Starting phenix.real_space_refine on Sat Sep 12 02:12:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ojl_12955/09_2026/7ojl_12955.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ojl_12955/09_2026/7ojl_12955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ojl_12955/09_2026/7ojl_12955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ojl_12955/09_2026/7ojl_12955.map" model { file = "/net/cci-nas-00/data/ceres_data/7ojl_12955/09_2026/7ojl_12955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ojl_12955/09_2026/7ojl_12955.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ojl_12955/09_2026/7ojl_12955.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ojl_12955/09_2026/7ojl_12955.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.029 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 Mn 1 7.51 5 P 31 5.49 5 S 67 5.16 5 C 8086 2.51 5 N 2182 2.21 5 O 2475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12842 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 12142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1498, 12142 Classifications: {'peptide': 1498} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 47, 'TRANS': 1450} Chain breaks: 12 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'RNAv2': 13} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 427 Classifications: {'RNAv2': 20} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 7} Link IDs: {'rna2p': 5, 'rna3p': 14} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.80, per 1000 atoms: 0.22 Number of scatterers: 12842 At special positions: 0 Unit cell: (102, 115.6, 111.35, 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) Mn 1 24.99 S 67 16.00 P 31 15.00 O 2475 8.00 N 2182 7.00 C 8086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS L 321 " - pdb=" SG CYS L 366 " 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: 0.95 Conformation dependent library (CDL) restraints added in 547.7 milliseconds 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2874 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 7 sheets defined 58.7% alpha, 4.9% beta 8 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'L' and resid 202 through 206 removed outlier: 3.935A pdb=" N VAL L 205 " --> pdb=" O SER L 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 213 through 221 removed outlier: 3.594A pdb=" N CYS L 221 " --> pdb=" O ILE L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 230 through 251 removed outlier: 3.757A pdb=" N LYS L 235 " --> pdb=" O ALA L 231 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 272 Processing helix chain 'L' and resid 284 through 293 Processing helix chain 'L' and resid 296 through 303 Processing helix chain 'L' and resid 321 through 336 removed outlier: 3.803A pdb=" N TYR L 325 " --> pdb=" O CYS L 321 " (cutoff:3.500A) Processing helix chain 'L' and resid 344 through 365 removed outlier: 3.515A pdb=" N ILE L 348 " --> pdb=" O LYS L 344 " (cutoff:3.500A) Processing helix chain 'L' and resid 385 through 404 Processing helix chain 'L' and resid 412 through 433 removed outlier: 3.780A pdb=" N MET L 420 " --> pdb=" O ILE L 416 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR L 424 " --> pdb=" O MET L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 438 through 442 Processing helix chain 'L' and resid 445 through 449 Processing helix chain 'L' and resid 453 through 459 Processing helix chain 'L' and resid 491 through 507 Processing helix chain 'L' and resid 521 through 527 removed outlier: 3.803A pdb=" N ALA L 524 " --> pdb=" O PHE L 521 " (cutoff:3.500A) Processing helix chain 'L' and resid 576 through 584 removed outlier: 3.509A pdb=" N TYR L 580 " --> pdb=" O PRO L 577 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N PHE L 581 " --> pdb=" O LYS L 578 " (cutoff:3.500A) Proline residue: L 582 - end of helix Processing helix chain 'L' and resid 588 through 601 removed outlier: 3.907A pdb=" N VAL L 601 " --> pdb=" O MET L 597 " (cutoff:3.500A) Processing helix chain 'L' and resid 607 through 609 No H-bonds generated for 'chain 'L' and resid 607 through 609' Processing helix chain 'L' and resid 610 through 628 removed outlier: 3.629A pdb=" N ILE L 614 " --> pdb=" O GLN L 610 " (cutoff:3.500A) Processing helix chain 'L' and resid 631 through 649 removed outlier: 3.593A pdb=" N LYS L 635 " --> pdb=" O LYS L 631 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU L 636 " --> pdb=" O ARG L 632 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU L 637 " --> pdb=" O SER L 633 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG L 641 " --> pdb=" O LEU L 637 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR L 642 " --> pdb=" O GLN L 638 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL L 648 " --> pdb=" O ILE L 644 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER L 649 " --> pdb=" O MET L 645 " (cutoff:3.500A) Processing helix chain 'L' and resid 656 through 661 Processing helix chain 'L' and resid 666 through 684 Processing helix chain 'L' and resid 691 through 705 Processing helix chain 'L' and resid 706 through 709 Processing helix chain 'L' and resid 715 through 735 Proline residue: L 730 - end of helix removed outlier: 3.628A pdb=" N GLY L 735 " --> pdb=" O LYS L 731 " (cutoff:3.500A) Processing helix chain 'L' and resid 746 through 761 removed outlier: 3.509A pdb=" N LEU L 761 " --> pdb=" O ALA L 757 " (cutoff:3.500A) Processing helix chain 'L' and resid 780 through 793 Processing helix chain 'L' and resid 798 through 803 