Starting phenix.real_space_refine on Sat Feb 7 01:17:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g2f_50975/02_2026/9g2f_50975.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g2f_50975/02_2026/9g2f_50975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9g2f_50975/02_2026/9g2f_50975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g2f_50975/02_2026/9g2f_50975.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9g2f_50975/02_2026/9g2f_50975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g2f_50975/02_2026/9g2f_50975.map" } resolution = 2.8 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= 0.003 sd= 0.036 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: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 17736 2.51 5 N 4820 2.21 5 O 5492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28158 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 13842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1752, 13842 Classifications: {'peptide': 1752} Link IDs: {'PTRANS': 65, 'TRANS': 1686} Chain: "B" Number of atoms: 13842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1752, 13842 Classifications: {'peptide': 1752} Link IDs: {'PTRANS': 65, 'TRANS': 1686} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.63, per 1000 atoms: 0.20 Number of scatterers: 28158 At special positions: 0 Unit cell: (151.89, 165.17, 146.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 5492 8.00 N 4820 7.00 C 17736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A1019 " - pdb=" SG CYS A1153 " distance=2.03 Simple disulfide: pdb=" SG CYS A1225 " - pdb=" SG CYS A1228 " distance=2.03 Simple disulfide: pdb=" SG CYS A1336 " - pdb=" SG CYS A1344 " distance=2.03 Simple disulfide: pdb=" SG CYS A1403 " - pdb=" SG CYS A1456 " distance=2.03 Simple disulfide: pdb=" SG CYS A1520 " - pdb=" SG CYS A1528 " distance=2.03 Simple disulfide: pdb=" SG CYS A1522 " - pdb=" SG CYS A1530 " distance=2.03 Simple disulfide: pdb=" SG CYS B1019 " - pdb=" SG CYS B1153 " distance=2.03 Simple disulfide: pdb=" SG CYS B1225 " - pdb=" SG CYS B1228 " distance=2.03 Simple disulfide: pdb=" SG CYS B1336 " - pdb=" SG CYS B1344 " distance=2.03 Simple disulfide: pdb=" SG CYS B1403 " - pdb=" SG CYS B1456 " distance=2.03 Simple disulfide: pdb=" SG CYS B1520 " - pdb=" SG CYS B1528 " distance=2.03 Simple disulfide: pdb=" SG CYS B1522 " - pdb=" SG CYS B1530 " 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 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN I 4 " - " MAN I 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA E 3 " - " MAN E 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A2801 " - " ASN A1993 " " NAG A2802 " - " ASN A1712 " " NAG A2803 " - " ASN A1807 " " NAG B2801 " - " ASN B1993 " " NAG B2802 " - " ASN B1712 " " NAG B2803 " - " ASN B1807 " " NAG C 1 " - " ASN A1616 " " NAG D 1 " - " ASN A1773 " " NAG E 1 " - " ASN A2337 " " NAG F 1 " - " ASN A1892 " " NAG G 1 " - " ASN A2648 " " NAG H 1 " - " ASN B1616 " " NAG I 1 " - " ASN B1773 " " NAG J 1 " - " ASN B2337 " " NAG K 1 " - " ASN B1892 " " NAG L 1 " - " ASN B2648 " Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.1 seconds 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6472 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 36 sheets defined 9.6% alpha, 53.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 1074 through 1076 No H-bonds generated for 'chain 'A' and resid 1074 through 1076' Processing helix chain 'A' and resid 1205 through 1207 No H-bonds generated for 'chain 'A' and resid 1205 through 1207' Processing helix chain 'A' and resid 1278 through 1282 Processing helix chain 'A' and resid 1321 through 1324 Processing helix chain 'A' and resid 1349 through 1353 Processing helix chain 'A' and resid 1410 through 1412 No H-bonds generated for 'chain 'A' and resid 1410 through 1412' Processing helix chain 'A' and resid 1453 through 1457 Processing helix chain 'A' and resid 1537 through 1541 Processing helix chain 'A' and resid 1684 through 1687 removed outlier: 4.275A pdb=" N GLY A1687 " --> pdb=" O GLY A1684 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1684 through 1687' Processing helix chain 'A' and resid 2410 through 2414 Processing helix chain 'A' and resid 2441 through 2443 No H-bonds generated for 'chain 'A' and resid 2441 through 2443' Processing helix chain 'A' and resid 2444 through 2449 removed outlier: 4.424A pdb=" N GLY A2449 " --> pdb=" O TRP A2445 " (cutoff:3.500A) Processing helix chain 'A' and resid 2471 through 2475 Processing helix chain 'A' and resid 2478 through 2486 Processing helix chain 'A' and resid 2489 through 2494 removed outlier: 4.276A pdb=" N ILE A2493 " --> pdb=" O GLN A2489 " (cutoff:3.500A) Processing helix chain 'A' and resid 2508 through 2517 Processing helix chain 'A' and resid 2524 through 2538 Processing helix chain 'A' and resid 2590 through 2601 Processing helix chain 'A' and resid 2627 through 2635 Processing helix chain 'A' and resid 2686 through 2716 removed outlier: 3.590A pdb=" N ARG A2702 " --> pdb=" O GLN A2698 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR A2706 " --> pdb=" O ARG A2702 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A2707 " --> pdb=" O ALA A2703 " (cutoff:3.500A) Processing helix chain 'A' and resid 2726 through 2737 Processing helix chain 'A' and resid 2753 through 2758 removed outlier: 3.644A pdb=" N ALA A2757 " --> pdb=" O PRO A2754 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP A2758 " --> pdb=" O GLU A2755 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2761 No H-bonds generated for 'chain 'A' and resid 2759 through 2761' Processing helix chain 'B' and resid 1074 through 1076 No H-bonds generated for 'chain 'B' and resid 1074 through 1076' Processing helix chain 'B' and resid 1205 through 1207 No H-bonds generated for 'chain 'B' and resid 1205 through 1207' Processing helix chain 'B' and resid 1278 through 1282 Processing helix chain 'B' and resid 1321 through 1324 Processing helix chain 'B' and resid 1349 through 1353 Processing helix chain 'B' and resid 1410 through 1412 No H-bonds generated for 'chain 'B' and resid 1410 through 1412' Processing helix chain 'B' and resid 1453 through 1457 Processing helix chain 'B' and resid 1537 through 1541 Processing helix chain 'B' and resid 2410 through 2414 Processing helix chain 'B' and resid 2444 through 2449 removed outlier: 4.557A pdb=" N GLY B2449 " --> pdb=" O TRP B2445 " (cutoff:3.500A) Processing helix chain 'B' and resid 2460 through 2464 Processing helix chain 'B' and resid 2471 through 2475 Processing helix chain 'B' and resid 2478 through 2486 Processing helix chain 'B' and resid 2489 through 2494 removed outlier: 4.171A pdb=" N ILE B2493 " --> pdb=" O GLN B2489 " (cutoff:3.500A) Processing helix chain 'B' and resid 2508 through 2517 Processing helix chain 'B' and resid 2524 through 2538 Processing helix chain 'B' and resid 2590 through 2601 Processing helix chain 'B' and resid 2627 through 2635 Processing helix chain 'B' and resid 2686 through 2716 removed outlier: 3.777A pdb=" N THR B2706 " --> pdb=" O ARG B2702 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B2707 " --> pdb=" O ALA B2703 " (cutoff:3.500A) Processing helix chain 'B' and resid 2726 through 2737 Processing helix chain 'B' and resid 2753 through 2758 removed outlier: 3.536A pdb=" N ALA B2757 " --> pdb=" O PRO B2754 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASP B2758 " --> pdb=" O GLU B2755 " (cutoff:3.500A) Processing helix chain 'B' and resid 2759 through 2761 No H-bonds generated for 'chain 'B' and resid 2759 through 2761' Processing sheet with id=AA1, first strand: chain 'A' and resid 1030 through 1033 Processing sheet with id=AA2, first strand: chain 'A' and resid 1049 through 1050 Processing sheet with id=AA3, first strand: chain 'A' and resid 1108 through 1114 Processing sheet with id=AA4, first strand: chain 'A' and resid 1186 through 1188 Processing sheet with id=AA5, first strand: chain 'A' and resid 1210 through 1216 removed outlier: 6.580A pdb=" N ILE A1567 " --> pdb=" O ILE A1214 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A1548 " --> pdb=" O ALA A1560 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1230 through 1231 removed outlier: 6.812A pdb=" N ILE A1259 " --> pdb=" O ILE A1271 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A1242 " --> pdb=" O GLY A1254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1289 through 1293 removed outlier: 5.263A pdb=" N LEU A1300 " --> pdb=" O VAL A1313 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A1309 " --> pdb=" O ASP A1304 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A1310 " --> pdb=" O VAL A1329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1358 through 1363 removed outlier: 4.225A pdb=" N VAL A1372 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE A1361 " --> pdb=" O TYR A1370 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N TYR A1370 " --> pdb=" O ILE A1361 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE A1377 " --> pdb=" O LEU A1389 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1407 through 1408 removed outlier: 6.560A pdb=" N ILE A1437 " --> pdb=" O ILE A1449 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP A1419 " --> pdb=" O LEU A1432 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1477 through 1482 removed outlier: 6.726A pdb=" N THR A1491 " --> pdb=" O SER A1478 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE A1480 " --> pdb=" O TYR A1489 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TYR A1489 " --> pdb=" O ILE A1480 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLN A1503 " --> pdb=" O LEU A1512 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU A1512 " --> pdb=" O GLN A1503 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1583 through 1587 removed outlier: 5.769A pdb=" N GLN A1603 " --> pdb=" O PHE A1617 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N SER A1607 " --> pdb=" O TYR A1613 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TYR A1613 " --> pdb=" O SER A1607 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU A1614 " --> pdb=" O ASP A1630 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP A1630 " --> pdb=" O LEU A1614 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN A1616 " --> pdb=" O LEU A1628 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU A1628 " --> pdb=" O ASN A1616 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR A1618 " --> pdb=" O THR A1626 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR A1626 " --> pdb=" O ILE A1638 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG A1647 " --> pdb=" O LEU A1659 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS A1668 " --> pdb=" O MET A1680 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASP A1683 " --> pdb=" O LEU A1689 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU A1689 " --> pdb=" O ASP A1683 " (cutoff:3.500A) removed outlier: 10.228A pdb=" N LEU A1688 " --> pdb=" O TYR A1704 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N TYR A1704 " --> pdb=" O LEU A1688 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ALA A1690 " --> pdb=" O TYR A1702 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N PHE A1701 " --> pdb=" O VAL A1713 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL A1713 " --> pdb=" O PHE A1701 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP A1703 " --> pdb=" O THR A1711 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR A1711 " --> pdb=" O LEU A1723 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A1805 " --> pdb=" O HIS A1789 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU A1791 " --> pdb=" O ILE A1803 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE A1803 " --> pdb=" O GLU A1791 " (cutoff:3.500A) removed outlier: 11.258A pdb=" N THR A1802 " --> pdb=" O LEU A1823 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N LEU A1823 " --> pdb=" O THR A1802 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLY A1804 " --> pdb=" O TRP A1821 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A1834 " --> pdb=" O GLU A1826 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE A1828 " --> pdb=" O VAL A1832 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL A1832 " --> pdb=" O ILE A1828 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A1847 " --> pdb=" O LEU A1839 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A1841 " --> pdb=" O ASN A1845 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ASN A1845 " --> pdb=" O VAL A1841 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N PHE A1880 " --> pdb=" O VAL A1893 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASN A1892 " --> pdb=" O LEU A1904 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU A1904 " --> pdb=" O ASN A1892 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N SER A1894 " --> pdb=" O ALA A1902 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ALA A1902 " --> pdb=" O THR A1913 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER A1910 " --> pdb=" O PHE A1926 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N PHE A1926 " --> pdb=" O SER A1910 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG A1912 " --> pdb=" O ARG A1924 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG A1924 " --> pdb=" O ARG A1912 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASP A1914 " --> pdb=" O VAL A1922 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL A1922 " --> pdb=" O TYR A1934 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N HIS A1962 " --> pdb=" O MET A1974 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE A1997 " --> pdb=" O THR A2009 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR A2009 " --> pdb=" O ILE A1997 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP A1999 " --> pdb=" O LEU A2007 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LEU A2007 " --> pdb=" O TYR A2020 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER A2029 " --> pdb=" O PHE A2040 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LYS A2050 " --> pdb=" O TYR A2065 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N SER A2060 " --> pdb=" O PHE A2079 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE A2079 " --> pdb=" O SER A2060 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR A2062 " --> pdb=" O TYR A2077 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR A2077 " --> pdb=" O THR A2062 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG A2064 " --> pdb=" O GLN A2075 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN A2075 " --> pdb=" O ARG A2064 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG A2066 " --> pdb=" O ASP A2073 " (cutoff:3.500A) removed outlier: 11.744A pdb=" N LEU A2071 " --> pdb=" O TYR A2093 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N TYR A2093 " --> pdb=" O LEU A2071 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ASP A2073 " --> pdb=" O TYR A2091 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG A2088 " --> pdb=" O PRO A2105 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP A2090 " --> pdb=" O ILE A2103 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE A2103 " --> pdb=" O ASP A2090 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR A2092 " --> pdb=" O ALA A2101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1583 through 1587 removed outlier: 5.769A pdb=" N GLN A1603 " --> pdb=" O PHE A1617 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N SER A1607 " --> pdb=" O TYR A1613 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TYR A1613 " --> pdb=" O SER A1607 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU A1614 " --> pdb=" O ASP A1630 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP A1630 " --> pdb=" O LEU A1614 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN A1616 " --> pdb=" O LEU A1628 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU A1628 " --> pdb=" O ASN A1616 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR A1618 " --> pdb=" O THR A1626 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR