Starting phenix.real_space_refine on Tue Jun 10 21:25:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oe3_12860/06_2025/7oe3_12860.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oe3_12860/06_2025/7oe3_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/cci-nas-00/data/ceres_data/7oe3_12860/06_2025/7oe3_12860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oe3_12860/06_2025/7oe3_12860.map" model { file = "/net/cci-nas-00/data/ceres_data/7oe3_12860/06_2025/7oe3_12860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oe3_12860/06_2025/7oe3_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-5710/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: 6.93, per 1000 atoms: 0.58 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: 2.84 Conformation dependent library (CDL) restraints added in 1.5 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: 1.52 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: 4.46 Time building geometry restraints manager: 3.40 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: 2.170 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: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 31.960 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.490 ------------------------------------------------------------------------------- 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 : 0.004 0.200 12138 Z= 0.149 Angle : 0.520 5.865 16376 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 Details of bonding type rmsd hydrogen bonds : bond 0.14669 ( 584) hydrogen bonds : angle 5.18298 ( 1680) metal coordination : bond 0.13595 ( 4) metal coordination : angle 2.47842 ( 2) SS BOND : bond 0.00209 ( 1) SS BOND : angle 0.88857 ( 2) covalent geometry : bond 0.00257 (12133) covalent geometry : angle 0.51939 (16372) *********************** 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 to be fit. rotamer outliers: 46 poor density : 84 time to evaluate : 1.432 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: 0.2287 time to fit residues: 44.1944 Evaluate side-chains 82 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.055238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.038645 restraints weight = 56769.650| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 4.14 r_work: 0.2619 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 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 12138 Z= 0.144 Angle : 0.548 9.026 16376 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 Details of bonding type rmsd hydrogen bonds : bond 0.04388 ( 584) hydrogen bonds : angle 4.06408 ( 1680) metal coordination : bond 0.00552 ( 4) metal coordination : angle 1.58940 ( 2) SS BOND : bond 0.00030 ( 1) SS BOND : angle 0.74821 ( 2) covalent geometry : bond 0.00321 (12133) covalent geometry : angle 0.54756 (16372) *********************** 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 to be fit. rotamer outliers: 39 poor density : 69 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 146 SER cc_start: 0.8901 (m) cc_final: 0.8589 (t) REVERT: L 155 TRP cc_start: 0.8438 (p-90) cc_final: 0.8107 (p-90) REVERT: L 178 PHE cc_start: 0.8776 (m-10) cc_final: 0.8551 (m-10) REVERT: L 185 ARG cc_start: 0.9259 (mtt-85) cc_final: 0.8915 (mmt90) REVERT: L 345 LEU cc_start: 0.9047 (mp) cc_final: 0.8463 (tt) REVERT: L 533 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8681 (mm-30) REVERT: L 555 GLU cc_start: 0.9258 (OUTLIER) cc_final: 0.8958 (mm-30) REVERT: L 1601 SER cc_start: 0.8730 (t) cc_final: 0.8402 (p) outliers start: 39 outliers final: 22 residues processed: 105 average time/residue: 0.2105 time to fit residues: 34.0150 Evaluate side-chains 86 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 533 GLU Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 541 LEU Chi-restraints excluded: chain L residue 555 GLU 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 118 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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** L 324 GLN ** L1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.053229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.036530 restraints weight = 58568.368| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 4.13 r_work: 0.2548 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 12138 Z= 0.271 Angle : 0.638 8.831 16376 Z= 0.329 Chirality : 0.042 0.175 1854 Planarity : 0.004 0.050 2075 Dihedral : 5.826 56.663 1610 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 3.76 % Allowed : 19.26 % 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: -0.57 (0.22), residues: 1458 helix: 1.43 (0.19), residues: 779 sheet: -0.67 (0.47), residues: 110 loop : -3.09 (0.22), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 155 HIS 0.006 0.001 HIS L1406 PHE 0.014 0.001 PHE L1400 TYR 0.015 0.001 TYR L 704 ARG 0.005 0.000 ARG L1821 Details of bonding type rmsd hydrogen bonds : bond 0.05585 ( 584) hydrogen bonds : angle 4.37579 ( 1680) metal coordination : bond 0.01448 ( 4) metal coordination : angle 1.57817 ( 2) SS BOND : bond 0.00197 ( 1) SS BOND : angle 0.78098 ( 2) covalent geometry : bond 0.00613 (12133) covalent geometry : angle 0.63745 (16372) *********************** 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 110 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 59 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 164 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9096 (mm) REVERT: L 178 PHE cc_start: 0.8826 (m-10) cc_final: 0.8574 (m-10) REVERT: L 185 ARG cc_start: 0.9267 (mtt-85) cc_final: 0.8977 (mmt90) REVERT: L 192 MET cc_start: 0.8996 (ttt) cc_final: 0.8627 (tmm) REVERT: L 345 LEU cc_start: 0.9093 (mp) cc_final: 0.8548 (tt) REVERT: L 533 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8632 (mm-30) outliers start: 51 outliers final: 32 residues processed: 108 average time/residue: 0.2162 time to fit residues: 36.2073 Evaluate side-chains 86 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 52 time to evaluate : 1.428 ------------------------------------------------------------------------------- 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 425 ILE Chi-restraints excluded: chain L residue 498 SER Chi-restraints excluded: chain L residue 507 SER Chi-restraints excluded: chain L residue 533 GLU 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 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 1114 THR Chi-restraints excluded: chain L residue 1246 VAL Chi-restraints excluded: chain L residue 1277 PHE Chi-restraints excluded: chain L residue 1286 VAL 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 1374 SER Chi-restraints excluded: chain L residue 1393 GLU Chi-restraints excluded: chain L residue 1424 ILE Chi-restraints excluded: chain L residue 1462 CYS Chi-restraints excluded: chain L residue 1497 LEU 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 Chi-restraints excluded: chain L residue 1777 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 77 optimal weight: 6.9990 chunk 137 optimal weight: 0.0980 chunk 140 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 114 optimal weight: 0.0770 chunk 124 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.056342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.039775 restraints weight = 56612.230| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 4.18 r_work: 0.2668 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12138 Z= 0.095 Angle : 0.514 8.938 16376 Z= 0.260 Chirality : 0.039 0.154 1854 Planarity : 0.004 0.055 2075 Dihedral : 5.293 57.755 1608 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.51 % Allowed : 20.81 % 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: -0.08 (0.23), residues: 1458 helix: 1.88 (0.19), residues: 777 sheet: -0.43 (0.47), residues: 110 loop : -2.92 (0.23), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L1547 HIS 0.003 0.000 HIS L 364 PHE 0.011 0.001 PHE L 120 TYR 0.009 0.001 TYR L 574 ARG 0.004 0.000 ARG L1804 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 584) hydrogen bonds : angle 3.73710 ( 1680) metal coordination : bond 0.00867 ( 4) metal coordination : angle 1.10826 ( 2) SS BOND : bond 0.00090 ( 1) SS BOND : angle 0.84544 ( 2) covalent geometry : bond 0.00193 (12133) covalent geometry : angle 0.51427 (16372) *********************** 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 103 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 69 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 185 ARG cc_start: 0.9227 (mtt-85) cc_final: 0.8945 (mmt90) REVERT: L 192 MET cc_start: 0.8883 (ttt) cc_final: 0.8542 (tmm) REVERT: L 345 LEU cc_start: 0.8950 (mp) cc_final: 0.8638 (mt) REVERT: L 533 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8607 (mm-30) REVERT: L 1393 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7895 (mm-30) outliers start: 34 outliers final: 17 residues processed: 97 average time/residue: 0.2164 time to fit residues: 33.0985 Evaluate side-chains 77 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 1.293 ------------------------------------------------------------------------------- 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 507 SER Chi-restraints excluded: chain L residue 533 GLU 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 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 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 1629 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 92 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 L1126 GLN ** L1179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1298 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.053949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.037226 restraints weight = 58072.002| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 4.16 r_work: 0.2576 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12138 Z= 0.215 Angle : 0.595 11.730 16376 Z= 0.301 Chirality : 0.040 0.144 1854 Planarity : 0.004 0.042 2075 Dihedral : 5.495 58.321 1607 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 