removed outlier: 4.032A pdb=" N LYS L 803 " --> pdb=" O GLU L 799 " (cutoff:3.500A) Processing helix chain 'L' and resid 842 through 860 Processing helix chain 'L' and resid 862 through 866 removed outlier: 3.578A pdb=" N LEU L 865 " --> pdb=" O GLY L 862 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU L 866 " --> pdb=" O LYS L 863 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 862 through 866' Processing helix chain 'L' and resid 870 through 884 Processing helix chain 'L' and resid 906 through 925 removed outlier: 4.572A pdb=" N TYR L 910 " --> pdb=" O GLY L 906 " (cutoff:3.500A) Processing helix chain 'L' and resid 942 through 949 Processing helix chain 'L' and resid 952 through 966 removed outlier: 3.509A pdb=" N ILE L 956 " --> pdb=" O ASN L 952 " (cutoff:3.500A) Processing helix chain 'L' and resid 977 through 991 removed outlier: 4.015A pdb=" N TYR L 981 " --> pdb=" O PRO L 977 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU L 982 " --> pdb=" O GLY L 978 " (cutoff:3.500A) Processing helix chain 'L' and resid 991 through 999 Processing helix chain 'L' and resid 1014 through 1023 Processing helix chain 'L' and resid 1025 through 1038 Processing helix chain 'L' and resid 1059 through 1068 removed outlier: 4.128A pdb=" N ARG L1068 " --> pdb=" O SER L1064 " (cutoff:3.500A) Processing helix chain 'L' and resid 1074 through 1085 removed outlier: 3.528A pdb=" N ALA L1078 " --> pdb=" O SER L1074 " (cutoff:3.500A) Processing helix chain 'L' and resid 1093 through 1097 Processing helix chain 'L' and resid 1137 through 1158 removed outlier: 3.592A pdb=" N ILE L1147 " --> pdb=" O PHE L1143 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN L1157 " --> pdb=" O ALA L1153 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU L1158 " --> pdb=" O LEU L1154 " (cutoff:3.500A) Processing helix chain 'L' and resid 1165 through 1182 Processing helix chain 'L' and resid 1193 through 1198 Processing helix chain 'L' and resid 1199 through 1208 removed outlier: 3.520A pdb=" N PHE L1203 " --> pdb=" O CYS L1199 " (cutoff:3.500A) Processing helix chain 'L' and resid 1218 through 1236 removed outlier: 4.024A pdb=" N LYS L1222 " --> pdb=" O GLN L1218 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP L1233 " --> pdb=" O THR L1229 " (cutoff:3.500A) Processing helix chain 'L' and resid 1242 through 1259 Processing helix chain 'L' and resid 1267 through 1278 removed outlier: 3.699A pdb=" N ASN L1276 " --> pdb=" O PHE L1272 " (cutoff:3.500A) Processing helix chain 'L' and resid 1297 through 1320 removed outlier: 3.502A pdb=" N ASP L1302 " --> pdb=" O HIS L1298 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE L1311 " --> pdb=" O ILE L1307 " (cutoff:3.500A) Processing helix chain 'L' and resid 1338 through 1348 Processing helix chain 'L' and resid 1348 through 1366 Processing helix chain 'L' and resid 1396 through 1406 removed outlier: 3.674A pdb=" N HIS L1406 " --> pdb=" O ALA L1402 " (cutoff:3.500A) Processing helix chain 'L' and resid 1412 through 1429 removed outlier: 3.763A pdb=" N GLU L1418 " --> pdb=" O HIS L1414 " (cutoff:3.500A) Processing helix chain 'L' and resid 1433 through 1451 removed outlier: 3.523A pdb=" N CYS L1437 " --> pdb=" O PRO L1433 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU L1439 " --> pdb=" O HIS L1435 " (cutoff:3.500A) removed outlier: 3.543A 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: 3.845A pdb=" N ILE L1478 " --> pdb=" O ARG L1474 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET L1479 " --> pdb=" O SER L1475 " (cutoff:3.500A) Processing helix chain 'L' and resid 1490 through 1507 removed outlier: 4.030A pdb=" N MET L1496 " --> pdb=" O ARG L1492 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS L1499 " --> pdb=" O SER L1495 " (cutoff:3.500A) Processing helix chain 'L' and resid 1511 through 1517 Processing helix chain 'L' and resid 1522 through 1533 removed outlier: 3.591A pdb=" N ASN L1528 " --> pdb=" O SER L1524 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU L1533 " --> pdb=" O LEU L1529 " (cutoff:3.500A) Processing helix chain 'L' and resid 1578 through 1589 Processing helix chain 'L' and resid 1612 through 1624 Processing helix chain 'L' and resid 1638 through 1649 removed outlier: 3.879A pdb=" N ILE L1649 " --> pdb=" O LEU L1645 " (cutoff:3.500A) Processing helix chain 'L' and resid 1668 through 1672 removed outlier: 3.965A pdb=" N ASP L1672 " --> pdb=" O ASN L1669 " (cutoff:3.500A) 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 1683 through 1697 Processing helix chain 'L' and resid 1700 through 1705 removed outlier: 3.867A pdb=" N VAL L1703 " --> pdb=" O GLY L1700 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU L1704 " --> pdb=" O ALA L1701 " (cutoff:3.500A) Processing helix chain 'L' and resid 1740 through 1745 Processing helix chain 'L' and resid 1751 through 1758 removed outlier: 3.548A pdb=" N PHE L1755 " --> pdb=" O TYR L1751 " (cutoff:3.500A) Processing helix chain 'L' and resid 1759 through 1763 removed outlier: 3.706A pdb=" N MET L1763 " --> pdb=" O LEU L1760 " (cutoff:3.500A) Processing helix chain 'L' and resid 1779 through 1787 removed outlier: 4.012A pdb=" N ALA L1785 " --> pdb=" O ASP L1781 " (cutoff:3.500A) Processing helix chain 'L' and resid 1796 through 1802 Processing helix chain 'L' and resid 1813 through 1818 Processing sheet with id=AA1, first strand: chain 'L' and resid 258 through 260 removed outlier: 3.597A pdb=" N VAL L1375 " --> pdb=" O SER L1188 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN L1333 " --> pdb=" O MET L1189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 374 through 376 removed outlier: 3.654A pdb=" N CYS L 571 " --> pdb=" O ILE L 562 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 468 through 469 Processing sheet with id=AA4, first strand: chain 'L' and resid 738 through 739 Processing sheet with id=AA5, first strand: chain 'L' and resid 827 through 829 Processing sheet with id=AA6, first strand: chain 'L' and resid 1653 through 1656 removed outlier: 8.389A pdb=" N GLN L1662 " --> pdb=" O LEU L1548 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU L1548 " --> pdb=" O GLN L1662 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 1723 through 1726 602 hydrogen bonds defined for protein. 