints excluded: chain L residue 1462 CYS Chi-restraints excluded: chain L residue 1509 LEU Chi-restraints excluded: chain L residue 1629 VAL Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1710 VAL Chi-restraints excluded: chain L residue 1783 CYS Chi-restraints excluded: chain L residue 1798 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 135 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12133 Z= 0.161 Angle : 0.539 11.288 16372 Z= 0.267 Chirality : 0.039 0.178 1854 Planarity : 0.003 0.036 2075 Dihedral : 4.636 57.182 1604 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.36 % Allowed : 20.89 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.18 (0.23), residues: 1458 helix: 2.02 (0.19), residues: 783 sheet: -0.29 (0.50), residues: 100 loop : -2.71 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 155 HIS 0.002 0.001 HIS L1510 PHE 0.016 0.001 PHE L 178 TYR 0.011 0.001 TYR L1751 ARG 0.003 0.000 ARG L 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 64 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: L 154 ASP cc_start: 0.8380 (p0) cc_final: 0.8043 (p0) REVERT: L 155 TRP cc_start: 0.8457 (p-90) cc_final: 0.8132 (p-90) REVERT: L 182 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8583 (mm-30) REVERT: L 185 ARG cc_start: 0.9288 (mtt-85) cc_final: 0.9036 (mmt90) REVERT: L 192 MET cc_start: 0.8415 (ttt) cc_final: 0.8059 (tmm) REVERT: L 345 LEU cc_start: 0.8815 (mp) cc_final: 0.8446 (mt) REVERT: L 432 LEU cc_start: 0.9545 (tp) cc_final: 0.9324 (tt) REVERT: L 1393 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: L 1496 MET cc_start: 0.9001 (tmm) cc_final: 0.8594 (tmm) REVERT: L 1804 ARG cc_start: 0.8125 (ttp80) cc_final: 0.7883 (ptm-80) outliers start: 32 outliers final: 29 residues processed: 93 average time/residue: 0.2081 time to fit residues: 30.2679 Evaluate side-chains 95 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 64 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 168 LEU Chi-restraints excluded: chain L residue 182 GLU Chi-restraints excluded: chain L residue 306 ILE Chi-restraints excluded: chain L residue 318 ILE Chi-restraints excluded: chain L residue 498 SER Chi-restraints excluded: chain L residue 507 SER Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 541 LEU Chi-restraints excluded: chain L residue 612 CYS Chi-restraints excluded: chain L residue 687 ASP Chi-restraints excluded: chain L residue 746 THR Chi-restraints excluded: chain L residue 795 SER Chi-restraints excluded: chain L residue 1109 SER Chi-restraints excluded: chain L residue 1277 PHE Chi-restraints excluded: chain L residue 1292 MET Chi-restraints excluded: chain L residue 1318 CYS Chi-restraints excluded: chain L residue 1375 VAL Chi-restraints excluded: chain L residue 1393 GLU Chi-restraints excluded: chain L residue 1397 LEU Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1424 ILE Chi-restraints excluded: chain L residue 1462 CYS Chi-restraints excluded: chain L residue 1479 MET Chi-restraints excluded: chain L residue 1509 LEU Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1710 VAL Chi-restraints excluded: chain L residue 1783 CYS Chi-restraints excluded: chain L residue 1798 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 134 optimal weight: 0.0010 chunk 116 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 0.0870 chunk 71 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.8170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12133 Z= 0.192 Angle : 0.566 10.987 16372 Z= 0.283 Chirality : 0.039 0.189 1854 Planarity : 0.003 0.037 2075 Dihedral : 4.645 58.375 1603 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 2.36 % Allowed : 20.89 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.23), residues: 1458 helix: 2.02 (0.19), residues: 784 sheet: -0.28 (0.50), residues: 100 loop : -2.68 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 155 HIS 0.003 0.001 HIS L1510 PHE 0.017 0.001 PHE L 178 TYR 0.009 0.001 TYR L1751 ARG 0.005 0.000 ARG L 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 64 time to evaluate : 1.414 Fit side-chains revert: symmetry clash REVERT: L 154 ASP cc_start: 0.8428 (p0) cc_final: 0.8051 (p0) REVERT: L 155 TRP cc_start: 0.8481 (p-90) cc_final: 0.8135 (p-90) REVERT: L 182 GLU cc_start: 0.9263 (OUTLIER) cc_final: 0.8582 (mm-30) REVERT: L 185 ARG cc_start: 0.9290 (mtt-85) cc_final: 0.9039 (mmt90) REVERT: L 192 MET cc_start: 0.8455 (ttt) cc_final: 0.8085 (tmm) REVERT: L 345 LEU cc_start: 0.8830 (mp) cc_final: 0.8461 (mt) REVERT: L 432 LEU cc_start: 0.9549 (tp) cc_final: 0.9325 (tt) REVERT: L 1393 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7693 (mm-30) REVERT: L 1496 MET cc_start: 0.9012 (tmm) cc_final: 0.8593 (tmm) outliers start: 32 outliers final: 27 residues processed: 94 average time/residue: 0.2090 time to fit residues: 30.6285 Evaluate side-chains 93 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 64 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 168 LEU Chi-restraints excluded: chain L residue 182 GLU Chi-restraints excluded: chain L residue 306 ILE Chi-restraints excluded: chain L residue 318 ILE Chi-restraints excluded: chain L residue 498 SER Chi-restraints excluded: chain L residue 507 SER Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 541 LEU Chi-restraints excluded: chain L residue 612 CYS Chi-restraints excluded: chain L residue 746 THR Chi-restraints excluded: chain L residue 795 SER Chi-restraints excluded: chain L residue 1109 SER Chi-restraints excluded: chain L residue 1277 PHE Chi-restraints excluded: chain L residue 1292 MET Chi-restraints excluded: chain L residue 1318 CYS Chi-restraints excluded: chain L residue 1375 VAL Chi-restraints excluded: chain L residue 1393 GLU Chi-restraints excluded: chain L residue 1397 LEU Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1424 ILE Chi-restraints excluded: chain L residue 1462 CYS Chi-restraints excluded: chain L residue 1509 LEU Chi-restraints excluded: chain L residue 1677 VAL Chi-restraints excluded: chain L residue 1710 VAL Chi-restraints excluded: chain L residue 1783 CYS Chi-restraints excluded: chain L residue 1798 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 17 optimal weight: 0.0570 chunk 32 optimal weight: 0.8980 chunk 116 optimal weight: 0.0670 chunk 48 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 58 ASN ** L1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1298 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.056975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.040481 restraints weight = 56163.731| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 4.21 r_work: 0.2696 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12133 Z= 0.124 Angle : 0.539 10.710 16372 Z= 0.267 Chirality : 0.038 0.175 1854 Planarity : 0.003 0.036 2075 Dihedral : 4.445 52.489 1603 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.85 % Allowed : 21.25 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.32 (0.23), residues: 1458 helix: 2.09 (0.19), residues: 786 sheet: -0.20 (0.51), residues: 100 loop : -2.59 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 155 HIS 0.002 0.000 HIS L 364 PHE 0.021 0.001 PHE L 178 TYR 0.010 0.001 TYR L1751 ARG 0.006 0.000 ARG L1804 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2261.54 seconds wall clock time: 42 minutes 13.02 seconds (2533.02 seconds total)