2.73 % Allowed : 21.11 % Favored : 76.16 % 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: -0.06 (0.23), residues: 1458 helix: 1.89 (0.19), residues: 775 sheet: -0.46 (0.47), residues: 110 loop : -2.88 (0.23), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 155 HIS 0.005 0.001 HIS L1406 PHE 0.013 0.001 PHE L 797 TYR 0.012 0.001 TYR L 704 ARG 0.004 0.000 ARG L 71 Details of bonding type rmsd hydrogen bonds : bond 0.04793 ( 584) hydrogen bonds : angle 4.05733 ( 1680) metal coordination : bond 0.01257 ( 4) metal coordination : angle 1.50790 ( 2) SS BOND : bond 0.00170 ( 1) SS BOND : angle 0.73216 ( 2) covalent geometry : bond 0.00486 (12133) covalent geometry : angle 0.59430 (16372) *********************** 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 97 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 60 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 182 GLU cc_start: 0.9360 (OUTLIER) cc_final: 0.8830 (mm-30) REVERT: L 185 ARG cc_start: 0.9245 (mtt-85) cc_final: 0.8950 (mmt90) REVERT: L 192 MET cc_start: 0.8951 (ttt) cc_final: 0.8646 (tmm) REVERT: L 345 LEU cc_start: 0.9056 (mp) cc_final: 0.8489 (tt) REVERT: L 432 LEU cc_start: 0.9648 (tp) cc_final: 0.9429 (tt) REVERT: L 533 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8611 (mm-30) REVERT: L 1530 CYS cc_start: 0.8997 (m) cc_final: 0.8662 (p) outliers start: 37 outliers final: 27 residues processed: 96 average time/residue: 0.2365 time to fit residues: 35.7364 Evaluate side-chains 89 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 78 ILE 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 533 GLU 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 649 SER 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 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 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 Chi-restraints excluded: chain L residue 1783 CYS Chi-restraints excluded: chain L residue 1798 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 114 optimal weight: 0.3980 chunk 55 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 126 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.055788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.039082 restraints weight = 57685.254| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 4.23 r_work: 0.2643 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12138 Z= 0.097 Angle : 0.515 10.207 16376 Z= 0.260 Chirality : 0.039 0.155 1854 Planarity : 0.003 0.042 2075 Dihedral : 5.181 57.587 1607 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.66 % Allowed : 20.96 % Favored : 76.38 % 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: 0.13 (0.23), residues: 1458 helix: 2.07 (0.19), residues: 772 sheet: -0.46 (0.47), residues: 112 loop : -2.79 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 155 HIS 0.003 0.001 HIS L 364 PHE 0.010 0.001 PHE L1151 TYR 0.008 0.001 TYR L 574 ARG 0.004 0.000 ARG L 71 Details of bonding type rmsd hydrogen bonds : bond 0.03421 ( 584) hydrogen bonds : angle 3.71659 ( 1680) metal coordination : bond 0.00369 ( 4) metal coordination : angle 1.02051 ( 2) SS BOND : bond 0.00021 ( 1) SS BOND : angle 0.74523 ( 2) covalent geometry : bond 0.00211 (12133) covalent geometry : angle 0.51479 (16372) *********************** 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 101 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 65 time to evaluate : 1.307 Fit side-chains revert: symmetry clash REVERT: L 155 TRP cc_start: 0.8487 (p-90) cc_final: 0.8197 (p-90) REVERT: L 185 ARG cc_start: 0.9196 (mtt-85) cc_final: 0.8934 (mmt90) REVERT: L 192 MET cc_start: 0.8875 (ttt) cc_final: 0.8544 (tmm) REVERT: L 432 LEU cc_start: 0.9609 (tp) cc_final: 0.9371 (tt) REVERT: L 533 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8580 (mm-30) REVERT: L 1393 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7942 (mm-30) REVERT: L 1751 TYR cc_start: 0.8905 (m-10) cc_final: 0.8701 (m-80) outliers start: 36 outliers final: 26 residues processed: 98 average time/residue: 0.2028 time to fit residues: 31.1950 Evaluate side-chains 90 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 103 CYS 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 533 GLU 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 649 SER Chi-restraints excluded: chain L residue 746 THR Chi-restraints excluded: chain L residue 795 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 1408 ILE 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 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 75 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 29 optimal weight: 0.0770 chunk 102 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 48 optimal weight: 0.0270 chunk 34 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- 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** L1819 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.056301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.039864 restraints weight = 