1707 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 2.76 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4012 1.34 - 1.46: 2641 1.46 - 1.58: 6344 1.58 - 1.70: 62 1.70 - 1.82: 100 Bond restraints: 13159 Sorted by residual: 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 8.35e-01 bond pdb=" C ASN L 379 " pdb=" N ASP L 380 " ideal model delta sigma weight residual 1.331 1.314 0.017 2.22e-02 2.03e+03 5.89e-01 bond pdb=" CG LEU L 626 " pdb=" CD1 LEU L 626 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.26e-01 bond pdb=" CA THR L 710 " pdb=" CB THR L 710 " ideal model delta sigma weight residual 1.532 1.546 -0.013 2.01e-02 2.48e+03 4.30e-01 bond pdb=" C1' A D 12 " pdb=" N9 A D 12 " ideal model delta sigma weight residual 1.478 1.465 0.013 2.00e-02 2.50e+03 4.09e-01 ... (remaining 13154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 17504 1.39 - 2.78: 296 2.78 - 4.17: 85 4.17 - 5.56: 21 5.56 - 6.95: 2 Bond angle restraints: 17908 Sorted by residual: angle pdb=" C SER L1329 " pdb=" N SER L1330 " pdb=" CA SER L1330 " ideal model delta sigma weight residual 121.54 126.70 -5.16 1.91e+00 2.74e-01 7.31e+00 angle pdb=" N ASP L 380 " pdb=" CA ASP L 380 " pdb=" C ASP L 380 " ideal model delta sigma weight residual 114.16 110.50 3.66 1.48e+00 4.57e-01 6.11e+00 angle pdb=" C3' A D 12 " pdb=" C2' A D 12 " pdb=" O2' A D 12 " ideal model delta sigma weight residual 109.80 114.57 -4.77 2.00e+00 2.50e-01 5.68e+00 angle pdb=" C3' G D 11 " pdb=" C2' G D 11 " pdb=" O2' G D 11 " ideal model delta sigma weight residual 109.80 114.57 -4.77 2.00e+00 2.50e-01 5.68e+00 angle pdb=" C3' G D 1 " pdb=" C2' G D 1 " pdb=" O2' G D 1 " ideal model delta sigma weight residual 109.80 114.48 -4.68 2.00e+00 2.50e-01 5.49e+00 ... (remaining 17903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 7352 17.23 - 34.47: 408 34.47 - 51.70: 108 51.70 - 68.94: 38 68.94 - 86.17: 9 Dihedral angle restraints: 7915 sinusoidal: 3493 harmonic: 4422 Sorted by residual: dihedral pdb=" C4' C D 6 " pdb=" C3' C D 6 " pdb=" C2' C D 6 " pdb=" C1' C D 6 " ideal model delta sinusoidal sigma weight residual 36.34 -36.92 73.26 1 3.10e+00 1.04e-01 7.11e+02 dihedral pdb=" C4' A D 12 " pdb=" C3' A D 12 " pdb=" C2' A D 12 " pdb=" C1' A D 12 " ideal model delta sinusoidal sigma weight residual 36.34 -35.77 72.11 1 3.10e+00 1.04e-01 6.92e+02 dihedral pdb=" C4' G D 11 " pdb=" C3' G D 11 " pdb=" C2' G D 11 " pdb=" C1' G D 11 " ideal model delta sinusoidal sigma weight residual 36.34 -35.28 71.62 1 3.10e+00 1.04e-01 6.84e+02 ... (remaining 7912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1768 0.055 - 0.111: 213 0.111 - 0.166: 20 0.166 - 0.222: 1 0.222 - 0.277: 40 Chirality restraints: 2042 Sorted by residual: chirality pdb=" C2' A D 12 " pdb=" C3' A D 12 " pdb=" O2' A D 12 " pdb=" C1' A D 12 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C2' C D 7 " pdb=" C3' C D 7 " pdb=" O2' C D 7 " pdb=" C1' C D 7 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" P A D 5 " pdb=" OP1 A D 5 " pdb=" OP2 A D 5 " pdb=" O5' A D 5 " both_signs ideal model delta sigma weight residual True 2.17 -2.44 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 2039 not shown) Planarity restraints: 2144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN L 720 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C GLN L 720 " 0.059 2.00e-02 2.50e+03 pdb=" O GLN L 720 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE L 721 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA L 503 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C ALA L 503 " -0.043 2.00e-02 2.50e+03 pdb=" O ALA L 503 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU L 504 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU L 541 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C LEU L 541 " -0.038 2.00e-02 2.50e+03 pdb=" O LEU L 541 " 0.014 2.00e-02 2.50e+03 pdb=" N SER L 542 " 0.013 2.00e-02 2.50e+03 ... (remaining 2141 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 72 2.44 - 3.06: 8647 3.06 - 3.67: 19062 3.67 - 4.29: 28996 4.29 - 4.90: 47475 Nonbonded interactions: 104252 Sorted by model distance: nonbonded pdb=" OD1 ASP L1332 " pdb="MN MN L2301 " model vdw 1.827 2.320 nonbonded pdb=" OE2 GLU L1382 " pdb="MN MN L2301 " model vdw 1.973 2.320 nonbonded pdb=" O ILE L 709 " pdb=" OG1 THR L 710 " model vdw 2.191 3.040 nonbonded pdb=" OG SER L 498 " pdb=" O ILE L 584 " model vdw 2.195 3.040 nonbonded pdb=" O LEU L1083 " pdb=" OG1 THR L1086 " model vdw 2.203 3.040 ... (remaining 104247 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.870 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 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 0.028 13160 Z= 0.114 Angle : 0.511 6.946 17910 Z= 0.256 Chirality : 0.050 0.277 2042 Planarity : 0.003 0.035 2144 Dihedral : 12.313 86.171 5038 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.15 % Favored : 91.78 % Rotamer: Outliers : 2.98 % Allowed : 4.80 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.19), residues: 1472 helix: -0.67 (0.17), residues: 793 sheet: -3.23 (0.45), residues: 92 loop : -3.29 (0.21), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 632 TYR 0.010 0.001 TYR L 642 PHE 0.011 0.001 PHE L 971 TRP 0.007 0.001 TRP L1547 HIS 0.003 0.001 HIS L 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (13159) covalent geometry : angle 0.51096 / 0.26 (17908) SS BOND : bond 0.00280 / 0.18 ( 1) SS BOND : angle 1.36159 / 0.47 ( 2) hydrogen bonds : bond 0.14141 / 9.59 ( 624) hydrogen bonds : angle 5.19550 / 3.81 ( 1751) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 483 MET cc_start: 0.8050 (mmt) cc_final: 0.7816 (mmt) REVERT: L 1075 ASN cc_start: 0.7916 (OUTLIER) cc_final: 0.7502 (m-40) REVERT: L 1085 LEU cc_start: 0.7510 (mm) cc_final: 0.6856 (pp) REVERT: L 1811 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8501 (mp) outliers start: 41 outliers final: 19 residues processed: 177 average time/residue: 0.1427 time to fit residues: 34.4885 Evaluate side-chains 100 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 462 VAL Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain L residue 513 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 601 VAL Chi-restraints excluded: chain L residue 658 ASP Chi-restraints excluded: chain L residue 743 ASP Chi-restraints excluded: chain L residue 828 VAL Chi-restraints excluded: chain L residue 830 ASN Chi-restraints excluded: chain L residue 1075 ASN Chi-restraints excluded: chain L residue 1230 LEU Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1394 VAL Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1456 ASP Chi-restraints excluded: chain L residue 1509 LEU Chi-restraints excluded: chain L residue 1687 ASP Chi-restraints excluded: chain L residue 1783 CYS Chi-restraints excluded: chain L residue 1811 LEU Chi-restraints excluded: chain L residue 1818 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1407 ASN L1481 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.076556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.058461 restraints weight = 34478.449| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.79 r_work: 0.2811 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13160 Z= 0.270 Angle : 0.711 14.334 17910 Z= 0.344 Chirality : 0.056 0.978 2042 Planarity : 0.004 0.052 2144 Dihedral : 10.568 149.008 2045 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.55 % Allowed : 9.02 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.21), residues: 1472 helix: 0.33 (0.18), residues: 804 sheet: -3.15 (0.45), residues: 100 loop : -2.77 (0.22), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L1557 TYR 0.013 0.002 TYR L 910 PHE 0.023 0.002 PHE L1022 TRP 0.008 0.001 TRP L1547 HIS 0.004 0.001 HIS L1234 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.27 (13159) covalent geometry : angle 0.71136 / 0.34 (17908) SS BOND : bond 0.00069 / 0.04 ( 1) SS BOND : angle 1.04368 / 0.37 ( 2) hydrogen bonds : bond 0.04402 / 2.91 ( 624) hydrogen bonds : angle 4.40795 / 3.29 ( 1751) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: L 483 MET cc_start: 0.8577 (mmt) cc_final: 0.7802 (mmt) REVERT: L 504 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9349 (tt) REVERT: L 513 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8948 (p) REVERT: L 944 ASN cc_start: 0.9382 (m-40) cc_final: 0.9139 (m-40) REVERT: L 1261 LYS cc_start: 0.8217 (tptt) cc_final: 0.7661 (tptt) REVERT: L 1811 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9232 (mp) outliers start: 35 outliers final: 19 residues processed: 111 average time/residue: 0.1077 time to fit residues: 17.8319 Evaluate side-chains 94 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 439 VAL Chi-restraints excluded: chain L residue 462 VAL Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain L residue 513 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 601 VAL Chi-restraints excluded: chain L residue 736 HIS Chi-restraints excluded: chain L residue 743 ASP Chi-restraints excluded: chain L residue 1234 HIS Chi-restraints excluded: chain L residue 1264 THR Chi-restraints excluded: chain L residue 1265 THR Chi-restraints excluded: chain L residue 1289 ILE Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1394 VAL Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1509 LEU Chi-restraints excluded: chain L residue 1629 VAL Chi-restraints excluded: chain L residue 1687 ASP Chi-restraints excluded: chain L residue 1783 CYS Chi-restraints excluded: chain L residue 1811 LEU Chi-restraints excluded: chain L residue 1818 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 104 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 116 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 60 optimal weight: 0.0970 chunk 33 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1407 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.078951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.060211 restraints weight = 34643.343| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.86 r_work: 0.2872 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13160 Z= 0.121 Angle : 0.576 9.415 17910 Z= 0.279 Chirality : 0.045 0.362 2042 Planarity : 0.003 0.039 2144 Dihedral : 10.370 155.712 2034 