A1626 " --> pdb=" O ILE A1638 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG A1647 " --> pdb=" O LEU A1659 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS A1668 " --> pdb=" O MET A1680 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASP A1683 " --> pdb=" O LEU A1689 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU A1689 " --> pdb=" O ASP A1683 " (cutoff:3.500A) removed outlier: 10.228A pdb=" N LEU A1688 " --> pdb=" O TYR A1704 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N TYR A1704 " --> pdb=" O LEU A1688 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ALA A1690 " --> pdb=" O TYR A1702 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N PHE A1701 " --> pdb=" O VAL A1713 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL A1713 " --> pdb=" O PHE A1701 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP A1703 " --> pdb=" O THR A1711 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR A1711 " --> pdb=" O LEU A1723 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A1805 " --> pdb=" O HIS A1789 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU A1791 " --> pdb=" O ILE A1803 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE A1803 " --> pdb=" O GLU A1791 " (cutoff:3.500A) removed outlier: 11.258A pdb=" N THR A1802 " --> pdb=" O LEU A1823 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N LEU A1823 " --> pdb=" O THR A1802 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLY A1804 " --> pdb=" O TRP A1821 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A1834 " --> pdb=" O GLU A1826 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE A1828 " --> pdb=" O VAL A1832 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL A1832 " --> pdb=" O ILE A1828 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A1847 " --> pdb=" O LEU A1839 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A1841 " --> pdb=" O ASN A1845 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ASN A1845 " --> pdb=" O VAL A1841 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N PHE A1880 " --> pdb=" O VAL A1893 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASN A1892 " --> pdb=" O LEU A1904 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU A1904 " --> pdb=" O ASN A1892 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N SER A1894 " --> pdb=" O ALA A1902 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ALA A1902 " --> pdb=" O THR A1913 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER A1910 " --> pdb=" O PHE A1926 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N PHE A1926 " --> pdb=" O SER A1910 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG A1912 " --> pdb=" O ARG A1924 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG A1924 " --> pdb=" O ARG A1912 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASP A1914 " --> pdb=" O VAL A1922 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL A1922 " --> pdb=" O TYR A1934 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N HIS A1962 " --> pdb=" O MET A1974 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE A1997 " --> pdb=" O THR A2009 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR A2009 " --> pdb=" O ILE A1997 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP A1999 " --> pdb=" O LEU A2007 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LEU A2007 " --> pdb=" O TYR A2020 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER A2029 " --> pdb=" O PHE A2040 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LYS A2050 " --> pdb=" O TYR A2065 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N SER A2060 " --> pdb=" O PHE A2079 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE A2079 " --> pdb=" O SER A2060 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR A2062 " --> pdb=" O TYR A2077 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR A2077 " --> pdb=" O THR A2062 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG A2064 " --> pdb=" O GLN A2075 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN A2075 " --> pdb=" O ARG A2064 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG A2066 " --> pdb=" O ASP A2073 " (cutoff:3.500A) removed outlier: 11.744A pdb=" N LEU A2071 " --> pdb=" O TYR A2093 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N TYR A2093 " --> pdb=" O LEU A2071 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ASP A2073 " --> pdb=" O TYR A2091 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG A2088 " --> pdb=" O PRO A2105 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP A2090 " --> pdb=" O ILE A2103 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE A2103 " --> pdb=" O ASP A2090 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR A2092 " --> pdb=" O ALA A2101 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ALA A2101 " --> pdb=" O TYR A2117 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU A2116 " --> pdb=" O PHE A2129 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE A2129 " --> pdb=" O LEU A2116 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG A2118 " --> pdb=" O GLU A2127 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU A2127 " --> pdb=" O VAL A2134 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LYS A2161 " --> pdb=" O VAL A2177 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N MET A2167 " --> pdb=" O LEU A2171 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU A2171 " --> pdb=" O MET A2167 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE A2186 " --> pdb=" O TYR A2203 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL A2216 " --> pdb=" O PRO A2220 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2225 through 2226 removed outlier: 6.491A pdb=" N SER A2225 " --> pdb=" O HIS A2233 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N HIS A2233 " --> pdb=" O LEU A2246 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU A2257 " --> pdb=" O PRO A2245 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG A2247 " --> pdb=" O THR A2255 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR A2255 " --> pdb=" O TYR A2262 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N CYS A2271 " --> pdb=" O PHE A2278 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N THR A2287 " --> pdb=" O TYR A2300 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N SER A2297 " --> pdb=" O THR A2313 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR A2313 " --> pdb=" O SER A2297 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLN A2299 " --> pdb=" O TYR A2311 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR A2311 " --> pdb=" O GLN A2299 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG A2301 " --> pdb=" O ALA A2309 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ALA A2309 " --> pdb=" O TYR A2321 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE A2355 " --> pdb=" O VAL A2367 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TYR A2366 " --> pdb=" O VAL A2378 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL A2378 " --> pdb=" O TYR A2366 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA A2368 " --> pdb=" O LEU A2376 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU A2376 " --> pdb=" O LEU A2389 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLN A2388 " --> pdb=" O ASP A2400 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASP A2400 " --> pdb=" O GLN A2388 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLN A2390 " --> pdb=" O TYR A2398 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2415 through 2417 removed outlier: 3.718A pdb=" N LEU A2422 " --> pdb=" O ASP A2417 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2572 through 2577 removed outlier: 3.616A pdb=" N ALA A2603 " --> pdb=" O VAL A2581 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2572 through 2577 removed outlier: 3.616A pdb=" N ALA A2603 " --> pdb=" O VAL A2581 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR A2666 " --> pdb=" O TYR A2681 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2655 through 2658 Processing sheet with id=AB9, first strand: chain 'A' and resid 2742 through 2746 Processing sheet with id=AC1, first strand: chain 'B' and resid 1030 through 1033 Processing sheet with id=AC2, first strand: chain 'B' and resid 1049 through 1050 Processing sheet with id=AC3, first strand: chain 'B' and resid 1108 through 1114 Processing sheet with id=AC4, first strand: chain 'B' and resid 1186 through 1188 Processing sheet with id=AC5, first strand: chain 'B' and resid 1210 through 1216 removed outlier: 6.705A pdb=" N ILE B1567 " --> pdb=" O ILE B1214 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP B1561 " --> pdb=" O ARG B1566 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TYR B1558 " --> pdb=" O LEU B1549 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU B1549 " --> pdb=" O TYR B1558 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA B1560 " --> pdb=" O SER B1547 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1230 through 1231 removed outlier: 6.808A pdb=" N ILE B1259 " --> pdb=" O ILE B1271 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1289 through 1293 removed outlier: 5.244A pdb=" N LEU B1300 " --> pdb=" O VAL B1313 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG B1309 " --> pdb=" O ASP B1304 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE B1310 " --> pdb=" O VAL B1329 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1358 through 1363 removed outlier: 4.242A pdb=" N VAL B1372 " --> pdb=" O ARG B1359 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE B1361 " --> pdb=" O TYR B1370 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR B1370 " --> pdb=" O ILE B1361 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE B1377 " --> pdb=" O LEU B1389 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1407 through 1408 removed outlier: 6.578A pdb=" N ILE B1437 " --> pdb=" O ILE B1449 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP B1419 " --> pdb=" O LEU B1432 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1477 through 1482 removed outlier: 6.749A pdb=" N THR B1491 " --> pdb=" O SER B1478 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE B1480 " --> pdb=" O TYR B1489 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR B1489 " --> pdb=" O ILE B1480 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLN B1503 " --> pdb=" O LEU B1512 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU B1512 " --> pdb=" O GLN B1503 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1583 through 1587 removed outlier: 8.066A pdb=" N GLN B1603 " --> pdb=" O ASN B1616 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASN B1616 " --> pdb=" O GLN B1603 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR B1605 " --> pdb=" O LEU B1614 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU B1614 " --> pdb=" O ASP B1630 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASP B1630 " --> pdb=" O LEU B1614 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN B1616 " --> pdb=" O LEU B1628 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU B1628 " --> pdb=" O ASN B1616 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B1618 " --> pdb=" O THR B1626 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR B1626 " --> pdb=" O ILE B1638 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ARG B1647 " --> pdb=" O LEU B1659 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LYS B1668 " --> pdb=" O MET B1680 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP B1683 " --> pdb=" O LEU B1689 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU B1689 " --> pdb=" O ASP B1683 " (cutoff:3.500A) removed outlier: 10.272A pdb=" N LEU B1688 " --> pdb=" O TYR B1704 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N TYR B1704 " --> pdb=" O LEU B1688 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA B1690 " --> pdb=" O TYR B1702 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN B1712 " --> pdb=" O ASP B1703 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR B1711 " --> pdb=" O LEU B1723 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA B1785 " --> pdb=" O ILE B1808 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE B1808 " --> pdb=" O ALA B1785 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER B1787 " --> pdb=" O CYS B1806 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N CYS B1806 " --> pdb=" O SER B1787 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N HIS B1789 " --> pdb=" O GLY B1804 " (cutoff:3.500A) removed outlier: 11.014A pdb=" N THR B1802 " --> pdb=" O LEU B1823 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N LEU B1823 " --> pdb=" O THR B1802 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY B1804 " --> pdb=" O TRP B1821 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N SER B1818 " --> pdb=" O VAL B1841 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL B1841 " --> pdb=" O SER B1818 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU B1820 " --> pdb=" O LEU B1839 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU B1839 " --> pdb=" O GLU B1820 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ARG B1822 " --> pdb=" O ARG B1837 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ARG B1837 " --> pdb=" O ARG B1822 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ARG B1824 " --> pdb=" O PHE B1835 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE B1835 " --> pdb=" O ARG B1824 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLU B1826 " --> pdb=" O THR B1833 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL B1841 " --> pdb=" O ASN B1845 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASN B1845 " --> pdb=" O VAL B1841 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N PHE B1880 " --> pdb=" O VAL B1893 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASN B1892 " --> pdb=" O LEU B1904 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU B1904 " --> pdb=" O ASN B1892 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER B1894 " --> pdb=" O ALA B1902 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA B1902 " --> pdb=" O THR B1913 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER B1910 " --> pdb=" O PHE B1926 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHE B1926 " --> pdb=" O SER B1910 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG B1912 " --> pdb=" O ARG B1924 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG B1924 " --> pdb=" O ARG B1912 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP B1914 " --> pdb=" O VAL B1922 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N VAL B1922 " --> pdb=" O TYR B1934 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N HIS B1962 " --> pdb=" O MET B1974 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE B1997 " --> pdb=" O THR B2009 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR B2009 " --> pdb=" O ILE B1997 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP B1999 " --> pdb=" O LEU B2007 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU B2007 " --> pdb=" O TYR B2020 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N SER B2029 " --> pdb=" O PHE B2040 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LYS B2050 " --> pdb=" O TYR B2065 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL B2068 " --> pdb=" O VAL B2072 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL B2072 " --> pdb=" O VAL B2068 " (cutoff:3.500A) removed outlier: 11.740A pdb=" N LEU B2071 " --> pdb=" O TYR B2093 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N TYR B2093 " --> pdb=" O LEU B2071 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ASP B2073 " --> pdb=" O TYR B2091 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARG B2088 " --> pdb=" O PRO B2105 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASP B2090 " --> pdb=" O ILE B2103 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE B2103 " --> pdb=" O ASP B2090 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR B2092 " --> pdb=" O