56743.364| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 4.18 r_work: 0.2669 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12138 Z= 0.091 Angle : 0.526 11.925 16376 Z= 0.261 Chirality : 0.038 0.185 1854 Planarity : 0.003 0.041 2075 Dihedral : 4.755 56.685 1605 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.36 % Allowed : 21.25 % Favored : 76.38 % 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: 0.14 (0.23), residues: 1458 helix: 2.05 (0.19), residues: 778 sheet: -0.46 (0.50), residues: 102 loop : -2.76 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 155 HIS 0.003 0.000 HIS L 364 PHE 0.028 0.001 PHE L1592 TYR 0.008 0.001 TYR L 574 ARG 0.003 0.000 ARG L 71 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 584) hydrogen bonds : angle 3.69728 ( 1680) metal coordination : bond 0.00218 ( 4) metal coordination : angle 0.69837 ( 2) SS BOND : bond 0.00016 ( 1) SS BOND : angle 0.72089 ( 2) covalent geometry : bond 0.00196 (12133) covalent geometry : angle 0.52605 (16372) *********************** 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 97 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 65 time to evaluate : 1.481 Fit side-chains revert: symmetry clash REVERT: L 155 TRP cc_start: 0.8565 (p-90) cc_final: 0.8247 (p-90) REVERT: L 182 GLU cc_start: 0.9362 (OUTLIER) cc_final: 0.8874 (mm-30) REVERT: L 185 ARG cc_start: 0.9171 (mtt-85) cc_final: 0.8913 (mmt90) REVERT: L 192 MET cc_start: 0.8871 (ttt) cc_final: 0.8493 (tmm) REVERT: L 432 LEU cc_start: 0.9601 (tp) cc_final: 0.9382 (tt) REVERT: L 533 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8601 (mm-30) REVERT: L 1393 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7912 (mm-30) REVERT: L 1751 TYR cc_start: 0.8902 (m-10) cc_final: 0.8674 (m-80) REVERT: L 1760 LEU cc_start: 0.9511 (mp) cc_final: 0.9305 (pp) outliers start: 32 outliers final: 24 residues processed: 96 average time/residue: 0.2234 time to fit residues: 33.5490 Evaluate side-chains 90 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 533 GLU 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 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 1497 LEU 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.82 > 50: distance: 15 - 19: 16.535 distance: 19 - 20: 25.989 distance: 20 - 21: 6.210 distance: 20 - 23: 32.256 distance: 21 - 22: 11.013 distance: 21 - 28: 18.701 distance: 23 - 24: 10.837 distance: 24 - 25: 4.682 distance: 25 - 26: 15.693 distance: 25 - 27: 31.001 distance: 28 - 29: 24.978 distance: 29 - 30: 15.743 distance: 29 - 32: 17.794 distance: 30 - 31: 40.473 distance: 32 - 33: 36.097 distance: 33 - 228: 16.592 distance: 34 - 35: 34.910 distance: 35 - 36: 9.622 distance: 35 - 38: 20.985 distance: 36 - 37: 15.154 distance: 36 - 43: 10.222 distance: 37 - 72: 39.209 distance: 38 - 39: 22.265 distance: 39 - 40: 19.452 distance: 40 - 41: 20.503 distance: 40 - 42: 17.333 distance: 43 - 44: 5.276 distance: 44 - 45: 16.966 distance: 44 - 47: 4.170 distance: 45 - 46: 25.714 distance: 45 - 51: 15.134 distance: 46 - 86: 44.864 distance: 47 - 48: 48.195 distance: 48 - 49: 31.000 distance: 49 - 50: 63.820 distance: 51 - 52: 15.544 distance: 52 - 53: 5.913 distance: 52 - 55: 15.956 distance: 53 - 54: 16.350 distance: 53 - 60: 29.579 distance: 54 - 97: 49.617 distance: 55 - 56: 23.412 distance: 56 - 57: 43.288 distance: 57 - 58: 4.085 distance: 60 - 61: 14.412 distance: 61 - 62: 17.950 distance: 61 - 64: 11.114 distance: 62 - 63: 39.041 distance: 62 - 72: 9.521 distance: 63 - 103: 45.323 distance: 64 - 65: 13.964 distance: 65 - 66: 8.436 distance: 65 - 67: 36.752 distance: 66 - 68: 8.402 distance: 67 - 69: 14.811 distance: 68 - 70: 27.167 distance: 69 - 70: 23.914 distance: 70 - 71: 15.524 distance: 72 - 73: 11.360 distance: 73 - 74: 21.866 distance: 73 - 76: 19.611 distance: 74 - 75: 12.221 distance: 74 - 86: 17.832 distance: 75 - 114: 23.965 distance: 76 - 77: 30.474 distance: 77 - 78: 20.836 distance: 77 - 79: 41.649 distance: 78 - 80: 23.837 distance: 79 - 81: 45.055 distance: 79 - 82: 38.515 distance: 80 - 81: 40.957 distance: 81 - 83: 30.804 distance: 82 - 84: 15.556 distance: 83 - 85: 12.838 distance: 84 - 85: 11.882 distance: 86 - 87: 15.094 distance: 87 - 88: 3.480 distance: 87 - 90: 9.146 distance: 88 - 89: 26.317 distance: 88 - 97: 24.048 distance: 89 - 121: 25.942 distance: 90 - 91: 15.654 distance: 91 - 92: 18.947 distance: 92 - 93: 10.348 distance: 93 - 94: 8.811 distance: 94 - 95: 25.747 distance: 94 - 96: 34.143 distance: 97 - 98: 13.786 distance: 98 - 99: 12.623 distance: 98 - 101: 7.226 distance: 99 - 100: 19.515 distance: 99 - 103: 22.090 distance: 100 - 129: 30.026 distance: 101 - 102: 10.160 distance: 103 - 104: 5.800 distance: 104 - 105: 14.196 distance: 104 - 107: 12.503 distance: 105 - 106: 23.741 distance: 105 - 114: 11.430 distance: 106 - 135: 32.986 distance: 107 - 108: 16.620 distance: 108 - 109: 11.513 distance: 108 - 110: 14.730 distance: 109 - 111: 5.766 distance: 110 - 112: 12.862 distance: 111 - 113: 13.699 distance: 112 - 113: 16.260