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.89 % Allowed : 10.26 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.22), residues: 1472 helix: 1.03 (0.18), residues: 801 sheet: -2.86 (0.45), residues: 100 loop : -2.42 (0.23), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 381 TYR 0.023 0.001 TYR L1517 PHE 0.016 0.001 PHE L1022 TRP 0.010 0.001 TRP L1802 HIS 0.003 0.001 HIS L 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (13159) covalent geometry : angle 0.57584 / 0.28 (17908) SS BOND : bond 0.00356 / 0.22 ( 1) SS BOND : angle 1.21892 / 0.42 ( 2) hydrogen bonds : bond 0.03490 / 2.29 ( 624) hydrogen bonds : angle 3.91779 / 2.95 ( 1751) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.496 Fit side-chains REVERT: L 483 MET cc_start: 0.8555 (mmt) cc_final: 0.8042 (mmt) REVERT: L 912 ASP cc_start: 0.9238 (m-30) cc_final: 0.8667 (p0) REVERT: L 1085 LEU cc_start: 0.7992 (mm) cc_final: 0.7516 (pp) REVERT: L 1261 LYS cc_start: 0.8225 (tptt) cc_final: 0.7688 (tptt) outliers start: 26 outliers final: 18 residues processed: 103 average time/residue: 0.1004 time to fit residues: 15.9358 Evaluate side-chains 91 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 439 VAL Chi-restraints excluded: chain L residue 462 VAL Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain L residue 513 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 601 VAL Chi-restraints excluded: chain L residue 736 HIS Chi-restraints excluded: chain L residue 743 ASP Chi-restraints excluded: chain L residue 1238 MET Chi-restraints excluded: chain L residue 1264 THR Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1394 VAL Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1509 LEU Chi-restraints excluded: chain L residue 1629 VAL Chi-restraints excluded: chain L residue 1687 ASP Chi-restraints excluded: chain L residue 1818 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 134 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 117 optimal weight: 0.1980 chunk 72 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1718 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.077833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.059635 restraints weight = 34366.103| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.81 r_work: 0.2850 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13160 Z= 0.159 Angle : 0.583 10.558 17910 Z= 0.282 Chirality : 0.044 0.391 2042 Planarity : 0.003 0.049 2144 Dihedral : 10.226 156.507 2029 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 1.97 % Allowed : 10.77 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.22), residues: 1472 helix: 1.25 (0.19), residues: 802 sheet: -2.46 (0.49), residues: 90 loop : -2.30 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L1072 TYR 0.011 0.001 TYR L1517 PHE 0.022 0.001 PHE L 858 TRP 0.007 0.001 TRP L1547 HIS 0.003 0.001 HIS L1234 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (13159) covalent geometry : angle 0.58253 / 0.28 (17908) SS BOND : bond 0.00226 / 0.14 ( 1) SS BOND : angle 1.14983 / 0.40 ( 2) hydrogen bonds : bond 0.03565 / 2.35 ( 624) hydrogen bonds : angle 3.93078 / 2.95 ( 1751) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.330 Fit side-chains REVERT: L 483 MET cc_start: 0.8606 (mmt) cc_final: 0.8062 (mmt) REVERT: L 860 ARG cc_start: 0.8401 (ttp-170) cc_final: 0.7905 (ptt90) REVERT: L 1079 LEU cc_start: 0.8768 (tp) cc_final: 0.8562 (mm) REVERT: L 1085 LEU cc_start: 0.8033 (mm) cc_final: 0.7567 (pp) REVERT: L 1261 LYS cc_start: 0.8333 (tptt) cc_final: 0.7754 (tptt) REVERT: L 1407 ASN cc_start: 0.8760 (t0) cc_final: 0.8546 (t0) outliers start: 27 outliers final: 21 residues processed: 108 average time/residue: 0.1029 time to fit residues: 17.0229 Evaluate side-chains 89 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 382 LEU Chi-restraints excluded: chain L residue 439 VAL Chi-restraints excluded: chain L residue 462 VAL Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 601 VAL Chi-restraints excluded: chain L residue 736 HIS Chi-restraints excluded: chain L residue 743 ASP Chi-restraints excluded: chain L residue 1227 LEU Chi-restraints excluded: chain L residue 1238 MET Chi-restraints excluded: chain L residue 1245 VAL Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1332 ASP Chi-restraints excluded: chain L residue 1394 VAL Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1466 VAL Chi-restraints excluded: chain L residue 1509 LEU Chi-restraints excluded: chain L residue 1629 VAL Chi-restraints excluded: chain L residue 1687 ASP Chi-restraints excluded: chain L residue 1818 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 22 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 88 optimal weight: 0.0980 chunk 129 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 634 GLN L 694 ASN ** L1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1481 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.080313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.061517 restraints weight = 34801.153| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.95 r_work: 0.2903 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 13160 Z= 0.095 Angle : 0.518 10.469 17910 Z= 0.255 Chirality : 0.042 0.321 2042 Planarity : 0.003 0.033 2144 Dihedral : 10.426 162.916 2028 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.04 % Allowed : 11.35 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.22), residues: 1472 helix: 1.49 (0.19), residues: 806 sheet: -2.23 (0.49), residues: 90 loop : -2.09 