ALA B2101 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1583 through 1587 removed outlier: 8.066A pdb=" N GLN B1603 " --> pdb=" O ASN B1616 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASN B1616 " --> pdb=" O GLN B1603 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR B1605 " --> pdb=" O LEU B1614 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU B1614 " --> pdb=" O ASP B1630 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASP B1630 " --> pdb=" O LEU B1614 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN B1616 " --> pdb=" O LEU B1628 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU B1628 " --> pdb=" O ASN B1616 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B1618 " --> pdb=" O THR B1626 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR B1626 " --> pdb=" O ILE B1638 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ARG B1647 " --> pdb=" O LEU B1659 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LYS B1668 " --> pdb=" O MET B1680 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP B1683 " --> pdb=" O LEU B1689 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU B1689 " --> pdb=" O ASP B1683 " (cutoff:3.500A) removed outlier: 10.272A pdb=" N LEU B1688 " --> pdb=" O TYR B1704 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N TYR B1704 " --> pdb=" O LEU B1688 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA B1690 " --> pdb=" O TYR B1702 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN B1712 " --> pdb=" O ASP B1703 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR B1711 " --> pdb=" O LEU B1723 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA B1785 " --> pdb=" O ILE B1808 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE B1808 " --> pdb=" O ALA B1785 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER B1787 " --> pdb=" O CYS B1806 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N CYS B1806 " --> pdb=" O SER B1787 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N HIS B1789 " --> pdb=" O GLY B1804 " (cutoff:3.500A) removed outlier: 11.014A pdb=" N THR B1802 " --> pdb=" O LEU B1823 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N LEU B1823 " --> pdb=" O THR B1802 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY B1804 " --> pdb=" O TRP B1821 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N SER B1818 " --> pdb=" O VAL B1841 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL B1841 " --> pdb=" O SER B1818 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU B1820 " --> pdb=" O LEU B1839 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU B1839 " --> pdb=" O GLU B1820 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ARG B1822 " --> pdb=" O ARG B1837 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ARG B1837 " --> pdb=" O ARG B1822 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ARG B1824 " --> pdb=" O PHE B1835 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE B1835 " --> pdb=" O ARG B1824 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLU B1826 " --> pdb=" O THR B1833 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL B1841 " --> pdb=" O ASN B1845 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASN B1845 " --> pdb=" O VAL B1841 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N PHE B1880 " --> pdb=" O VAL B1893 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASN B1892 " --> pdb=" O LEU B1904 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU B1904 " --> pdb=" O ASN B1892 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER B1894 " --> pdb=" O ALA B1902 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA B1902 " --> pdb=" O THR B1913 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER B1910 " --> pdb=" O PHE B1926 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHE B1926 " --> pdb=" O SER B1910 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG B1912 " --> pdb=" O ARG B1924 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG B1924 " --> pdb=" O ARG B1912 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP B1914 " --> pdb=" O VAL B1922 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N VAL B1922 " --> pdb=" O TYR B1934 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N HIS B1962 " --> pdb=" O MET B1974 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE B1997 " --> pdb=" O THR B2009 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR B2009 " --> pdb=" O ILE B1997 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP B1999 " --> pdb=" O LEU B2007 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU B2007 " --> pdb=" O TYR B2020 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N SER B2029 " --> pdb=" O PHE B2040 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LYS B2050 " --> pdb=" O TYR B2065 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL B2068 " --> pdb=" O VAL B2072 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL B2072 " --> pdb=" O VAL B2068 " (cutoff:3.500A) removed outlier: 11.740A pdb=" N LEU B2071 " --> pdb=" O TYR B2093 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N TYR B2093 " --> pdb=" O LEU B2071 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ASP B2073 " --> pdb=" O TYR B2091 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARG B2088 " --> pdb=" O PRO B2105 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASP B2090 " --> pdb=" O ILE B2103 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE B2103 " --> pdb=" O ASP B2090 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR B2092 " --> pdb=" O ALA B2101 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA B2101 " --> pdb=" O TYR B2117 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU B2116 " --> pdb=" O PHE B2129 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE B2129 " --> pdb=" O LEU B2116 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG B2118 " --> pdb=" O GLU B2127 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLU B2127 " --> pdb=" O VAL B2134 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYS B2161 " --> pdb=" O VAL B2177 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N MET B2167 " --> pdb=" O LEU B2171 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU B2171 " --> pdb=" O MET B2167 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE B2186 " --> pdb=" O TYR B2203 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL B2216 " --> pdb=" O PRO B2220 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 2225 through 2226 removed outlier: 5.384A pdb=" N HIS B2233 " --> pdb=" O LEU B2246 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU B2257 " --> pdb=" O PRO B2245 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG B2247 " --> pdb=" O THR B2255 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR B2255 " --> pdb=" O TYR B2262 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLN B2261 " --> pdb=" O ARG B2273 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG B2273 " --> pdb=" O GLN B2261 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS B2263 " --> pdb=" O CYS B2271 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N CYS B2271 " --> pdb=" O PHE B2278 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N SER B2297 " --> pdb=" O THR B2313 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR B2313 " --> pdb=" O SER B2297 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLN B2299 " --> pdb=" O TYR B2311 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TYR B2311 " --> pdb=" O GLN B2299 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG B2301 " --> pdb=" O ALA B2309 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ALA B2309 " --> pdb=" O TYR B2321 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE B2355 " --> pdb=" O VAL B2367 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TYR B2366 " --> pdb=" O VAL B2378 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL B2378 " --> pdb=" O TYR B2366 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA B2368 " --> pdb=" O LEU B2376 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LEU B2376 " --> pdb=" O LEU B2389 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLN B2388 " --> pdb=" O ASP B2400 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP B2400 " --> pdb=" O GLN B2388 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN B2390 " --> pdb=" O TYR B2398 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 2415 through 2417 removed outlier: 3.731A pdb=" N LEU B2422 " --> pdb=" O ASP B2417 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 2572 through 2577 removed outlier: 3.734A pdb=" N ALA B2603 " --> pdb=" O VAL B2581 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 2572 through 2577 removed outlier: 3.734A pdb=" N ALA B2603 " --> pdb=" O VAL B2581 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR B2666 " --> pdb=" O TYR B2681 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY B2639 " --> pdb=" O VAL B2651 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 2655 through 2658 Processing sheet with id=AD9, first strand: chain 'B' and resid 2742 through 2746 1459 hydrogen bonds defined for protein. 3858 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: 12.26 Time building geometry restraints manager: 3.03 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: 9134 1.34 - 1.46: 6745 1.46 - 1.58: 12685 1.58 - 1.70: 0 1.70 - 1.83: 186 Bond restraints: 28750 Sorted by residual: bond pdb=" C2 MAN D 4 " pdb=" O2 MAN D 4 " ideal model delta sigma weight residual 1.407 1.470 -0.063 2.00e-02 2.50e+03 9.88e+00 bond pdb=" C3 BMA D 3 " pdb=" O3 BMA D 3 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.64e+00 bond pdb=" C1 NAG A2803 " pdb=" O5 NAG A2803 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.76e+00 bond pdb=" C1 NAG A2802 " pdb=" O5 NAG A2802 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.72e+00 bond pdb=" C1 MAN D 4 " pdb=" C2 MAN D 4 " ideal model delta sigma weight residual 1.526 1.575 -0.049 2.00e-02 2.50e+03 6.11e+00 ... (remaining 28745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 37766 1.92 - 3.84: 1065 3.84 - 5.76: 132 5.76 - 7.68: 28 7.68 - 9.60: 7 Bond angle restraints: 38998 Sorted by residual: angle pdb=" CA CYS B1225 " pdb=" CB CYS B1225 " pdb=" SG CYS B1225 " ideal model delta sigma weight residual 114.40 124.00 -9.60 2.30e+00 1.89e-01 1.74e+01 angle pdb=" CA CYS A1225 " pdb=" CB CYS A1225 " pdb=" SG CYS A1225 " ideal model delta sigma weight residual 114.40 123.88 -9.48 2.30e+00 1.89e-01 1.70e+01 angle pdb=" C PRO B1990 " pdb=" N GLU B1991 " pdb=" CA GLU B1991 " ideal model delta sigma weight residual 122.82 127.94 -5.12 1.42e+00 4.96e-01 1.30e+01 angle pdb=" CA ASN B1712 " pdb=" CB ASN B1712 " pdb=" CG ASN B1712 " ideal model delta sigma weight residual 112.60 116.03 -3.43 1.00e+00 1.00e+00 1.18e+01 angle pdb=" C ASP A1494 " pdb=" N GLU A1495 " pdb=" CA GLU A1495 " ideal model delta sigma weight residual 121.54 127.92 -6.38 1.91e+00 2.74e-01 1.12e+01 ... (remaining 38993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.13: 16179 23.13 - 46.26: 1137 46.26 - 69.38: 237 69.38 - 92.51: 58 92.51 - 115.64: 33 Dihedral angle restraints: 17644 sinusoidal: 7474 harmonic: 10170 Sorted by residual: dihedral pdb=" CD ARG B1343 " pdb=" NE ARG B1343 " pdb=" CZ ARG B1343 " pdb=" NH1 ARG B1343 " ideal model delta sinusoidal sigma weight residual 0.00 -70.46 70.46 1 1.00e+01 1.00e-02 6.39e+01 dihedral pdb=" CD ARG A1343 " pdb=" NE ARG A1343 " pdb=" CZ ARG A1343 " pdb=" NH1 ARG A1343 " ideal model delta sinusoidal sigma weight residual 0.00 -70.35 70.35 1 1.00e+01 1.00e-02 6.37e+01 dihedral pdb=" CB CYS B1225 " pdb=" SG CYS B1225 " pdb=" SG CYS B1228 " pdb=" CB CYS B1228 " ideal model delta sinusoidal sigma weight residual -86.00 -137.74 51.74 1 1.00e+01 1.00e-02 3.66e+01 ... (remaining 17641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.198: 4417 0.198 - 0.397: 15 0.397 - 0.595: 1 0.595 - 0.793: 0 0.793 - 0.991: 1 Chirality restraints: 4434 Sorted by residual: chirality pdb=" C1 NAG A2802 " pdb=" ND2 ASN A1712 " pdb=" C2 NAG A2802 " pdb=" O5 NAG A2802 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" C1 NAG B2802 " pdb=" ND2 ASN B1712 " pdb=" C2 NAG B2802 " pdb=" O5 NAG B2802 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.75e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B1773 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 4431 not shown) Planarity restraints: 5010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B1343 " -0.870 9.50e-02 1.11e+02 3.91e-01 1.05e+02 pdb=" NE ARG B1343 " 0.075 2.00e-02 2.50e+03 pdb=" CZ ARG B1343 " -0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG B1343 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG B1343 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1343 " 0.869 9.50e-02 1.11e+02 3.91e-01 1.05e+02 pdb=" NE ARG A1343 " -0.075 2.00e-02 2.50e+03 pdb=" CZ ARG A1343 " 0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG A1343 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A1343 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B2499 " 0.486 9.50e-02 1.11e+02 2.19e-01 3.67e+01 pdb=" NE ARG B2499 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG B2499 " 0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG B2499 " -0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG B2499 " 0.001 2.00e-02 2.50e+03 ... (remaining 5007 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5722 2.79 - 3.32: 22832 3.32 - 3.84: 46860 3.84 - 4.37: 55358 4.37 - 4.90: 98041 Nonbonded interactions: 228813 Sorted by model distance: nonbonded pdb=" O ASP B1255 " pdb=" OH TYR B1289 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR B2014 " pdb=" OD2 ASP B2267 " model vdw 2.285 3.040 nonbonded pdb=" OG1 THR A2014 " pdb=" OD2 ASP A2267 " model vdw 2.289 3.040 nonbonded pdb=" O ASP A1255 " pdb=" OH TYR A1289 " model vdw 2.294 3.040 nonbonded pdb=" O SER A1947 " pdb=" OG SER A1947 " model vdw 2.299 3.040 ... (remaining 228808 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 32.570 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 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 0.082 28798 Z= 0.204 Angle : 0.766 22.125 39130 Z= 0.396 Chirality : 0.057 0.991 4434 Planarity : 0.012 0.391 4994 Dihedral : 17.269 115.639 11136 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.45 % Allowed : 18.21 % Favored : 80.34 % 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: -0.54 (0.14), residues: 3500 helix: -1.35 (0.30), residues: 224 sheet: 0.33 (0.14), residues: 1348 loop : -0.71 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.061 0.002 ARG A1343 TYR 0.027 0.002 TYR A1258 PHE 0.027 0.002 PHE B1788 TRP 0.025 0.002 TRP A2560 HIS 0.017 0.002 HIS A1962 Details of bonding type rmsd covalent geometry : bond 0.00442 (28750) covalent geometry : angle 0.73436 (38998) SS BOND : bond 0.00275 ( 12) SS BOND : angle 1.69609 ( 24) hydrogen bonds : bond 0.19908 ( 1065) hydrogen bonds : angle 7.75280 ( 3858) link_ALPHA1-2 : bond 0.01572 ( 2) link_ALPHA1-2 : angle 1.75980 ( 6) link_ALPHA1-3 : bond 0.00744 ( 4) link_ALPHA1-3 : angle 1.76715 ( 12) link_BETA1-4 : bond 0.00919 ( 14) link_BETA1-4 : angle 2.46176 ( 42) link_NAG-ASN : bond 0.00639 ( 16) link_NAG-ASN : angle 5.64663 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 776 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1043 SER cc_start: 0.8468 (t) cc_final: 0.8141 (p) REVERT: A 1105 VAL cc_start: 0.8681 (t) cc_final: 0.8356 (p) REVERT: A 1122 TYR cc_start: 0.8168 (t80) cc_final: 0.7951 (t80) REVERT: A 1210 ILE cc_start: 0.8629 (pt) cc_final: 0.8426 (mp) REVERT: A 1340 ASP cc_start: 0.3965 (OUTLIER) cc_final: 0.3631 (m-30) REVERT: A 1376 MET cc_start: 0.6939 (mtm) cc_final: 0.6691 (mtm) REVERT: A 1379 LYS cc_start: 0.8088 (pttt) cc_final: 0.7372 (ptpp) REVERT: A 1554 ASP cc_start: 0.7284 (p0) cc_final: 0.7072 (p0) REVERT: A 1676 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7170 (mm-30) REVERT: A 1742 ASP cc_start: 0.7849 (p0) cc_final: 0.7582 (p0) REVERT: A 1748 THR cc_start: 0.8567 (m) cc_final: 0.8192 (p) REVERT: A 1875 GLN cc_start: 0.7824 (pm20) cc_final: 0.7513 (pm20) REVERT: A 1917 LYS cc_start: 0.8313 (mmtm) cc_final: 0.8045 (mmtm) REVERT: A 1941 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8282 (ttp) REVERT: A 1969 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8186 (t) REVERT: A 1991 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7673 (mt-10) REVERT: A 2080 SER cc_start: 0.8630 (m) cc_final: 0.8383 (t) REVERT: A 2175 MET cc_start: 0.8681 (ttp) cc_final: 0.8452 (ttt) REVERT: A 2243 LEU cc_start: 0.8587 (mt) cc_final: 0.8369 (mm) REVERT: A 2260 VAL cc_start: 0.8751 (p) cc_final: 0.8532 (m) REVERT: A 2471 ASP cc_start: 0.7865 (t0) cc_final: 0.7533 (t0) REVERT: A 2531 GLU cc_start: 0.8019 (tp30) cc_final: 0.7717 (tp30) REVERT: A 2543 GLN cc_start: 0.8549 (tt0) cc_final: 0.8339 (tt0) REVERT: A 2553 ILE cc_start: 0.8486 (mm) cc_final: 0.8158 (tt) REVERT: A 2573 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8013 (tmm) REVERT: A 2595 LYS cc_start: 0.8664 (mttt) cc_final: 0.8453 (mttt) REVERT: A 2681 TYR cc_start: 0.8663 (m-80) cc_final: 0.8434 (m-80) REVERT: A 2732 GLN cc_start: 0.7921 (mt0) cc_final: 0.7689 (tt0) REVERT: A 2760 SER cc_start: 0.8743 (m) cc_final: 0.8541 (p) REVERT: B 1043 SER cc_start: 0.8524 (t) cc_final: 0.8320 (p) REVERT: B 1105 VAL cc_start: 0.8619 (t) cc_final: 0.8244 (p) REVERT: B 1118 PRO cc_start: 0.8063 (Cg_endo) cc_final: 0.7861 (Cg_exo) REVERT: B 1210 ILE cc_start: 0.8539 (pt) cc_final: 0.8103 (mm) REVERT: B 1217 ASN cc_start: 0.7067 (p0) cc_final: 0.6478 (p0) REVERT: B 1340 ASP cc_start: 0.4508 (OUTLIER) cc_final: 0.4218 (m-30) REVERT: B 1376 MET cc_start: 0.6779 (mtm) cc_final: 0.6503 (mtm) REVERT: B 1379 LYS cc_start: 0.7966 (pttt) cc_final: 0.7308 (ptpp) REVERT: B 1595 VAL cc_start: 0.9160 (t) cc_final: 0.8630 (m) REVERT: B 1742 ASP cc_start: 0.7747 (p0) cc_final: 0.7473 (p0) REVERT: B 1875 GLN cc_start: 0.7918 (pm20) cc_final: 0.7642 (pm20) REVERT: B 1914 ASP cc_start: 0.8035 (m-30) cc_final: 0.7834 (m-30) REVERT: B 1931 VAL cc_start: 0.9243 (OUTLIER) cc_final: 0.8988 (t) REVERT: B 1941 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8398 (ttp) REVERT: B 1969 VAL cc_start: 0.8265 (OUTLIER) cc_final: 0.8020 (t) REVERT: B 1982 TYR cc_start: 0.8550 (p90) cc_final: 0.8156 (p90) REVERT: B 2044 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7652 (mm-30) REVERT: B 2080 SER cc_start: 0.8625 (m) cc_final: 0.8424 (t) REVERT: B 2104 LYS cc_start: 0.8660 (tptm) cc_final: 0.8437 (tptm) REVERT: B 2243 LEU cc_start: 0.8557 (mt) cc_final: 0.8324 (mm) REVERT: B 2288 ARG cc_start: 0.8458 (mtp180) cc_final: 0.8171 (ttt180) REVERT: B 2347 TYR cc_start: 0.8808 (m-80) cc_final: 0.8606 (m-80) REVERT: B 2364 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7220 (mt-10) REVERT: B 2471 ASP cc_start: 0.7900 (t0) cc_final: 0.7568 (t0) REVERT: B 2553 ILE cc_start: 0.8551 (mm) cc_final: 0.8284 (tt) REVERT: B 2573 MET cc_start: 0.8592 (tmt) cc_final: 0.8135 (tmm) REVERT: B 2595 LYS cc_start: 0.8690 (mttt) cc_final: 0.8459 (mttp) REVERT: B 2681 TYR cc_start: 0.8627 (m-80) cc_final: 0.8386 (m-80) REVERT: B 2719 ARG cc_start: 0.7468 (mtt180) cc_final: 0.7256 (mtt-85) REVERT: B 2720 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7336 (mt-10) outliers start: 44 outliers final: 19 residues processed: 806 average time/residue: 0.6581 time to fit residues: 611.6565 Evaluate side-chains 657 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 630 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1340 ASP Chi-restraints excluded: chain A residue 1343 ARG Chi-restraints excluded: chain A residue 1457 GLN Chi-restraints excluded: chain A residue 1604 TYR Chi-restraints excluded: chain A residue 1749 ASN Chi-restraints excluded: chain A residue 1941 MET Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 2573 MET Chi-restraints excluded: chain A residue 2655 THR Chi-restraints excluded: chain A residue 2657 LEU Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain B residue 1337 LEU Chi-restraints excluded: chain B residue 1340 ASP Chi-restraints excluded: chain B residue 1341 GLU Chi-restraints excluded: chain B residue 1343 ARG Chi-restraints excluded: chain B residue 1457 GLN Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1749 ASN Chi-restraints excluded: chain B residue 1931 VAL Chi-restraints excluded: chain B residue 1941 MET Chi-restraints excluded: chain B residue 1969 VAL Chi-restraints excluded: chain B residue 2128 HIS Chi-restraints excluded: chain B residue 2588 ILE Chi-restraints excluded: chain B residue 2655 THR Chi-restraints excluded: chain B residue 2657 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1573 ASN A1673 GLN A1749 ASN A1814 ASN A1946 GLN A1962 HIS A2153 HIS A2447 ASN A2489 GLN A2527 GLN A2534 ASN A2550 HIS A2559 HIS A2712 GLN A2752 GLN B1188 ASN B1484 HIS B1573 ASN B1591 GLN B1749 ASN B1946 GLN B1962 HIS B2053 ASN B2096 ASN B2447 ASN B2464 ASN B2527 GLN B2534 ASN B2550 HIS B2712 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.128876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.101847 restraints weight = 40510.242| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.14 r_work: 0.3208 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 28798 Z= 0.215 Angle : 0.628 15.070 39130 Z= 0.323 Chirality : 0.049 0.570 4434 Planarity : 0.004 0.046 4994 Dihedral : 10.180 104.776 4696 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.52 % Allowed : 21.07 % Favored : 75.41 % 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: -0.04 (0.14), residues: 3500 helix: 0.31 (0.34), residues: 226 sheet: 0.52 (0.14), residues: 1338 loop : -0.41 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B1912 TYR 0.018 0.002 TYR A2262 PHE 0.019 0.002 PHE A1110 TRP 0.020 0.001 TRP A2560 HIS 0.008 0.001 HIS A1484 Details of bonding type rmsd covalent geometry : bond 0.00492 (28750) covalent geometry : angle 0.60554 (38998) SS BOND : bond 0.00324 ( 12) SS BOND : angle 1.64753 ( 24) hydrogen bonds : bond 0.04275 ( 1065) hydrogen bonds : angle 5.37225 ( 3858) link_ALPHA1-2 : bond 0.01682 ( 2) link_ALPHA1-2 : angle 1.51553 ( 6) link_ALPHA1-3 : bond 0.01218 ( 4) link_ALPHA1-3 : angle 2.41929 ( 12) link_BETA1-4 : bond 0.00471 ( 14) link_BETA1-4 : angle 2.03687 ( 42) link_NAG-ASN : bond 0.00473 ( 16) link_NAG-ASN : angle 4.11219 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 640 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1105 VAL cc_start: 0.8626 (t) cc_final: 0.8384 (p) REVERT: A 1122 TYR cc_start: 0.8283 (t80) cc_final: 0.8037 (t80) REVERT: A 1210 ILE cc_start: 0.8599 (pt) cc_final: 0.8388 (mp) REVERT: A 1215 MET cc_start: 0.7688 (tpp) cc_final: 0.7235 (tpp) REVERT: A 1340 ASP cc_start: 0.4037 (OUTLIER) cc_final: 0.3796 (m-30) REVERT: A 1356 MET cc_start: 0.5106 (mtp) cc_final: 0.4865 (mtp) REVERT: A 1376 MET cc_start: 0.7082 (mtm) cc_final: 0.6724 (mtm) REVERT: A 1467 LYS cc_start: 0.7707 (mmpt) cc_final: 0.7316 (mmmm) REVERT: A 1488 LEU cc_start: 0.8635 (tp) cc_final: 0.8380 (tt) REVERT: A 1542 ILE cc_start: 0.8390 (mt) cc_final: 0.8116 (mp) REVERT: A 1671 SER cc_start: 0.8779 (p) cc_final: 0.8398 (m) REVERT: A 1676 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7174 (mm-30) REVERT: A 1680 MET cc_start: 0.8801 (mpp) cc_final: 0.8425 (mtm) REVERT: A 1742 ASP cc_start: 0.8037 (p0) cc_final: 0.7733 (p0) REVERT: A 1791 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: A 1844 ARG cc_start: 0.8194 (ptp-170) cc_final: 0.7863 (ttp80) REVERT: A 1875 GLN cc_start: 0.8046 (pm20) cc_final: 0.7766 (pm20) REVERT: A 1917 LYS cc_start: 0.8445 (mmtm) cc_final: 0.8192 (mmtm) REVERT: A 1969 VAL cc_start: 0.8610 (t) cc_final: 0.8341 (t) REVERT: A 2074 LYS cc_start: 0.8921 (ttmt) cc_final: 0.8717 (ttmt) REVERT: A 2080 SER cc_start: 0.8744 (m) cc_final: 0.8476 (t) REVERT: A 2175 MET cc_start: 0.8817 (ttp) cc_final: 0.8581 (ttt) REVERT: A 2227 ASP cc_start: 0.7740 (t0) cc_final: 0.7521 (t0) REVERT: A 2243 LEU cc_start: 0.8664 (mt) cc_final: 0.8414 (mm) REVERT: A 2260 VAL cc_start: 0.8799 (p) cc_final: 0.8563 (m) REVERT: A 2272 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8285 (tt0) REVERT: A 2471 ASP cc_start: 0.7902 (t0) cc_final: 0.7551 (t0) REVERT: A 2531 GLU cc_start: 0.8258 (tp30) cc_final: 0.7870 (tp30) REVERT: A 2553 ILE cc_start: 0.8606 (mm) cc_final: 0.8231 (tt) REVERT: A 2573 MET cc_start: 0.8618 (tmt) cc_final: 0.8133 (tmm) REVERT: A 2574 PHE cc_start: 0.8817 (t80) cc_final: 0.8506 (t80) REVERT: A 2614 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8102 (mm-30) REVERT: A 2681 TYR cc_start: 0.8667 (m-80) cc_final: 0.8464 (m-80) REVERT: A 2696 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8331 (mm) REVERT: B 1102 MET cc_start: 0.8458 (mtt) cc_final: 0.8257 (mtp) REVERT: B 1105 VAL cc_start: 0.8551 (t) cc_final: 0.8242 (p) REVERT: B 1210 ILE cc_start: 0.8548 (pt) cc_final: 0.8113 (mm) REVERT: B 1217 ASN cc_start: 0.7194 (p0) cc_final: 0.6879 (p0) REVERT: B 1236 LYS cc_start: 0.6553 (mtpp) cc_final: 0.6145 (mmmt) REVERT: B 1327 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6982 (pp20) REVERT: B 1376 MET cc_start: 0.6783 (mtm) cc_final: 0.6412 (mtm) REVERT: B 1379 LYS cc_start: 0.7871 (pttt) cc_final: 0.7173 (ptpp) REVERT: B 1500 ARG cc_start: 0.8104 (ptt-90) cc_final: 0.7834 (ptt-90) REVERT: B 1509 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7180 (pt0) REVERT: B 1542 ILE cc_start: 0.8349 (mt) cc_final: 0.8077 (mm) REVERT: B 1671 SER cc_start: 0.8802 (p) cc_final: 0.8581 (m) REVERT: B 1742 ASP cc_start: 0.7878 (p0) cc_final: 0.7499 (p0) REVERT: B 1875 GLN cc_start: 0.8157 (pm20) cc_final: 0.7905 (pm20) REVERT: B 1931 VAL cc_start: 0.9234 (OUTLIER) cc_final: 0.8988 (t) REVERT: B 2044 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8112 (mm-30) REVERT: B 2064 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8240 (mtp85) REVERT: B 2080 SER cc_start: 0.8772 (m) cc_final: 0.8509 (t) REVERT: B 2219 ARG cc_start: 0.7720 (ttp80) cc_final: 0.7513 (ttp80) REVERT: B 2242 ARG cc_start: 0.7567 (mtt180) cc_final: 0.7313 (mtm110) REVERT: B 2288 ARG cc_start: 0.8594 (mtp180) cc_final: 0.8342 (ttt180) REVERT: B 2357 MET cc_start: 0.9017 (mtm) cc_final: 0.8814 (mtp) REVERT: B 2471 ASP cc_start: 0.7930 (t0) cc_final: 0.7613 (t0) REVERT: B 2499 ARG cc_start: 0.7932 (ttm-80) cc_final: 0.7687 (ttm-80) REVERT: B 2531 GLU cc_start: 0.8348 (tp30) cc_final: 0.7946 (tp30) REVERT: B 2574 PHE cc_start: 0.8822 (t80) cc_final: 0.8456 (t80) REVERT: B 2614 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8106 (mm-30) REVERT: B 2681 TYR cc_start: 0.8653 (m-80) cc_final: 0.8420 (m-80) REVERT: B 2713 GLN cc_start: 0.8548 (tp40) cc_final: 0.8168 (mm-40) REVERT: B 2732 GLN cc_start: 0.7370 (tt0) cc_final: 0.7158 (tt0) REVERT: B 2739 VAL cc_start: 0.7072 (OUTLIER) cc_final: 0.6853 (m) REVERT: B 2765 PHE cc_start: 0.8638 (m-80) cc_final: 0.8257 (m-80) outliers start: 107 outliers final: 33 residues processed: 693 average time/residue: 0.7688 time to fit residues: 615.0693 Evaluate side-chains 649 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 608 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1340 ASP Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1511 CYS Chi-restraints excluded: chain A residue 1534 ASP Chi-restraints excluded: chain A residue 1576 VAL Chi-restraints excluded: chain A residue 1628 LEU Chi-restraints excluded: chain A residue 1663 THR Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1736 GLU Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1769 GLN Chi-restraints excluded: chain A residue 1791 GLU Chi-restraints excluded: chain A residue 1909 MET Chi-restraints excluded: chain A residue 2024 LYS Chi-restraints excluded: chain A residue 2112 LEU Chi-restraints excluded: chain A residue 2272 GLN Chi-restraints excluded: chain A residue 2448 VAL Chi-restraints excluded: chain A residue 2678 SER Chi-restraints excluded: chain A residue 2696 LEU Chi-restraints excluded: chain B residue 1030 ILE Chi-restraints excluded: chain B residue 1327 GLU Chi-restraints excluded: chain B residue 1341 GLU Chi-restraints excluded: chain B residue 1511 CYS Chi-restraints excluded: chain B residue 1730 SER Chi-restraints excluded: chain B residue 1736 GLU Chi-restraints excluded: chain B residue 1931 VAL Chi-restraints excluded: chain B residue 1935 SER Chi-restraints excluded: chain B residue 2064 ARG Chi-restraints excluded: chain B residue 2112 LEU Chi-restraints excluded: chain B residue 2114 VAL Chi-restraints excluded: chain B residue 2339 SER Chi-restraints excluded: chain B residue 2490 LEU Chi-restraints excluded: chain B residue 2559 HIS Chi-restraints excluded: chain B residue 2585 VAL Chi-restraints excluded: chain B residue 2588 ILE Chi-restraints excluded: chain B residue 2655 THR Chi-restraints excluded: chain B residue 2678 SER Chi-restraints excluded: chain B residue 2696 LEU Chi-restraints excluded: chain B residue 2724 LEU Chi-restraints excluded: chain B residue 2739 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 326 optimal weight: 0.8980 chunk 328 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 269 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1195 HIS ** A1484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1962 HIS A2550 HIS A2559 HIS A2701 GLN A2752 GLN B1962 HIS B2233 HIS B2701 GLN ** B2732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.127911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.101158 restraints weight = 40791.262| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.14 r_work: 0.3202 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28798 Z= 0.186 Angle : 0.591 15.890 39130 Z= 0.302 Chirality : 0.048 0.468 4434 Planarity : 0.004 0.049 4994 Dihedral : 8.344 105.032 4647 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.35 % Allowed : 22.19 % Favored : 74.46 % 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: 0.16 (0.14), residues: 3500 helix: 0.95 (0.35), residues: 224 sheet: 0.59 (0.14), residues: 1342 loop : -0.29 (0.15), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1912 TYR 0.018 0.002 TYR A2077 PHE 0.018 0.002 PHE A1114 TRP 0.011 0.001 TRP A2560 HIS 0.007 0.001 HIS B2233 Details of bonding type rmsd covalent geometry : bond 0.00423 (28750) covalent geometry : angle 0.56619 (38998) SS BOND : bond 0.00228 ( 12) SS BOND : angle 1.01860 ( 24) hydrogen bonds : bond 0.04132 ( 1065) hydrogen bonds : angle 5.05902 ( 3858) link_ALPHA1-2 : bond 0.01540 ( 2) link_ALPHA1-2 : angle 1.83398 ( 6) link_ALPHA1-3 : bond 0.01395 ( 4) link_ALPHA1-3 : angle 1.82288 ( 12) link_BETA1-4 : bond 0.00584 ( 14) link_BETA1-4 : angle 1.84183 ( 42) link_NAG-ASN : bond 0.00509 ( 16) link_NAG-ASN : angle 4.37230 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 620 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1105 VAL cc_start: 0.8731 (OUTLIER) cc_final: 0.8465 (p) REVERT: A 1122 TYR cc_start: 0.8350 (t80) cc_final: 0.8121 (t80) REVERT: A 1210 ILE cc_start: 0.8588 (pt) cc_final: 0.8376 (mp) REVERT: A 1215 MET cc_start: 0.7717 (tpp) cc_final: 0.7287 (tpp) REVERT: A 1340 ASP cc_start: 0.4216 (OUTLIER) cc_final: 0.3954 (m-30) REVERT: A 1356 MET cc_start: 0.5071 (mtp) cc_final: 0.4798 (mtp) REVERT: A 1376 MET cc_start: 0.7136 (mtm) cc_final: 0.6630 (mtm) REVERT: A 1454 MET cc_start: 0.6458 (pmm) cc_final: 0.6175 (pmm) REVERT: A 1467 LYS cc_start: 0.7720 (mmpt) cc_final: 0.7409 (mmmm) REVERT: A 1488 LEU cc_start: 0.8643 (tp) cc_final: 0.8366 (tt) REVERT: A 1542 ILE cc_start: 0.8447 (mt) cc_final: 0.8174 (mp) REVERT: A 1651 MET cc_start: 0.8634 (mmt) cc_final: 0.8391 (mmm) REVERT: A 1671 SER cc_start: 0.8758 (p) cc_final: 0.8401 (m) REVERT: A 1676 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7131 (mm-30) REVERT: A 1680 MET cc_start: 0.8845 (mpp) cc_final: 0.8431 (mtm) REVERT: A 1742 ASP cc_start: 0.7964 (p0) cc_final: 0.7559 (p0) REVERT: A 1875 GLN cc_start: 0.8009 (pm20) cc_final: 0.7750 (pm20) REVERT: A 1917 LYS cc_start: 0.8494 (mmtm) cc_final: 0.8257 (mmtm) REVERT: A 1969 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8458 (t) REVERT: A 2080 SER cc_start: 0.8753 (m) cc_final: 0.8464 (t) REVERT: A 2109 GLU cc_start: 0.7910 (mp0) cc_final: 0.7695 (mp0) REVERT: A 2272 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: A 2346 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8248 (mt) REVERT: A 2471 ASP cc_start: 0.7908 (t0) cc_final: 0.7589 (t0) REVERT: A 2531 GLU cc_start: 0.8218 (tp30) cc_final: 0.7866 (tp30) REVERT: A 2544 VAL cc_start: 0.8986 (p) cc_final: 0.8770 (t) REVERT: A 2553 ILE cc_start: 0.8631 (mm) cc_final: 0.8240 (tt) REVERT: A 2573 MET cc_start: 0.8607 (tmt) cc_final: 0.8154 (tmm) REVERT: A 2574 PHE cc_start: 0.8827 (t80) cc_final: 0.8481 (t80) REVERT: A 2614 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8099 (mm-30) REVERT: A 2681 TYR cc_start: 0.8662 (m-80) cc_final: 0.8441 (m-80) REVERT: A 2713 GLN cc_start: 0.8508 (tp-100) cc_final: 0.8158 (mm-40) REVERT: B 1105 VAL cc_start: 0.8609 (t) cc_final: 0.8296 (p) REVERT: B 1210 ILE cc_start: 0.8537 (pt) cc_final: 0.8127 (mm) REVERT: B 1217 ASN cc_start: 0.7140 (p0) cc_final: 0.6785 (p0) REVERT: B 1236 LYS cc_start: 0.6574 (mtpp) cc_final: 0.6237 (mmmt) REVERT: B 1327 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7080 (pp20) REVERT: B 1344 CYS cc_start: 0.7146 (m) cc_final: 0.6413 (m) REVERT: B 1376 MET cc_start: 0.6783 (mtm) cc_final: 0.6303 (mtm) REVERT: B 1509 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7239 (pt0) REVERT: B 1542 ILE cc_start: 0.8466 (mt) cc_final: 0.8189 (mp) REVERT: B 1671 SER cc_start: 0.8766 (p) cc_final: 0.8540 (m) REVERT: B 1742 ASP cc_start: 0.7862 (p0) cc_final: 0.7515 (p0) REVERT: B 1822 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8214 (mtt90) REVERT: B 1840 ARG cc_start: 0.8787 (mtp-110) cc_final: 0.8525 (mtp-110) REVERT: B 1875 GLN cc_start: 0.8166 (pm20) cc_final: 0.7896 (pm20) REVERT: B 1931 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.8990 (t) REVERT: B 1969 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8450 (t) REVERT: B 2044 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8076 (mm-30) REVERT: B 2080 SER cc_start: 0.8792 (m) cc_final: 0.8500 (t) REVERT: B 2219 ARG cc_start: 0.7699 (ttp80) cc_final: 0.7486 (ttp80) REVERT: B 2227 ASP cc_start: 0.7795 (t0) cc_final: 0.7571 (t0) REVERT: B 2242 ARG cc_start: 0.7700 (mtt180) cc_final: 0.7422 (mtm110) REVERT: B 2263 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7403 (ttpp) REVERT: B 2288 ARG cc_start: 0.8632 (mtp180) cc_final: 0.8333 (ttt180) REVERT: B 2357 MET cc_start: 0.9022 (mtm) cc_final: 0.8800 (mtp) REVERT: B 2451 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7986 (mt-10) REVERT: B 2471 ASP cc_start: 0.7950 (t0) cc_final: 0.7617 (t0) REVERT: B 2531 GLU cc_start: 0.8384 (tp30) cc_final: 0.7982 (tp30) REVERT: B 2574 PHE cc_start: 0.8784 (t80) cc_final: 0.8426 (t80) REVERT: B 2614 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8125 (mm-30) REVERT: B 2681 TYR cc_start: 0.8617 (m-80) cc_final: 0.8370 (m-80) REVERT: B 2690 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8149 (mt-10) REVERT: B 2713 GLN cc_start: 0.8544 (tp40) cc_final: 0.8231 (mm-40) REVERT: B 2719 ARG cc_start: 0.7711 (mtt-85) cc_final: 0.7450 (mtt-85) REVERT: B 2730 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7814 (ttmm) REVERT: B 2765 PHE cc_start: 0.8641 (m-80) cc_final: 0.8240 (m-80) outliers start: 102 outliers final: 52 residues processed: 666 average time/residue: 0.7557 time to fit residues: 581.1463 Evaluate side-chains 662 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 599 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1340 ASP Chi-restraints excluded: chain A residue 1511 CYS Chi-restraints excluded: chain A residue 1534 ASP Chi-restraints excluded: chain A residue 1576 VAL Chi-restraints excluded: chain A residue 1628 LEU Chi-restraints excluded: chain A residue 1663 THR Chi-restraints excluded: chain A residue 1712 ASN Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1736 GLU Chi-restraints excluded: chain A residue 1909 MET Chi-restraints excluded: chain A residue 1935 SER Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 2002 ASP Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2112 LEU Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2148 MET Chi-restraints excluded: chain A residue 2272 GLN Chi-restraints excluded: chain A residue 2346 LEU Chi-restraints excluded: chain A residue 2427 GLN Chi-restraints excluded: chain A residue 2678 SER Chi-restraints excluded: chain A residue 2724 LEU Chi-restraints excluded: chain B residue 1030 ILE Chi-restraints excluded: chain B residue 1327 GLU Chi-restraints excluded: chain B residue 1337 LEU Chi-restraints excluded: chain B residue 1341 GLU Chi-restraints excluded: chain B residue 1485 THR Chi-restraints excluded: chain B residue 1511 CYS Chi-restraints excluded: chain B residue 1534 ASP Chi-restraints excluded: chain B residue 1557 ILE Chi-restraints excluded: chain B residue 1576 VAL Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1641 ASP Chi-restraints excluded: chain B residue 1663 THR Chi-restraints excluded: chain B residue 1693 SER Chi-restraints excluded: chain B residue 1730 SER Chi-restraints excluded: chain B residue 1736 GLU Chi-restraints excluded: chain B residue 1746 VAL Chi-restraints excluded: chain B residue 1769 GLN Chi-restraints excluded: chain B residue 1822 ARG Chi-restraints excluded: chain B residue 1931 VAL Chi-restraints excluded: chain B residue 1935 SER Chi-restraints excluded: chain B residue 1969 VAL Chi-restraints excluded: chain B residue 2114 VAL Chi-restraints excluded: chain B residue 2128 HIS Chi-restraints excluded: chain B residue 2148 MET Chi-restraints excluded: chain B residue 2263 LYS Chi-restraints excluded: chain B residue 2339 SER Chi-restraints excluded: chain B residue 2478 ASP Chi-restraints excluded: chain B residue 2490 LEU Chi-restraints excluded: chain B residue 2553 ILE Chi-restraints excluded: chain B residue 2559 HIS Chi-restraints excluded: chain B residue 2573 MET Chi-restraints excluded: chain B residue 2585 VAL Chi-restraints excluded: chain B residue 2622 VAL Chi-restraints excluded: chain B residue 2638 ILE Chi-restraints excluded: chain B residue 2655 THR Chi-restraints excluded: chain B residue 2678 SER Chi-restraints excluded: chain B residue 2696 LEU Chi-restraints excluded: chain B residue 2724 LEU Chi-restraints excluded: chain B residue 2730 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 41 optimal weight: 6.9990 chunk 146 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 199 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 173 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 348 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1471 HIS A1962 HIS A2299 GLN A2559 HIS A2701 GLN B1763 GLN ** B1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1948 GLN B1962 HIS B2233 HIS B2534 ASN B2701 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.127175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.100900 restraints weight = 40754.511| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.09 r_work: 0.3199 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 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 : 0.004 0.039 28798 Z= 0.182 Angle : 0.584 15.406 39130 Z= 0.298 Chirality : 0.047 0.480 4434 Planarity : 0.004 0.056 4994 Dihedral : 7.414 99.058 4645 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.81 % Allowed : 21.89 % Favored : 74.29 % 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: 0.19 (0.14), residues: 3500 helix: 1.04 (0.35), residues: 224 sheet: 0.62 (0.14), residues: 1342 loop : -0.28 (0.15), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B1912 TYR 0.017 0.001 TYR A2262 PHE 0.014 0.001 PHE B2129 TRP 0.010 0.001 TRP A2296 HIS 0.007 0.001 HIS B2233 Details of bonding type rmsd covalent geometry : bond 0.00415 (28750) covalent geometry : angle 0.56020 (38998) SS BOND : bond 0.00176 ( 12) SS BOND : angle 0.97747 ( 24) hydrogen bonds : bond 0.03864 ( 1065) hydrogen bonds : angle 4.94875 ( 3858) link_ALPHA1-2 : bond 0.01106 ( 2) link_ALPHA1-2 : angle 2.30295 ( 6) link_ALPHA1-3 : bond 0.01247 ( 4) link_ALPHA1-3 : angle 1.73111 ( 12) link_BETA1-4 : bond 0.00493 ( 14) link_BETA1-4 : angle 1.84286 ( 42) link_NAG-ASN : bond 0.00472 ( 16) link_NAG-ASN : angle 4.26958 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 609 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1105 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8472 (p) REVERT: A 1122 TYR cc_start: 0.8383 (t80) cc_final: 0.8127 (t80) REVERT: A 1210 ILE cc_start: 0.8570 (pt) cc_final: 0.8367 (mp) REVERT: A 1215 MET cc_start: 0.7721 (tpp) cc_final: 0.7324 (tpp) REVERT: A 1340 ASP cc_start: 0.4413 (OUTLIER) cc_final: 0.4093 (m-30) REVERT: A 1356 MET cc_start: 0.5058 (mtp) cc_final: 0.4808 (mtp) REVERT: A 1369 MET cc_start: 0.7956 (tmm) cc_final: 0.7710 (tmm) REVERT: A 1376 MET cc_start: 0.7141 (mtm) cc_final: 0.6607 (mtm) REVERT: A 1454 MET cc_start: 0.6471 (pmm) cc_final: 0.6173 (pmm) REVERT: A 1467 LYS cc_start: 0.7843 (mmpt) cc_final: 0.7550 (mmmm) REVERT: A 1488 LEU cc_start: 0.8643 (tp) cc_final: 0.8369 (tt) REVERT: A 1542 ILE cc_start: 0.8502 (mt) cc_final: 0.8204 (mp) REVERT: A 1676 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7231 (mm-30) REVERT: A 1680 MET cc_start: 0.8864 (mpp) cc_final: 0.8596 (mtm) REVERT: A 1742 ASP cc_start: 0.7922 (p0) cc_final: 0.7537 (p0) REVERT: A 1791 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7572 (mt-10) REVERT: A 1875 GLN cc_start: 0.7989 (pm20) cc_final: 0.7746 (pm20) REVERT: A 1917 LYS cc_start: 0.8519 (mmtm) cc_final: 0.8275 (mmtm) REVERT: A 1969 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8533 (t) REVERT: A 2074 LYS cc_start: 0.8836 (ttmp) cc_final: 0.8574 (ttmm) REVERT: A 2080 SER cc_start: 0.8767 (m) cc_final: 0.8463 (t) REVERT: A 2227 ASP cc_start: 0.7747 (t0) cc_final: 0.7517 (t0) REVERT: A 2272 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8293 (tt0) REVERT: A 2346 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8271 (mt) REVERT: A 2471 ASP cc_start: 0.7901 (t0) cc_final: 0.7612 (t0) REVERT: A 2531 GLU cc_start: 0.8205 (tp30) cc_final: 0.7846 (tp30) REVERT: A 2544 VAL cc_start: 0.9012 (p) cc_final: 0.8776 (t) REVERT: A 2553 ILE cc_start: 0.8661 (mm) cc_final: 0.8276 (tt) REVERT: A 2573 MET cc_start: 0.8606 (tmt) cc_final: 0.8166 (tmm) REVERT: A 2574 PHE cc_start: 0.8797 (t80) cc_final: 0.8469 (t80) REVERT: A 2614 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8085 (mm-30) REVERT: A 2657 LEU cc_start: 0.4601 (OUTLIER) cc_final: 0.4256 (tm) REVERT: A 2713 GLN cc_start: 0.8492 (tp-100) cc_final: 0.8133 (mm-40) REVERT: B 1105 VAL cc_start: 0.8650 (t) cc_final: 0.8344 (p) REVERT: B 1210 ILE cc_start: 0.8516 (pt) cc_final: 0.8110 (mm) REVERT: B 1236 LYS cc_start: 0.6715 (mtpp) cc_final: 0.6355 (mmpt) REVERT: B 1327 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6930 (pp20) REVERT: B 1344 CYS cc_start: 0.7115 (m) cc_final: 0.6409 (m) REVERT: B 1376 MET cc_start: 0.6785 (mtm) cc_final: 0.6297 (mtm) REVERT: B 1542 ILE cc_start: 0.8463 (mt) cc_final: 0.8202 (mp) REVERT: B 1742 ASP cc_start: 0.7830 (p0) cc_final: 0.7470 (p0) REVERT: B 1822 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8209 (mtt90) REVERT: B 1875 GLN cc_start: 0.8161 (pm20) cc_final: 0.7885 (pm20) REVERT: B 1931 VAL cc_start: 0.9223 (OUTLIER) cc_final: 0.8994 (t) REVERT: B 1969 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8520 (t) REVERT: B 2044 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8059 (mm-30) REVERT: B 2064 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8243 (mtp85) REVERT: B 2080 SER cc_start: 0.8803 (m) cc_final: 0.8515 (t) REVERT: B 2219 ARG cc_start: 0.7712 (ttp80) cc_final: 0.7462 (ttp80) REVERT: B 2242 ARG cc_start: 0.7734 (mtt180) cc_final: 0.7460 (mtm110) REVERT: B 2288 ARG cc_start: 0.8642 (mtp180) cc_final: 0.8314 (ttt180) REVERT: B 2357 MET cc_start: 0.9007 (mtm) cc_final: 0.8781 (mtp) REVERT: B 2451 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7992 (mt-10) REVERT: B 2471 ASP cc_start: 0.8000 (t0) cc_final: 0.7668 (t0) REVERT: B 2531 GLU cc_start: 0.8387 (tp30) cc_final: 0.7979 (tp30) REVERT: B 2574 PHE cc_start: 0.8792 (t80) cc_final: 0.8536 (t80) REVERT: B 2614 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8143 (mm-30) REVERT: B 2681 TYR cc_start: 0.8619 (m-80) cc_final: 0.8398 (m-80) REVERT: B 2690 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8133 (mt-10) REVERT: B 2713 GLN cc_start: 0.8511 (tp40) cc_final: 0.8226 (mm-40) REVERT: B 2730 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7765 (ttmm) REVERT: B 2765 PHE cc_start: 0.8645 (m-80) cc_final: 0.8286 (m-80) outliers start: 116 outliers final: 69 residues processed: 671 average time/residue: 0.7724 time to fit residues: 598.6499 Evaluate side-chains 682 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 600 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1115 GLN Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1340 ASP Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1511 CYS Chi-restraints excluded: chain A residue 1534 ASP Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1576 VAL Chi-restraints excluded: chain A residue 1591 GLN Chi-restraints excluded: chain A residue 1628 LEU Chi-restraints excluded: chain A residue 1663 THR Chi-restraints excluded: chain A residue 1712 ASN Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1736 GLU Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1791 GLU Chi-restraints excluded: chain A residue 1834 ILE Chi-restraints excluded: chain A residue 1866 LYS Chi-restraints excluded: chain A residue 1909 MET Chi-restraints excluded: chain A residue 1935 SER Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1973 SER Chi-restraints excluded: chain A residue 2002 ASP Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2112 LEU Chi-restraints excluded: chain A residue 2122 ILE Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2148 MET Chi-restraints excluded: chain A residue 2272 GLN Chi-restraints excluded: chain A residue 2346 LEU Chi-restraints excluded: chain A residue 2427 GLN Chi-restraints excluded: chain A residue 2632 VAL Chi-restraints excluded: chain A residue 2638 ILE Chi-restraints excluded: chain A residue 2657 LEU Chi-restraints excluded: chain A residue 2666 THR Chi-restraints excluded: chain A residue 2678 SER Chi-restraints excluded: chain A residue 2697 ASP Chi-restraints excluded: chain A residue 2724 LEU Chi-restraints excluded: chain B residue 1030 ILE Chi-restraints excluded: chain B residue 1153 CYS Chi-restraints excluded: chain B residue 1327 GLU Chi-restraints excluded: chain B residue 1337 LEU Chi-restraints excluded: chain B residue 1341 GLU Chi-restraints excluded: chain B residue 1485 THR Chi-restraints excluded: chain B residue 1505 THR Chi-restraints excluded: chain B residue 1511 CYS Chi-restraints excluded: chain B residue 1534 ASP Chi-restraints excluded: chain B residue 1557 ILE Chi-restraints excluded: chain B residue 1576 VAL Chi-restraints excluded: chain B residue 1601 ILE Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1641 ASP Chi-restraints excluded: chain B residue 1663 THR Chi-restraints excluded: chain B residue 1693 SER Chi-restraints excluded: chain B residue 1730 SER Chi-restraints excluded: chain B residue 1736 GLU Chi-restraints excluded: chain B residue 1746 VAL Chi-restraints excluded: chain B residue 1769 GLN Chi-restraints excluded: chain B residue 1822 ARG Chi-restraints excluded: chain B residue 1931 VAL Chi-restraints excluded: chain B residue 1935 SER Chi-restraints excluded: chain B residue 1947 SER Chi-restraints excluded: chain B residue 1969 VAL Chi-restraints excluded: chain B residue 2029 SER Chi-restraints excluded: chain B residue 2064 ARG Chi-restraints excluded: chain B residue 2112 LEU Chi-restraints excluded: chain B residue 2122 ILE Chi-restraints excluded: chain B residue 2128 HIS Chi-restraints excluded: chain B residue 2148 MET Chi-restraints excluded: chain B residue 