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 381 TYR 0.029 0.001 TYR L1517 PHE 0.017 0.001 PHE L1513 TRP 0.008 0.001 TRP L1547 HIS 0.003 0.001 HIS L 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 (13159) covalent geometry : angle 0.51758 / 0.25 (17908) SS BOND : bond 0.00389 / 0.24 ( 1) SS BOND : angle 1.22430 / 0.42 ( 2) hydrogen bonds : bond 0.03022 / 1.98 ( 624) hydrogen bonds : angle 3.74121 / 2.83 ( 1751) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: L 483 MET cc_start: 0.8610 (mmt) cc_final: 0.8240 (mmt) REVERT: L 504 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9351 (tt) REVERT: L 942 SER cc_start: 0.8809 (m) cc_final: 0.8586 (p) REVERT: L 1085 LEU cc_start: 0.7996 (mm) cc_final: 0.7523 (pp) REVERT: L 1261 LYS cc_start: 0.8305 (tptt) cc_final: 0.7762 (tptt) REVERT: L 1407 ASN cc_start: 0.8672 (t0) cc_final: 0.8468 (t0) outliers start: 28 outliers final: 19 residues processed: 102 average time/residue: 0.1034 time to fit residues: 16.3140 Evaluate side-chains 90 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 382 LEU Chi-restraints excluded: chain L residue 462 VAL Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 601 VAL Chi-restraints excluded: chain L residue 736 HIS Chi-restraints excluded: chain L residue 743 ASP Chi-restraints excluded: chain L residue 1189 MET Chi-restraints excluded: chain L residue 1238 MET Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1394 VAL Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1509 LEU Chi-restraints excluded: chain L residue 1575 GLU Chi-restraints excluded: chain L residue 1629 VAL Chi-restraints excluded: chain L residue 1687 ASP Chi-restraints excluded: chain L residue 1783 CYS Chi-restraints excluded: chain L residue 1818 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 143 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 694 ASN ** L1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1633 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.078421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.059630 restraints weight = 34680.237| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.86 r_work: 0.2857 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13160 Z= 0.159 Angle : 0.555 10.743 17910 Z= 0.271 Chirality : 0.043 0.384 2042 Planarity : 0.003 0.051 2144 Dihedral : 10.504 161.452 2028 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.11 % Allowed : 12.15 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.22), residues: 1472 helix: 1.50 (0.19), residues: 803 sheet: -2.18 (0.50), residues: 90 loop : -2.04 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L1072 TYR 0.018 0.001 TYR L1517 PHE 0.015 0.001 PHE L1358 TRP 0.006 0.001 TRP L1547 HIS 0.003 0.001 HIS L1406 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (13159) covalent geometry : angle 0.55525 / 0.27 (17908) SS BOND : bond 0.00178 / 0.11 ( 1) SS BOND : angle 1.09750 / 0.38 ( 2) hydrogen bonds : bond 0.03416 / 2.26 ( 624) hydrogen bonds : angle 3.84678 / 2.89 ( 1751) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: L 483 MET cc_start: 0.8657 (mmt) cc_final: 0.8129 (mmt) REVERT: L 504 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9345 (tt) REVERT: L 620 MET cc_start: 0.9163 (mtp) cc_final: 0.8939 (mtp) REVERT: L 942 SER cc_start: 0.8861 (m) cc_final: 0.8656 (p) REVERT: L 1085 LEU cc_start: 0.8030 (mm) cc_final: 0.7531 (pp) REVERT: L 1261 LYS cc_start: 0.8325 (tptt) cc_final: 0.7774 (tptt) outliers start: 29 outliers final: 20 residues processed: 100 average time/residue: 0.1104 time to fit residues: 16.4709 Evaluate side-chains 88 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 382 LEU Chi-restraints excluded: chain L residue 439 VAL Chi-restraints excluded: chain L residue 462 VAL Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 601 VAL Chi-restraints excluded: chain L residue 736 HIS Chi-restraints excluded: chain L residue 743 ASP Chi-restraints excluded: chain L residue 1238 MET Chi-restraints excluded: chain L residue 1245 VAL Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1332 ASP Chi-restraints excluded: chain L residue 1394 VAL Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1509 LEU Chi-restraints excluded: chain L residue 1629 VAL Chi-restraints excluded: chain L residue 1687 ASP Chi-restraints excluded: chain L residue 1783 CYS Chi-restraints excluded: chain L residue 1818 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 119 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 59 optimal weight: 0.0670 chunk 4 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 944 ASN ** L1299 ASN ** 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 = 0.3419 r_free = 0.3419 target = 0.078783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.060416 restraints weight = 34441.948| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.85 r_work: 0.2879 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13160 Z= 0.119 Angle : 0.530 8.286 17910 Z= 0.262 Chirality : 0.042 0.350 2042 Planarity : 0.003 0.041 2144 Dihedral : 10.503 163.663 2028 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.75 % Allowed : 12.37 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.22), residues: 1472 helix: 1.60 (0.19), residues: 802 sheet: -2.35 (0.46), residues: 100 loop : -1.94 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L1072 TYR 0.019 0.001 TYR L1751 PHE 0.017 0.001 PHE L 858 TRP 0.007 0.001 TRP L1547 HIS 0.003 0.001 HIS L1406 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (13159) covalent geometry : angle 0.53033 / 0.26 (17908) SS BOND : bond 0.00311 / 0.19 ( 1) SS BOND : angle 1.15112 / 0.40 ( 2) hydrogen bonds : bond 0.03171 / 2.09 ( 624) hydrogen bonds : angle 3.74760 / 2.82 ( 1751) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: L 483 MET cc_start: 0.8686 (mmt) cc_final: 0.8271 (mmt) REVERT: L 504 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9351 (tt) REVERT: L 620 MET cc_start: 0.9162 (mtp) cc_final: 0.8925 (mtp) REVERT: L 1085 LEU cc_start: 0.7950 (mm) cc_final: 0.7511 (pp) REVERT: L 1261 LYS cc_start: 0.8309 (tptt) cc_final: 0.7764 (tptt) REVERT: L 1407 ASN cc_start: 0.8732 (t0) cc_final: 0.8514 (t0) outliers start: 24 outliers final: 21 residues processed: 94 average time/residue: 0.1142 time to fit residues: 16.2466 Evaluate side-chains 88 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 382 LEU Chi-restraints excluded: chain L residue 439 VAL Chi-restraints excluded: chain L residue 462 VAL Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 601 VAL Chi-restraints excluded: chain L residue 682 LEU Chi-restraints excluded: chain L residue 736 HIS Chi-restraints excluded: chain L residue 743 ASP Chi-restraints excluded: chain L residue 1238 MET Chi-restraints excluded: chain L residue 1245 VAL Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1394 VAL Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1466 VAL Chi-restraints excluded: chain L residue 1509 LEU Chi-restraints excluded: chain L residue 1629 VAL Chi-restraints excluded: chain L residue 1687 ASP Chi-restraints excluded: chain L residue 1783 CYS Chi-restraints excluded: chain L residue 1818 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 944 ASN ** L1299 ASN ** 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 = 0.3425 r_free = 0.3425 target = 0.079267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.060961 restraints weight = 33980.685| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.83 r_work: 0.2885 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13160 Z= 0.116 Angle : 0.520 8.391 17910 Z= 0.256 Chirality : 0.042 0.347 2042 Planarity : 0.003 0.041 2144 Dihedral : 10.480 165.341 2028 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.89 % Allowed : 12.45 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.22), residues: 1472 helix: 1.67 (0.19), residues: 804 sheet: -2.04 (0.50), residues: 90 loop : -1.92 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L1072 TYR 0.016 0.001 TYR L1751 PHE 0.013 0.001 PHE L1358 TRP 0.007 0.001 TRP L1547 HIS 0.003 0.001 HIS L1406 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (13159) covalent geometry : angle 0.52000 / 0.26 (17908) SS BOND : bond 0.00271 / 0.17 ( 1) SS BOND : angle 1.15069 / 0.40 ( 2) hydrogen bonds : bond 0.03120 / 2.06 ( 624) hydrogen bonds : angle 3.70148 / 2.79 ( 1751) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: L 483 MET cc_start: 0.8711 (mmt) cc_final: 0.8285 (mmt) REVERT: L 504 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9343 (tt) REVERT: L 1085 LEU cc_start: 0.7921 (mm) cc_final: 0.7479 (pp) REVERT: L 1261 LYS cc_start: 0.8317 (tptt) cc_final: 0.7807 (tptt) REVERT: L 1407 ASN cc_start: 0.8708 (t0) cc_final: 0.8496 (t0) outliers start: 26 outliers final: 23 residues processed: 96 average time/residue: 0.1139 time to fit residues: 16.5402 Evaluate side-chains 92 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 382 LEU Chi-restraints excluded: chain L residue 439 VAL Chi-restraints excluded: chain L residue 462 VAL Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain L residue 528 VAL Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 601 VAL Chi-restraints excluded: chain L residue 682 LEU Chi-restraints excluded: chain L residue 736 HIS Chi-restraints excluded: chain L residue 743 ASP Chi-restraints excluded: chain L residue 1238 MET Chi-restraints excluded: chain L residue 1245 VAL Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1332 ASP Chi-restraints excluded: chain L residue 1394 VAL Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1466 VAL Chi-restraints excluded: chain L residue 1509 LEU Chi-restraints excluded: chain L residue 1629 VAL Chi-restraints excluded: chain L residue 1687 ASP Chi-restraints excluded: chain L residue 1740 LEU Chi-restraints excluded: chain L residue 1783 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 151 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 81 optimal weight: 0.4980 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 940 GLN ** L1299 ASN ** 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 = 0.3403 r_free = 0.3403 target = 0.078122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.059800 restraints weight = 34446.524| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.84 r_work: 0.2859 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13160 Z= 0.153 Angle : 0.552 8.066 17910 Z= 0.272 Chirality : 0.043 0.378 2042 Planarity : 0.003 0.044 2144 Dihedral : 10.462 163.129 2027 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.97 % Allowed : 12.66 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.22), residues: 1472 helix: 1.61 (0.19), residues: 804 sheet: -2.03 (0.50), residues: 90 loop : -1.93 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 695 TYR 0.016 0.001 TYR L1751 PHE 0.016 0.001 PHE L 858 TRP 0.006 0.001 TRP L1547 HIS 0.003 0.001 HIS L1406 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (13159) covalent geometry : angle 0.55217 / 0.27 (17908) SS BOND : bond 0.00190 / 0.12 ( 1) SS BOND : angle 1.10170 / 0.38 ( 2) hydrogen bonds : bond 0.03321 / 2.19 ( 624) hydrogen bonds : angle 3.77422 / 2.83 ( 1751) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: L 483 MET cc_start: 0.8716 (mmt) cc_final: 0.8123 (mmt) REVERT: L 504 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9345 (tt) REVERT: L 1085 LEU cc_start: 0.7883 (mm) cc_final: 0.7462 (pp) REVERT: L 1261 LYS cc_start: 0.8302 (tptt) cc_final: 0.7832 (tptt) outliers start: 27 outliers final: 24 residues processed: 96 average time/residue: 0.1158 time to fit residues: 16.7092 Evaluate side-chains 92 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 382 LEU Chi-restraints excluded: chain L residue 439 VAL Chi-restraints excluded: chain L residue 462 VAL Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain L residue 504 LEU Chi-restraints excluded: chain L residue 528 VAL Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 601 VAL Chi-restraints excluded: chain L residue 736 HIS Chi-restraints excluded: chain L residue 743 ASP Chi-restraints excluded: chain L residue 1238 MET Chi-restraints excluded: chain L residue 1245 VAL Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1332 ASP Chi-restraints excluded: chain L residue 1394 VAL Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1466 VAL Chi-restraints excluded: chain L residue 1509 LEU Chi-restraints excluded: chain L residue 1629 VAL Chi-restraints excluded: chain L residue 1687 ASP Chi-restraints excluded: chain L residue 1740 LEU Chi-restraints excluded: chain L residue 1783 CYS Chi-restraints excluded: chain L residue 1784 VAL Chi-restraints excluded: chain L residue 1818 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 110 optimal weight: 0.0470 chunk 103 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1407 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.080725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.062528 restraints weight = 34279.350| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.85 r_work: 0.2926 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13160 Z= 0.092 Angle : 0.508 7.971 17910 Z= 0.251 Chirality : 0.041 0.303 2042 Planarity : 0.003 0.035 2144 Dihedral : 10.463 169.567 2027 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.60 % Allowed : 12.95 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.23), residues: 1472 helix: 1.77 (0.19), residues: 806 sheet: -1.90 (0.50), residues: 90 loop : -1.84 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 695 TYR 0.014 0.001 TYR L1226 PHE 0.013 0.001 PHE L1513 TRP 0.008 0.001 TRP L1547 HIS 0.004 0.001 HIS L 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (13159) covalent geometry : angle 0.50796 / 0.25 (17908) SS BOND : bond 0.00287 / 0.18 ( 1) SS BOND : angle 1.13794 / 0.39 ( 2) hydrogen bonds : bond 0.02865 / 1.89 ( 624) hydrogen bonds : angle 3.61061 / 2.73 ( 1751) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: L 483 MET cc_start: 0.8708 (mmt) cc_final: 0.8353 (mmt) REVERT: L 1071 GLU cc_start: 0.8556 (mp0) cc_final: 0.7900 (mp0) REVERT: L 1085 LEU cc_start: 0.7838 (mm) cc_final: 0.7423 (pp) REVERT: L 1261 LYS cc_start: 0.8333 (tptt) cc_final: 0.7885 (tptt) outliers start: 22 outliers final: 17 residues processed: 91 average time/residue: 0.1151 time to fit residues: 15.8280 Evaluate side-chains 85 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 382 LEU Chi-restraints excluded: chain L residue 439 VAL Chi-restraints excluded: chain L residue 462 VAL Chi-restraints excluded: chain L residue 466 VAL Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain L residue 601 VAL Chi-restraints excluded: chain L residue 682 LEU Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1394 VAL Chi-restraints excluded: chain L residue 1408 ILE Chi-restraints excluded: chain L residue 1509 LEU Chi-restraints excluded: chain L residue 1629 VAL Chi-restraints excluded: chain L residue 1687 ASP Chi-restraints excluded: chain L residue 1740 LEU Chi-restraints excluded: chain L residue 1784 VAL Chi-restraints excluded: chain L residue 1818 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 56 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L1299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1407 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 = 0.3438 r_free = 0.3438 target = 0.080211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.061234 restraints weight = 34691.791| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.95 r_work: 0.2890 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13160 Z= 0.116 Angle : 0.526 8.144 17910 Z= 0.260 Chirality : 0.042 0.333 2042 Planarity : 0.003 0.033 2144 Dihedral : 10.354 168.307 2025 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.60 % Allowed : 13.03 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.22), residues: 1472 helix: 1.77 (0.19), residues: 804 sheet: -1.88 (0.50), residues: 90 loop : -1.81 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 997 TYR 0.014 0.001 TYR L1751 PHE 0.015 0.001 PHE L 858 TRP 0.007 0.001 TRP L1547 HIS 0.003 0.001 HIS L 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (13159) covalent geometry : angle 0.52608 / 0.26 (17908) SS BOND : bond 0.00157 / 0.10 ( 1) SS BOND : angle 0.88509 / 0.31 ( 2) hydrogen bonds : bond 0.03039 / 2.01 ( 624) hydrogen bonds : angle 3.65016 / 2.75 ( 1751) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2415.65 seconds wall clock time: 42 minutes 33.20 seconds (2553.20 seconds total)