2478 ASP Chi-restraints excluded: chain B residue 2490 LEU Chi-restraints excluded: chain B residue 2553 ILE Chi-restraints excluded: chain B residue 2559 HIS Chi-restraints excluded: chain B residue 2573 MET Chi-restraints excluded: chain B residue 2585 VAL Chi-restraints excluded: chain B residue 2622 VAL Chi-restraints excluded: chain B residue 2678 SER Chi-restraints excluded: chain B residue 2696 LEU Chi-restraints excluded: chain B residue 2724 LEU Chi-restraints excluded: chain B residue 2730 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 251 optimal weight: 1.9990 chunk 232 optimal weight: 0.8980 chunk 309 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 291 optimal weight: 0.9990 chunk 313 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1471 HIS A1962 HIS A2559 HIS A2701 GLN ** B1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1962 HIS B2233 HIS B2299 GLN B2701 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.127019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.100724 restraints weight = 40789.576| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.10 r_work: 0.3200 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 28798 Z= 0.164 Angle : 0.570 15.248 39130 Z= 0.292 Chirality : 0.047 0.461 4434 Planarity : 0.004 0.063 4994 Dihedral : 7.005 95.192 4644 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.91 % Allowed : 22.65 % Favored : 73.44 % 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: 0.21 (0.14), residues: 3500 helix: 0.98 (0.35), residues: 226 sheet: 0.66 (0.14), residues: 1324 loop : -0.27 (0.15), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B1912 TYR 0.016 0.001 TYR B2077 PHE 0.014 0.001 PHE B2129 TRP 0.010 0.001 TRP A2296 HIS 0.007 0.001 HIS B2233 Details of bonding type rmsd covalent geometry : bond 0.00375 (28750) covalent geometry : angle 0.54677 (38998) SS BOND : bond 0.00175 ( 12) SS BOND : angle 0.91647 ( 24) hydrogen bonds : bond 0.03719 ( 1065) hydrogen bonds : angle 4.86943 ( 3858) link_ALPHA1-2 : bond 0.01035 ( 2) link_ALPHA1-2 : angle 2.39967 ( 6) link_ALPHA1-3 : bond 0.01272 ( 4) link_ALPHA1-3 : angle 1.94861 ( 12) link_BETA1-4 : bond 0.00520 ( 14) link_BETA1-4 : angle 1.74372 ( 42) link_NAG-ASN : bond 0.00464 ( 16) link_NAG-ASN : angle 4.20287 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 599 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1098 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.6889 (mmp-170) REVERT: A 1105 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8511 (p) REVERT: A 1122 TYR cc_start: 0.8411 (t80) cc_final: 0.8210 (t80) REVERT: A 1210 ILE cc_start: 0.8570 (pt) cc_final: 0.8361 (mp) REVERT: A 1215 MET cc_start: 0.7766 (tpp) cc_final: 0.7356 (tpp) REVERT: A 1337 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5575 (mm) REVERT: A 1340 ASP cc_start: 0.4413 (OUTLIER) cc_final: 0.4102 (m-30) REVERT: A 1356 MET cc_start: 0.5054 (mtp) cc_final: 0.4811 (mtp) REVERT: A 1369 MET cc_start: 0.7927 (tmm) cc_final: 0.7686 (tmm) REVERT: A 1376 MET cc_start: 0.7130 (mtm) cc_final: 0.6579 (mtm) REVERT: A 1454 MET cc_start: 0.6519 (pmm) cc_final: 0.6236 (pmm) REVERT: A 1467 LYS cc_start: 0.7893 (mmpt) cc_final: 0.7593 (mmmm) REVERT: A 1488 LEU cc_start: 0.8629 (tp) cc_final: 0.8361 (tt) REVERT: A 1542 ILE cc_start: 0.8510 (mt) cc_final: 0.8208 (mp) REVERT: A 1676 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7274 (mm-30) REVERT: A 1742 ASP cc_start: 0.7926 (p0) cc_final: 0.7523 (p0) REVERT: A 1791 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7575 (mt-10) REVERT: A 1819 ILE cc_start: 0.8789 (mt) cc_final: 0.8531 (tt) REVERT: A 1917 LYS cc_start: 0.8526 (mmtm) cc_final: 0.8289 (mmtm) REVERT: A 2080 SER cc_start: 0.8757 (m) cc_final: 0.8451 (t) REVERT: A 2109 GLU cc_start: 0.7891 (mp0) cc_final: 0.7685 (mp0) REVERT: A 2227 ASP cc_start: 0.7756 (t0) cc_final: 0.7542 (t0) REVERT: A 2272 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8285 (tt0) REVERT: A 2346 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8279 (mt) REVERT: A 2471 ASP cc_start: 0.7921 (t0) cc_final: 0.7623 (t0) REVERT: A 2531 GLU cc_start: 0.8182 (tp30) cc_final: 0.7816 (tp30) REVERT: A 2544 VAL cc_start: 0.9019 (p) cc_final: 0.8779 (t) REVERT: A 2553 ILE cc_start: 0.8656 (mm) cc_final: 0.8248 (tt) REVERT: A 2573 MET cc_start: 0.8635 (tmt) cc_final: 0.8185 (tmm) REVERT: A 2574 PHE cc_start: 0.8788 (t80) cc_final: 0.8508 (t80) REVERT: A 2657 LEU cc_start: 0.4677 (OUTLIER) cc_final: 0.4342 (tm) REVERT: A 2673 SER cc_start: 0.8854 (OUTLIER) cc_final: 0.8608 (t) REVERT: A 2713 GLN cc_start: 0.8470 (tp-100) cc_final: 0.8109 (mm-40) REVERT: B 1105 VAL cc_start: 0.8674 (t) cc_final: 0.8363 (p) REVERT: B 1175 ASN cc_start: 0.8833 (t0) cc_final: 0.8416 (t0) REVERT: B 1210 ILE cc_start: 0.8510 (pt) cc_final: 0.8106 (mm) REVERT: B 1236 LYS cc_start: 0.6738 (mtpp) cc_final: 0.6489 (mmmm) REVERT: B 1327 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7055 (pp20) REVERT: B 1344 CYS cc_start: 0.7094 (m) cc_final: 0.6386 (m) REVERT: B 1376 MET cc_start: 0.6823 (mtm) cc_final: 0.6314 (mtm) REVERT: B 1509 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7365 (pt0) REVERT: B 1542 ILE cc_start: 0.8456 (mt) cc_final: 0.8180 (mp) REVERT: B 1742 ASP cc_start: 0.7831 (p0) cc_final: 0.7479 (p0) REVERT: B 1765 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8086 (mtm180) REVERT: B 1822 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8239 (mtt90) REVERT: B 1875 GLN cc_start: 0.8154 (pm20) cc_final: 0.7878 (pm20) REVERT: B 1931 VAL cc_start: 0.9216 (OUTLIER) cc_final: 0.8998 (t) REVERT: B 2024 LYS cc_start: 0.8778 (ttpp) cc_final: 0.8555 (mtpt) REVERT: B 2044 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8021 (mm-30) REVERT: B 2064 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8203 (mtp85) REVERT: B 2080 SER cc_start: 0.8809 (m) cc_final: 0.8469 (t) REVERT: B 2114 VAL cc_start: 0.8537 (p) cc_final: 0.8298 (t) REVERT: B 2127 GLU cc_start: 0.8232 (mt-10) cc_final: 0.8006 (mt-10) REVERT: B 2242 ARG cc_start: 0.7770 (mtt180) cc_final: 0.7503 (mtm110) REVERT: B 2263 LYS cc_start: 0.8133 (ttpt) cc_final: 0.7884 (ttpp) REVERT: B 2451 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7991 (mt-10) REVERT: B 2471 ASP cc_start: 0.8006 (t0) cc_final: 0.7680 (t0) REVERT: B 2531 GLU cc_start: 0.8384 (tp30) cc_final: 0.7980 (tp30) REVERT: B 2553 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8577 (tt) REVERT: B 2574 PHE cc_start: 0.8780 (t80) cc_final: 0.8529 (t80) REVERT: B 2614 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8144 (mm-30) REVERT: B 2681 TYR cc_start: 0.8629 (m-80) cc_final: 0.8428 (m-80) REVERT: B 2690 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8111 (mt-10) REVERT: B 2700 ARG cc_start: 0.8535 (ttt-90) cc_final: 0.8331 (ttt90) REVERT: B 2713 GLN cc_start: 0.8533 (tp40) cc_final: 0.8220 (mm-40) REVERT: B 2730 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7773 (ttmm) REVERT: B 2765 PHE cc_start: 0.8637 (m-80) cc_final: 0.8152 (m-80) outliers start: 119 outliers final: 70 residues processed: 664 average time/residue: 0.7322 time to fit residues: 562.2774 Evaluate side-chains 680 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 594 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1098 ARG Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1115 GLN Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1340 ASP Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1505 THR Chi-restraints excluded: chain A residue 1511 CYS Chi-restraints excluded: chain A residue 1534 ASP Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1576 VAL Chi-restraints excluded: chain A residue 1591 GLN Chi-restraints excluded: chain A residue 1628 LEU Chi-restraints excluded: chain A residue 1663 THR Chi-restraints excluded: chain A residue 1712 ASN Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1736 GLU Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1791 GLU Chi-restraints excluded: chain A residue 1834 ILE Chi-restraints excluded: chain A residue 1866 LYS Chi-restraints excluded: chain A residue 1909 MET Chi-restraints excluded: chain A residue 1935 SER Chi-restraints excluded: chain A residue 1975 SER Chi-restraints excluded: chain A residue 2002 ASP Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2112 LEU Chi-restraints excluded: chain A residue 2122 ILE Chi-restraints excluded: chain A residue 2126 VAL Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2148 MET Chi-restraints excluded: chain A residue 2272 GLN Chi-restraints excluded: chain A residue 2346 LEU Chi-restraints excluded: chain A residue 2412 HIS Chi-restraints excluded: chain A residue 2427 GLN Chi-restraints excluded: chain A residue 2450 LYS Chi-restraints excluded: chain A residue 2638 ILE Chi-restraints excluded: chain A residue 2657 LEU Chi-restraints excluded: chain A residue 2666 THR Chi-restraints excluded: chain A residue 2673 SER Chi-restraints excluded: chain A residue 2676 LEU Chi-restraints excluded: chain A residue 2678 SER Chi-restraints excluded: chain A residue 2724 LEU Chi-restraints excluded: chain B residue 1030 ILE Chi-restraints excluded: chain B residue 1068 LYS Chi-restraints excluded: chain B residue 1153 CYS Chi-restraints excluded: chain B residue 1327 GLU Chi-restraints excluded: chain B residue 1337 LEU Chi-restraints excluded: chain B residue 1341 GLU Chi-restraints excluded: chain B residue 1485 THR Chi-restraints excluded: chain B residue 1511 CYS Chi-restraints excluded: chain B residue 1557 ILE Chi-restraints excluded: chain B residue 1576 VAL Chi-restraints excluded: chain B residue 1601 ILE Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1663 THR Chi-restraints excluded: chain B residue 1693 SER Chi-restraints excluded: chain B residue 1730 SER Chi-restraints excluded: chain B residue 1736 GLU Chi-restraints excluded: chain B residue 1746 VAL Chi-restraints excluded: chain B residue 1765 ARG Chi-restraints excluded: chain B residue 1769 GLN Chi-restraints excluded: chain B residue 1822 ARG Chi-restraints excluded: chain B residue 1931 VAL Chi-restraints excluded: chain B residue 1935 SER Chi-restraints excluded: chain B residue 1947 SER Chi-restraints excluded: chain B residue 2029 SER Chi-restraints excluded: chain B residue 2064 ARG Chi-restraints excluded: chain B residue 2112 LEU Chi-restraints excluded: chain B residue 2122 ILE Chi-restraints excluded: chain B residue 2128 HIS Chi-restraints excluded: chain B residue 2148 MET Chi-restraints excluded: chain B residue 2339 SER Chi-restraints excluded: chain B residue 2478 ASP Chi-restraints excluded: chain B residue 2490 LEU Chi-restraints excluded: chain B residue 2553 ILE Chi-restraints excluded: chain B residue 2559 HIS Chi-restraints excluded: chain B residue 2573 MET Chi-restraints excluded: chain B residue 2585 VAL Chi-restraints excluded: chain B residue 2622 VAL Chi-restraints excluded: chain B residue 2638 ILE Chi-restraints excluded: chain B residue 2678 SER Chi-restraints excluded: chain B residue 2696 LEU Chi-restraints excluded: chain B residue 2724 LEU Chi-restraints excluded: chain B residue 2730 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 304 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 213 optimal weight: 10.0000 chunk 226 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1471 HIS A1962 HIS A2299 GLN A2318 HIS A2474 ASN ** A2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2559 HIS A2701 GLN B1195 HIS B1962 HIS B2233 HIS B2550 HIS B2701 GLN ** B2732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.125043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.098780 restraints weight = 40850.470| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.09 r_work: 0.3163 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 28798 Z= 0.331 Angle : 0.667 16.079 39130 Z= 0.340 Chirality : 0.051 0.506 4434 Planarity : 0.005 0.061 4994 Dihedral : 7.051 96.135 4644 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.08 % Allowed : 22.58 % Favored : 73.34 % 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: 0.08 (0.14), residues: 3500 helix: 0.64 (0.35), residues: 226 sheet: 0.57 (0.14), residues: 1336 loop : -0.34 (0.15), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B1912 TYR 0.023 0.002 TYR B2262 PHE 0.028 0.002 PHE A1371 TRP 0.012 0.002 TRP B1698 HIS 0.008 0.002 HIS A2128 Details of bonding type rmsd covalent geometry : bond 0.00768 (28750) covalent geometry : angle 0.64121 (38998) SS BOND : bond 0.00226 ( 12) SS BOND : angle 0.85629 ( 24) hydrogen bonds : bond 0.04497 ( 1065) hydrogen bonds : angle 5.12323 ( 3858) link_ALPHA1-2 : bond 0.01475 ( 2) link_ALPHA1-2 : angle 2.79671 ( 6) link_ALPHA1-3 : bond 0.01122 ( 4) link_ALPHA1-3 : angle 1.59464 ( 12) link_BETA1-4 : bond 0.00621 ( 14) link_BETA1-4 : angle 2.10203 ( 42) link_NAG-ASN : bond 0.00566 ( 16) link_NAG-ASN : angle 4.77469 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 598 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1098 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.6836 (mmp-170) REVERT: A 1105 VAL cc_start: 0.8820 (t) cc_final: 0.8535 (p) REVERT: A 1210 ILE cc_start: 0.8584 (pt) cc_final: 0.8376 (mp) REVERT: A 1215 MET cc_start: 0.7737 (tpp) cc_final: 0.7310 (tpp) REVERT: A 1337 LEU cc_start: 0.5906 (OUTLIER) cc_final: 0.5604 (mm) REVERT: A 1340 ASP cc_start: 0.4557 (OUTLIER) cc_final: 0.4213 (m-30) REVERT: A 1356 MET cc_start: 0.5092 (mtp) cc_final: 0.4855 (mtp) REVERT: A 1369 MET cc_start: 0.7935 (tmm) cc_final: 0.7651 (tmm) REVERT: A 1376 MET cc_start: 0.7147 (mtm) cc_final: 0.6584 (mtm) REVERT: A 1454 MET cc_start: 0.6585 (pmm) cc_final: 0.6300 (pmm) REVERT: A 1467 LYS cc_start: 0.8004 (mmpt) cc_final: 0.7684 (mmmm) REVERT: A 1488 LEU cc_start: 0.8663 (tp) cc_final: 0.8415 (tt) REVERT: A 1502 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7476 (mtm180) REVERT: A 1542 ILE cc_start: 0.8505 (mt) cc_final: 0.8198 (mp) REVERT: A 1647 ARG cc_start: 0.8182 (mmm-85) cc_final: 0.7887 (mmt-90) REVERT: A 1676 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7321 (mm-30) REVERT: A 1680 MET cc_start: 0.8772 (mpp) cc_final: 0.8489 (mtm) REVERT: A 1742 ASP cc_start: 0.7857 (p0) cc_final: 0.7476 (p0) REVERT: A 1791 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7603 (mt-10) REVERT: A 1917 LYS cc_start: 0.8576 (mmtm) cc_final: 0.8323 (mmtm) REVERT: A 2080 SER cc_start: 0.8797 (m) cc_final: 0.8450 (t) REVERT: A 2131 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8706 (pttt) REVERT: A 2227 ASP cc_start: 0.7796 (t0) cc_final: 0.7567 (t0) REVERT: A 2346 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8345 (mt) REVERT: A 2471 ASP cc_start: 0.7937 (t0) cc_final: 0.7653 (t0) REVERT: A 2531 GLU cc_start: 0.8259 (tp30) cc_final: 0.7888 (tp30) REVERT: A 2553 ILE cc_start: 0.8722 (mm) cc_final: 0.8336 (tt) REVERT: A 2574 PHE cc_start: 0.8868 (t80) cc_final: 0.8603 (t80) REVERT: A 2657 LEU cc_start: 0.4687 (OUTLIER) cc_final: 0.4350 (tm) REVERT: A 2673 SER cc_start: 0.8831 (OUTLIER) cc_final: 0.8582 (t) REVERT: A 2700 ARG cc_start: 0.8519 (ttt-90) cc_final: 0.8300 (ttt90) REVERT: A 2713 GLN cc_start: 0.8496 (tp-100) cc_final: 0.8121 (mm-40) REVERT: B 1105 VAL cc_start: 0.8733 (t) cc_final: 0.8431 (p) REVERT: B 1210 ILE cc_start: 0.8572 (pt) cc_final: 0.8167 (mm) REVERT: B 1327 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7029 (pp20) REVERT: B 1376 MET cc_start: 0.6828 (mtm) cc_final: 0.6315 (mtm) REVERT: B 1509 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7371 (pt0) REVERT: B 1542 ILE cc_start: 0.8447 (mt) cc_final: 0.8179 (mp) REVERT: B 1742 ASP cc_start: 0.7784 (p0) cc_final: 0.7424 (p0) REVERT: B 1762 ASP cc_start: 0.8243 (t0) cc_final: 0.7987 (t0) REVERT: B 1765 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8154 (mtm180) REVERT: B 1822 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8242 (mtt90) REVERT: B 1875 GLN cc_start: 0.8182 (pm20) cc_final: 0.7964 (pm20) REVERT: B 1931 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.8993 (t) REVERT: B 1938 ASP cc_start: 0.7211 (t0) cc_final: 0.6995 (t0) REVERT: B 2044 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8080 (mm-30) REVERT: B 2064 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8261 (mtp85) REVERT: B 2080 SER cc_start: 0.8821 (m) cc_final: 0.8451 (t) REVERT: B 2263 LYS cc_start: 0.8136 (ttpt) cc_final: 0.7701 (ttpp) REVERT: B 2471 ASP cc_start: 0.8042 (t0) cc_final: 0.7742 (t0) REVERT: B 2499 ARG cc_start: 0.7989 (ttm-80) cc_final: 0.7782 (ttm-80) REVERT: B 2531 GLU cc_start: 0.8374 (tp30) cc_final: 0.7997 (tp30) REVERT: B 2554 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7865 (ttp-110) REVERT: B 2614 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8141 (mm-30) REVERT: B 2690 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8102 (mt-10) REVERT: B 2700 ARG cc_start: 0.8527 (ttt-90) cc_final: 0.8300 (ttt90) REVERT: B 2713 GLN cc_start: 0.8525 (tp40) cc_final: 0.8177 (mm-40) REVERT: B 2730 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7852 (ttmm) REVERT: B 2765 PHE cc_start: 0.8663 (m-80) cc_final: 0.8289 (m-80) outliers start: 124 outliers final: 78 residues processed: 665 average time/residue: 0.7304 time to fit residues: 561.1908 Evaluate side-chains 677 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 583 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1098 ARG Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1340 ASP Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1502 ARG Chi-restraints excluded: chain A residue 1505 THR Chi-restraints excluded: chain A residue 1511 CYS Chi-restraints excluded: chain A residue 1534 ASP Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1576 VAL Chi-restraints excluded: chain A residue 1591 GLN Chi-restraints excluded: chain A residue 1628 LEU Chi-restraints excluded: chain A residue 1663 THR Chi-restraints excluded: chain A residue 1691 THR Chi-restraints excluded: chain A residue 1712 ASN Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1791 GLU Chi-restraints excluded: chain A residue 1834 ILE Chi-restraints excluded: chain A residue 1866 LYS Chi-restraints excluded: chain A residue 1909 MET Chi-restraints excluded: chain A residue 1935 SER Chi-restraints excluded: chain A residue 1947 SER Chi-restraints excluded: chain A residue 1975 SER Chi-restraints excluded: chain A residue 2002 ASP Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2112 LEU Chi-restraints excluded: chain A residue 2122 ILE Chi-restraints excluded: chain A residue 2126 VAL Chi-restraints excluded: chain A residue 2131 LYS Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2272 GLN Chi-restraints excluded: chain A residue 2346 LEU Chi-restraints excluded: chain A residue 2412 HIS Chi-restraints excluded: chain A residue 2427 GLN Chi-restraints excluded: chain A residue 2444 MET Chi-restraints excluded: chain A residue 2448 VAL Chi-restraints excluded: chain A residue 2450 LYS Chi-restraints excluded: chain A residue 2490 LEU Chi-restraints excluded: chain A residue 2638 ILE Chi-restraints excluded: chain A residue 2657 LEU Chi-restraints excluded: chain A residue 2666 THR Chi-restraints excluded: chain A residue 2673 SER Chi-restraints excluded: chain A residue 2678 SER Chi-restraints excluded: chain A residue 2697 ASP Chi-restraints excluded: chain A residue 2724 LEU Chi-restraints excluded: chain B residue 1030 ILE Chi-restraints excluded: chain B residue 1087 MET Chi-restraints excluded: chain B residue 1153 CYS Chi-restraints excluded: chain B residue 1327 GLU Chi-restraints excluded: chain B residue 1337 LEU Chi-restraints excluded: chain B residue 1341 GLU Chi-restraints excluded: chain B residue 1485 THR Chi-restraints excluded: chain B residue 1511 CYS Chi-restraints excluded: chain B residue 1534 ASP Chi-restraints excluded: chain B residue 1557 ILE Chi-restraints excluded: chain B residue 1576 VAL Chi-restraints excluded: chain B residue 1601 ILE Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1663 THR Chi-restraints excluded: chain B residue 1693 SER Chi-restraints excluded: chain B residue 1730 SER Chi-restraints excluded: chain B residue 1736 GLU Chi-restraints excluded: chain B residue 1746 VAL Chi-restraints excluded: chain B residue 1750 LEU Chi-restraints excluded: chain B residue 1765 ARG Chi-restraints excluded: chain B residue 1769 GLN Chi-restraints excluded: chain B residue 1822 ARG Chi-restraints excluded: chain B residue 1931 VAL Chi-restraints excluded: chain B residue 1935 SER Chi-restraints excluded: chain B residue 1947 SER Chi-restraints excluded: chain B residue 2064 ARG Chi-restraints excluded: chain B residue 2112 LEU Chi-restraints excluded: chain B residue 2122 ILE Chi-restraints excluded: chain B residue 2128 HIS Chi-restraints excluded: chain B residue 2360 SER Chi-restraints excluded: chain B residue 2478 ASP Chi-restraints excluded: chain B residue 2490 LEU Chi-restraints excluded: chain B residue 2493 ILE Chi-restraints excluded: chain B residue 2553 ILE Chi-restraints excluded: chain B residue 2554 ARG Chi-restraints excluded: chain B residue 2559 HIS Chi-restraints excluded: chain B residue 2573 MET Chi-restraints excluded: chain B residue 2585 VAL Chi-restraints excluded: chain B residue 2587 SER Chi-restraints excluded: chain B residue 2622 VAL Chi-restraints excluded: chain B residue 2638 ILE Chi-restraints excluded: chain B residue 2678 SER Chi-restraints excluded: chain B residue 2696 LEU Chi-restraints excluded: chain B residue 2724 LEU Chi-restraints excluded: chain B residue 2730 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 59 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 chunk 251 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 315 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1471 HIS A1962 HIS A2299 GLN A2468 ASN A2474 ASN A2550 HIS A2559 HIS A2701 GLN ** B1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1948 GLN B1962 HIS B2233 HIS B2299 GLN B2550 HIS B2701 GLN B2732 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.127788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.101060 restraints weight = 40293.750| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.12 r_work: 0.3191 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28798 Z= 0.142 Angle : 0.583 15.163 39130 Z= 0.298 Chirality : 0.046 0.444 4434 Planarity : 0.004 0.073 4994 Dihedral : 6.681 93.803 4644 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.12 % Allowed : 23.77 % Favored : 73.11 % 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: 0.20 (0.14), residues: 3500 helix: 0.91 (0.35), residues: 226 sheet: 0.61 (0.14), residues: 1338 loop : -0.25 (0.15), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B1912 TYR 0.015 0.001 TYR B2119 PHE 0.027 0.001 PHE A1371 TRP 0.009 0.001 TRP B2296 HIS 0.007 0.001 HIS A2233 Details of bonding type rmsd covalent geometry : bond 0.00320 (28750) covalent geometry : angle 0.55989 (38998) SS BOND : bond 0.00169 ( 12) SS BOND : angle 0.69536 ( 24) hydrogen bonds : bond 0.03608 ( 1065) hydrogen bonds : angle 4.87968 ( 3858) link_ALPHA1-2 : bond 0.01053 ( 2) link_ALPHA1-2 : angle 2.56819 ( 6) link_ALPHA1-3 : bond 0.01280 ( 4) link_ALPHA1-3 : angle 1.77553 ( 12) link_BETA1-4 : bond 0.00505 ( 14) link_BETA1-4 : angle 1.76506 ( 42) link_NAG-ASN : bond 0.00468 ( 16) link_NAG-ASN : angle 4.21281 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 603 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1105 VAL cc_start: 0.8798 (t) cc_final: 0.8524 (p) REVERT: A 1210 ILE cc_start: 0.8562 (pt) cc_final: 0.8338 (mp) REVERT: A 1215 MET cc_start: 0.7767 (tpp) cc_final: 0.7334 (tpp) REVERT: A 1356 MET cc_start: 0.5093 (mtp) cc_final: 0.4861 (mtp) REVERT: A 1369 MET cc_start: 0.7881 (tmm) cc_final: 0.7597 (tmm) REVERT: A 1371 PHE cc_start: 0.7878 (p90) cc_final: 0.7614 (p90) REVERT: A 1376 MET cc_start: 0.7123 (mtm) cc_final: 0.6512 (mtm) REVERT: A 1454 MET cc_start: 0.6695 (pmm) cc_final: 0.6489 (pmm) REVERT: A 1467 LYS cc_start: 0.7965 (mmpt) cc_final: 0.7646 (mmmm) REVERT: A 1488 LEU cc_start: 0.8636 (tp) cc_final: 0.8378 (tt) REVERT: A 1676 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7365 (mm-30) REVERT: A 1742 ASP cc_start: 0.7858 (p0) cc_final: 0.7485 (p0) REVERT: A 1791 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7586 (mt-10) REVERT: A 1870 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8166 (mtp180) REVERT: A 1917 LYS cc_start: 0.8560 (mmtm) cc_final: 0.8306 (mmtm) REVERT: A 2059 PHE cc_start: 0.8107 (m-10) cc_final: 0.7803 (m-10) REVERT: A 2080 SER cc_start: 0.8752 (m) cc_final: 0.8410 (t) REVERT: A 2081 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7865 (mm-30) REVERT: A 2227 ASP cc_start: 0.7752 (t0) cc_final: 0.7525 (t0) REVERT: A 2272 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: A 2346 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8332 (mt) REVERT: A 2471 ASP cc_start: 0.7930 (t0) cc_final: 0.7653 (t0) REVERT: A 2531 GLU cc_start: 0.8230 (tp30) cc_final: 0.7863 (tp30) REVERT: A 2553 ILE cc_start: 0.8691 (mm) cc_final: 0.8311 (tt) REVERT: A 2573 MET cc_start: 0.8560 (tmt) cc_final: 0.8192 (tmm) REVERT: A 2574 PHE cc_start: 0.8820 (t80) cc_final: 0.8551 (t80) REVERT: A 2657 LEU cc_start: 0.4735 (OUTLIER) cc_final: 0.4407 (tm) REVERT: A 2673 SER cc_start: 0.8843 (m) cc_final: 0.8597 (t) REVERT: A 2696 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8185 (mp) REVERT: A 2713 GLN cc_start: 0.8419 (tp-100) cc_final: 0.8067 (mm-40) REVERT: B 1032 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8663 (tt) REVERT: B 1105 VAL cc_start: 0.8733 (t) cc_final: 0.8434 (p) REVERT: B 1175 ASN cc_start: 0.8800 (t0) cc_final: 0.8344 (t0) REVERT: B 1210 ILE cc_start: 0.8525 (pt) cc_final: 0.8112 (mm) REVERT: B 1327 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6930 (pp20) REVERT: B 1376 MET cc_start: 0.6798 (mtm) cc_final: 0.6266 (mtm) REVERT: B 1509 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7371 (pt0) REVERT: B 1542 ILE cc_start: 0.8367 (mt) cc_final: 0.8069 (mp) REVERT: B 1609 VAL cc_start: 0.8860 (OUTLIER) cc_final: 0.8656 (t) REVERT: B 1668 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8598 (mptp) REVERT: B 1742 ASP cc_start: 0.7818 (p0) cc_final: 0.7467 (p0) REVERT: B 1762 ASP cc_start: 0.8299 (t0) cc_final: 0.8062 (t0) REVERT: B 1791 GLU cc_start: 0.8026 (mp0) cc_final: 0.7375 (mp0) REVERT: B 1805 ARG cc_start: 0.8802 (mtm-85) cc_final: 0.8436 (mtm-85) REVERT: B 1819 ILE cc_start: 0.8922 (mm) cc_final: 0.8368 (tt) REVERT: B 1822 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8193 (mtt90) REVERT: B 1875 GLN cc_start: 0.8190 (pm20) cc_final: 0.7943 (pm20) REVERT: B 1931 VAL cc_start: 0.9214 (OUTLIER) cc_final: 0.8993 (t) REVERT: B 1938 ASP cc_start: 0.7176 (t0) cc_final: 0.6959 (t0) REVERT: B 2024 LYS cc_start: 0.8772 (ttpp) cc_final: 0.8469 (mtmt) REVERT: B 2044 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7994 (mm-30) REVERT: B 2064 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8263 (mtp85) REVERT: B 2080 SER cc_start: 0.8792 (m) cc_final: 0.8441 (t) REVERT: B 2082 GLU cc_start: 0.7849 (tp30) cc_final: 0.7364 (tp30) REVERT: B 2127 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8037 (mt-10) REVERT: B 2263 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7841 (ttpp) REVERT: B 2471 ASP cc_start: 0.7984 (t0) cc_final: 0.7682 (t0) REVERT: B 2531 GLU cc_start: 0.8389 (tp30) cc_final: 0.7953 (tp30) REVERT: B 2553 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8642 (tt) REVERT: B 2574 PHE cc_start: 0.8799 (t80) cc_final: 0.8516 (t80) REVERT: B 2713 GLN cc_start: 0.8481 (tp40) cc_final: 0.8065 (mm-40) REVERT: B 2730 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7787 (ttmm) REVERT: B 2765 PHE cc_start: 0.8617 (m-80) cc_final: 0.8279 (m-80) outliers start: 95 outliers final: 55 residues processed: 655 average time/residue: 0.7259 time to fit residues: 547.8075 Evaluate side-chains 653 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 582 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1115 GLN Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1255 ASP Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1511 CYS Chi-restraints excluded: chain A residue 1534 ASP Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1591 GLN Chi-restraints excluded: chain A residue 1628 LEU Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1791 GLU Chi-restraints excluded: chain A residue 1834 ILE Chi-restraints excluded: chain A residue 1866 LYS Chi-restraints excluded: chain A residue 1870 ARG Chi-restraints excluded: chain A residue 1909 MET Chi-restraints excluded: chain A residue 1975 SER Chi-restraints excluded: chain A residue 2002 ASP Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2112 LEU Chi-restraints excluded: chain A residue 2122 ILE Chi-restraints excluded: chain A residue 2126 VAL Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2272 GLN Chi-restraints excluded: chain A residue 2346 LEU Chi-restraints excluded: chain A residue 2412 HIS Chi-restraints excluded: chain A residue 2427 GLN Chi-restraints excluded: chain A residue 2448 VAL Chi-restraints excluded: chain A residue 2657 LEU Chi-restraints excluded: chain A residue 2676 LEU Chi-restraints excluded: chain A residue 2678 SER Chi-restraints excluded: chain A residue 2696 LEU Chi-restraints excluded: chain A residue 2697 ASP Chi-restraints excluded: chain B residue 1030 ILE Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain B residue 1087 MET Chi-restraints excluded: chain B residue 1327 GLU Chi-restraints excluded: chain B residue 1337 LEU Chi-restraints excluded: chain B residue 1341 GLU Chi-restraints excluded: chain B residue 1485 THR Chi-restraints excluded: chain B residue 1511 CYS Chi-restraints excluded: chain B residue 1557 ILE Chi-restraints excluded: chain B residue 1601 ILE Chi-restraints excluded: chain B residue 1609 VAL Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1663 THR Chi-restraints excluded: chain B residue 1668 LYS Chi-restraints excluded: chain B residue 1730 SER Chi-restraints excluded: chain B residue 1736 GLU Chi-restraints excluded: chain B residue 1746 VAL Chi-restraints excluded: chain B residue 1769 GLN Chi-restraints excluded: chain B residue 1822 ARG Chi-restraints excluded: chain B residue 1931 VAL Chi-restraints excluded: chain B residue 1935 SER Chi-restraints excluded: chain B residue 1947 SER Chi-restraints excluded: chain B residue 2002 ASP Chi-restraints excluded: chain B residue 2064 ARG Chi-restraints excluded: chain B residue 2112 LEU Chi-restraints excluded: chain B residue 2122 ILE Chi-restraints excluded: chain B residue 2128 HIS Chi-restraints excluded: chain B residue 2148 MET Chi-restraints excluded: chain B residue 2263 LYS Chi-restraints excluded: chain B residue 2478 ASP Chi-restraints excluded: chain B residue 2553 ILE Chi-restraints excluded: chain B residue 2559 HIS Chi-restraints excluded: chain B residue 2573 MET Chi-restraints excluded: chain B residue 2622 VAL Chi-restraints excluded: chain B residue 2678 SER Chi-restraints excluded: chain B residue 2724 LEU Chi-restraints excluded: chain B residue 2730 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 281 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 286 optimal weight: 1.9990 chunk 68 optimal weight: 0.0970 chunk 199 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1827 GLN A1962 HIS A2299 GLN A2474 ASN A2550 HIS A2559 HIS A2701 GLN B1817 ASN B1948 GLN B1962 HIS B2233 HIS B2299 GLN B2550 HIS B2701 GLN B2732 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.127007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.100675 restraints weight = 40987.856| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.11 r_work: 0.3194 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28798 Z= 0.143 Angle : 0.576 15.047 39130 Z= 0.293 Chirality : 0.046 0.425 4434 Planarity : 0.004 0.075 4994 Dihedral : 6.422 92.326 4642 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.19 % Allowed : 24.06 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.35 (0.14), residues: 3500 helix: 1.20 (0.35), residues: 224 sheet: 0.93 (0.15), residues: 1190 loop : -0.26 (0.14), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B1912 TYR 0.016 0.001 TYR B2119 PHE 0.025 0.001 PHE A1371 TRP 0.009 0.001 TRP B2296 HIS 0.008 0.001 HIS A2233 Details of bonding type rmsd covalent geometry : bond 0.00323 (28750) covalent geometry : angle 0.55345 (38998) SS BOND : bond 0.00257 ( 12) SS BOND : angle 0.63563 ( 24) hydrogen bonds : bond 0.03532 ( 1065) hydrogen bonds : angle 4.78942 ( 3858) link_ALPHA1-2 : bond 0.01039 ( 2) link_ALPHA1-2 : angle 2.58727 ( 6) link_ALPHA1-3 : bond 0.01187 ( 4) link_ALPHA1-3 : angle 1.65727 ( 12) link_BETA1-4 : bond 0.00517 ( 14) link_BETA1-4 : angle 1.67233 ( 42) link_NAG-ASN : bond 0.00453 ( 16) link_NAG-ASN : angle 4.17612 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 588 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1105 VAL cc_start: 0.8805 (t) cc_final: 0.8528 (p) REVERT: A 1210 ILE cc_start: 0.8586 (pt) cc_final: 0.8356 (mp) REVERT: A 1215 MET cc_start: 0.7881 (tpp) cc_final: 0.7473 (tpp) REVERT: A 1344 CYS cc_start: 0.7035 (m) cc_final: 0.6480 (m) REVERT: A 1356 MET cc_start: 0.5069 (mtp) cc_final: 0.4832 (mtp) REVERT: A 1369 MET cc_start: 0.7869 (tmm) cc_final: 0.7619 (tmm) REVERT: A 1371 PHE cc_start: 0.7882 (p90) cc_final: 0.7569 (p90) REVERT: A 1376 MET cc_start: 0.7159 (mtm) cc_final: 0.6598 (mtm) REVERT: A 1454 MET cc_start: 0.6709 (pmm) cc_final: 0.6508 (pmm) REVERT: A 1467 LYS cc_start: 0.7986 (mmpt) cc_final: 0.7666 (mmmm) REVERT: A 1488 LEU cc_start: 0.8623 (tp) cc_final: 0.8357 (tt) REVERT: A 1647 ARG cc_start: 0.8137 (mmm-85) cc_final: 0.7843 (mmt-90) REVERT: A 1676 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7387 (mm-30) REVERT: A 1680 MET cc_start: 0.8701 (mpp) cc_final: 0.8358 (mtm) REVERT: A 1742 ASP cc_start: 0.7880 (p0) cc_final: 0.7504 (p0) REVERT: A 1819 ILE cc_start: 0.8863 (mt) cc_final: 0.8586 (tt) REVERT: A 1870 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8193 (mtp180) REVERT: A 1917 LYS cc_start: 0.8540 (mmtm) cc_final: 0.8296 (mmtm) REVERT: A 2080 SER cc_start: 0.8764 (m) cc_final: 0.8420 (t) REVERT: A 2227 ASP cc_start: 0.7776 (t0) cc_final: 0.7572 (t0) REVERT: A 2272 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: A 2346 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8313 (mt) REVERT: A 2471 ASP cc_start: 0.7939 (t0) cc_final: 0.7670 (t0) REVERT: A 2531 GLU cc_start: 0.8229 (tp30) cc_final: 0.7862 (tp30) REVERT: A 2553 ILE cc_start: 0.8665 (mm) cc_final: 0.8303 (tt) REVERT: A 2574 PHE cc_start: 0.8792 (t80) cc_final: 0.8551 (t80) REVERT: A 2657 LEU cc_start: 0.4712 (OUTLIER) cc_final: 0.4373 (tm) REVERT: A 2673 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8608 (t) REVERT: A 2700 ARG cc_start: 0.8385 (ttt-90) cc_final: 0.8093 (ttt-90) REVERT: A 2713 GLN cc_start: 0.8430 (tp-100) cc_final: 0.8140 (mm-40) REVERT: B 1032 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8688 (tt) REVERT: B 1105 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8428 (p) REVERT: B 1175 ASN cc_start: 0.8818 (t0) cc_final: 0.8385 (t0) REVERT: B 1210 ILE cc_start: 0.8540 (pt) cc_final: 0.8114 (mm) REVERT: B 1327 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7086 (pp20) REVERT: B 1376 MET cc_start: 0.6822 (mtm) cc_final: 0.6311 (mtm) REVERT: B 1509 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7396 (pt0) REVERT: B 1542 ILE cc_start: 0.8432 (mt) cc_final: 0.8141 (mp) REVERT: B 1609 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8671 (t) REVERT: B 1742 ASP cc_start: 0.7802 (p0) cc_final: 0.7443 (p0) REVERT: B 1791 GLU cc_start: 0.8056 (mp0) cc_final: 0.7524 (mp0) REVERT: B 1805 ARG cc_start: 0.8826 (mtm-85) cc_final: 0.8489 (mtm-85) REVERT: B 1822 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8222 (mtt90) REVERT: B 1875 GLN cc_start: 0.8214 (pm20) cc_final: 0.7950 (pm20) REVERT: B 1931 VAL cc_start: 0.9212 (OUTLIER) cc_final: 0.9012 (t) REVERT: B 1938 ASP cc_start: 0.7141 (t0) cc_final: 0.6932 (t0) REVERT: B 2044 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8019 (mm-30) REVERT: B 2064 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8251 (mtp85) REVERT: B 2080 SER cc_start: 0.8783 (m) cc_final: 0.8436 (t) REVERT: B 2082 GLU cc_start: 0.7872 (tp30) cc_final: 0.7388 (tp30) REVERT: B 2114 VAL cc_start: 0.8562 (p) cc_final: 0.8312 (t) REVERT: B 2118 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.5827 (ttp-110) REVERT: B 2127 GLU cc_start: 0.8266 (mt-10) cc_final: 0.8003 (mt-10) REVERT: B 2263 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7759 (ttpp) REVERT: B 2471 ASP cc_start: 0.7977 (t0) cc_final: 0.7685 (t0) REVERT: B 2531 GLU cc_start: 0.8389 (tp30) cc_final: 0.7957 (tp30) REVERT: B 2553 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8644 (tt) REVERT: B 2574 PHE cc_start: 0.8795 (t80) cc_final: 0.8536 (t80) REVERT: B 2690 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8148 (mt-10) REVERT: B 2713 GLN cc_start: 0.8496 (tp40) cc_final: 0.8039 (mm-40) REVERT: B 2730 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7826 (ttmm) REVERT: B 2765 PHE cc_start: 0.8611 (m-80) cc_final: 0.8289 (m-80) outliers start: 97 outliers final: 57 residues processed: 645 average time/residue: 0.7006 time to fit residues: 521.3339 Evaluate side-chains 653 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 580 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1115 GLN Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1255 ASP Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1511 CYS Chi-restraints excluded: chain A residue 1534 ASP Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1591 GLN Chi-restraints excluded: chain A residue 1628 LEU Chi-restraints excluded: chain A residue 1712 ASN Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1834 ILE Chi-restraints excluded: chain A residue 1866 LYS Chi-restraints excluded: chain A residue 1868 THR Chi-restraints excluded: chain A residue 1870 ARG Chi-restraints excluded: chain A residue 1909 MET Chi-restraints excluded: chain A residue 2002 ASP Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2112 LEU Chi-restraints excluded: chain A residue 2122 ILE Chi-restraints excluded: chain A residue 2126 VAL Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2244 MET Chi-restraints excluded: chain A residue 2272 GLN Chi-restraints excluded: chain A residue 2346 LEU Chi-restraints excluded: chain A residue 2412 HIS Chi-restraints excluded: chain A residue 2427 GLN Chi-restraints excluded: chain A residue 2448 VAL Chi-restraints excluded: chain A residue 2493 ILE Chi-restraints excluded: chain A residue 2657 LEU Chi-restraints excluded: chain A residue 2673 SER Chi-restraints excluded: chain A residue 2676 LEU Chi-restraints excluded: chain A residue 2678 SER Chi-restraints excluded: chain A residue 2697 ASP Chi-restraints excluded: chain A residue 2712 GLN Chi-restraints excluded: chain B residue 1030 ILE Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain B residue 1087 MET Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1327 GLU Chi-restraints excluded: chain B residue 1337 LEU Chi-restraints excluded: chain B residue 1341 GLU Chi-restraints excluded: chain B residue 1511 CYS Chi-restraints excluded: chain B residue 1557 ILE Chi-restraints excluded: chain B residue 1609 VAL Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1663 THR Chi-restraints excluded: chain B residue 1691 THR Chi-restraints excluded: chain B residue 1730 SER Chi-restraints excluded: chain B residue 1736 GLU Chi-restraints excluded: chain B residue 1746 VAL Chi-restraints excluded: chain B residue 1769 GLN Chi-restraints excluded: chain B residue 1822 ARG Chi-restraints excluded: chain B residue 1931 VAL Chi-restraints excluded: chain B residue 1935 SER Chi-restraints excluded: chain B residue 2064 ARG Chi-restraints excluded: chain B residue 2112 LEU Chi-restraints excluded: chain B residue 2118 ARG Chi-restraints excluded: chain B residue 2122 ILE Chi-restraints excluded: chain B residue 2128 HIS Chi-restraints excluded: chain B residue 2148 MET Chi-restraints excluded: chain B residue 2263 LYS Chi-restraints excluded: chain B residue 2345 SER Chi-restraints excluded: chain B residue 2478 ASP Chi-restraints excluded: chain B residue 2553 ILE Chi-restraints excluded: chain B residue 2559 HIS Chi-restraints excluded: chain B residue 2573 MET Chi-restraints excluded: chain B residue 2622 VAL Chi-restraints excluded: chain B residue 2678 SER Chi-restraints excluded: chain B residue 2730 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 196 optimal weight: 5.9990 chunk 284 optimal weight: 0.7980 chunk 177 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 chunk 93 optimal weight: 0.6980 chunk 158 optimal weight: 0.2980 chunk 211 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 288 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1827 GLN A1946 GLN A1962 HIS A2468 ASN A2474 ASN A2559 HIS A2701 GLN A2732 GLN B1948 GLN B1962 HIS B2233 HIS B2299 GLN B2550 HIS B2701 GLN B2732 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.127676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.101413 restraints weight = 40870.382| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.11 r_work: 0.3211 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28798 Z= 0.116 Angle : 0.564 14.780 39130 Z= 0.288 Chirality : 0.046 0.405 4434 Planarity : 0.004 0.080 4994 Dihedral : 6.189 90.601 4642 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.76 % Allowed : 24.92 % Favored : 72.32 % 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: 0.42 (0.14), residues: 3500 helix: 1.32 (0.35), residues: 224 sheet: 0.96 (0.15), residues: 1190 loop : -0.21 (0.14), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B1912 TYR 0.015 0.001 TYR B2119 PHE 0.023 0.001 PHE A1371 TRP 0.009 0.001 TRP A2296 HIS 0.009 0.001 HIS A2233 Details of bonding type rmsd covalent geometry : bond 0.00259 (28750) covalent geometry : angle 0.54262 (38998) SS BOND : bond 0.00138 ( 12) SS BOND : angle 0.62122 ( 24) hydrogen bonds : bond 0.03322 ( 1065) hydrogen bonds : angle 4.69312 ( 3858) link_ALPHA1-2 : bond 0.01118 ( 2) link_ALPHA1-2 : angle 2.51338 ( 6) link_ALPHA1-3 : bond 0.01160 ( 4) link_ALPHA1-3 : angle 1.57407 ( 12) link_BETA1-4 : bond 0.00520 ( 14) link_BETA1-4 : angle 1.53852 ( 42) link_NAG-ASN : bond 0.00461 ( 16) link_NAG-ASN : angle 4.03527 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 588 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1105 VAL cc_start: 0.8780 (t) cc_final: 0.8515 (p) REVERT: A 1210 ILE cc_start: 0.8588 (pt) cc_final: 0.8358 (mp) REVERT: A 1215 MET cc_start: 0.7806 (tpp) cc_final: 0.7422 (tpp) REVERT: A 1344 CYS cc_start: 0.6968 (m) cc_final: 0.6442 (m) REVERT: A 1356 MET cc_start: 0.5072 (mtp) cc_final: 0.4838 (mtp) REVERT: A 1369 MET cc_start: 0.7879 (tmm) cc_final: 0.7638 (tmm) REVERT: A 1371 PHE cc_start: 0.7843 (p90) cc_final: 0.7541 (p90) REVERT: A 1376 MET cc_start: 0.7163 (mtm) cc_final: 0.6616 (mtm) REVERT: A 1467 LYS cc_start: 0.7950 (mmpt) cc_final: 0.7697 (mmmm) REVERT: A 1488 LEU cc_start: 0.8631 (tp) cc_final: 0.8354 (tt) REVERT: A 1647 ARG cc_start: 0.8172 (mmm-85) cc_final: 0.7890 (mmt-90) REVERT: A 1676 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7415 (mm-30) REVERT: A 1742 ASP cc_start: 0.7869 (p0) cc_final: 0.7486 (p0) REVERT: A 1819 ILE cc_start: 0.8825 (mt) cc_final: 0.8590 (tt) REVERT: A 1870 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8178 (mtp180) REVERT: A 1917 LYS cc_start: 0.8554 (mmtm) cc_final: 0.8323 (mmtm) REVERT: A 1941 MET cc_start: 0.8570 (ttm) cc_final: 0.8300 (ttp) REVERT: A 2080 SER cc_start: 0.8791 (m) cc_final: 0.8440 (t) REVERT: A 2148 MET cc_start: 0.8927 (ptm) cc_final: 0.8511 (ppp) REVERT: A 2272 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: A 2346 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8305 (mt) REVERT: A 2471 ASP cc_start: 0.7947 (t0) cc_final: 0.7676 (t0) REVERT: A 2531 GLU cc_start: 0.8219 (tp30) cc_final: 0.7849 (tp30) REVERT: A 2553 ILE cc_start: 0.8666 (mm) cc_final: 0.8317 (tt) REVERT: A 2657 LEU cc_start: 0.4706 (OUTLIER) cc_final: 0.4366 (tm) REVERT: A 2673 SER cc_start: 0.8859 (OUTLIER) cc_final: 0.8608 (t) REVERT: A 2696 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8049 (mp) REVERT: A 2713 GLN cc_start: 0.8480 (tp-100) cc_final: 0.8160 (mm-40) REVERT: B 1105 VAL cc_start: 0.8715 (OUTLIER) cc_final: 0.8416 (p) REVERT: B 1175 ASN cc_start: 0.8803 (t0) cc_final: 0.8402 (t0) REVERT: B 1210 ILE cc_start: 0.8537 (pt) cc_final: 0.8113 (mm) REVERT: B 1260 ARG cc_start: 0.7121 (pmm-80) cc_final: 0.6344 (mtt180) REVERT: B 1376 MET cc_start: 0.6853 (mtm) cc_final: 0.6356 (mtm) REVERT: B 1509 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7403 (pt0) REVERT: B 1542 ILE cc_start: 0.8422 (mt) cc_final: 0.8140 (mp) REVERT: B 1609 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8663 (t) REVERT: B 1742 ASP cc_start: 0.7840 (p0) cc_final: 0.7472 (p0) REVERT: B 1791 GLU cc_start: 0.8057 (mp0) cc_final: 0.7529 (mp0) REVERT: B 1805 ARG cc_start: 0.8813 (mtm-85) cc_final: 0.8533 (mtm-85) REVERT: B 1822 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8239 (mtt90) REVERT: B 1875 GLN cc_start: 0.8218 (pm20) cc_final: 0.7934 (pm20) REVERT: B 1954 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8123 (mt-10) REVERT: B 2044 GLU cc_start: 0.8246 (mm-30) cc_final: 0.8029 (mm-30) REVERT: B 2064 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8224 (mtp85) REVERT: B 2080 SER cc_start: 0.8780 (m) cc_final: 0.8439 (t) REVERT: B 2082 GLU cc_start: 0.7877 (tp30) cc_final: 0.7393 (tp30) REVERT: B 2114 VAL cc_start: 0.8554 (p) cc_final: 0.8290 (t) REVERT: B 2127 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7987 (mt-10) REVERT: B 2148 MET cc_start: 0.8900 (ptm) cc_final: 0.8553 (ppp) REVERT: B 2242 ARG cc_start: 0.7733 (mtt180) cc_final: 0.7474 (mtm110) REVERT: B 2263 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7756 (ttpp) REVERT: B 2471 ASP cc_start: 0.7969 (t0) cc_final: 0.7690 (t0) REVERT: B 2489 GLN cc_start: 0.8600 (mt0) cc_final: 0.8387 (mt0) REVERT: B 2531 GLU cc_start: 0.8375 (tp30) cc_final: 0.7935 (tp30) REVERT: B 2553 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8671 (tt) REVERT: B 2574 PHE cc_start: 0.8740 (t80) cc_final: 0.8525 (t80) REVERT: B 2631 LEU cc_start: 0.8795 (mt) cc_final: 0.8534 (tp) REVERT: B 2690 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8169 (mt-10) REVERT: B 2713 GLN cc_start: 0.8481 (tp40) cc_final: 0.8094 (mm-40) REVERT: B 2730 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7825 (ttmm) REVERT: B 2765 PHE cc_start: 0.8609 (m-80) cc_final: 0.8173 (m-80) outliers start: 84 outliers final: 55 residues processed: 633 average time/residue: 0.7160 time to fit residues: 523.8314 Evaluate side-chains 645 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 577 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1115 GLN Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1255 ASP Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1511 CYS Chi-restraints excluded: chain A residue 1534 ASP Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1591 GLN Chi-restraints excluded: chain A residue 1712 ASN Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1834 ILE Chi-restraints excluded: chain A residue 1868 THR Chi-restraints excluded: chain A residue 1870 ARG Chi-restraints excluded: chain A residue 1935 SER Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2112 LEU Chi-restraints excluded: chain A residue 2122 ILE Chi-restraints excluded: chain A residue 2126 VAL Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2272 GLN Chi-restraints excluded: chain A residue 2346 LEU Chi-restraints excluded: chain A residue 2412 HIS Chi-restraints excluded: chain A residue 2427 GLN Chi-restraints excluded: chain A residue 2448 VAL Chi-restraints excluded: chain A residue 2450 LYS Chi-restraints excluded: chain A residue 2657 LEU Chi-restraints excluded: chain A residue 2673 SER Chi-restraints excluded: chain A residue 2676 LEU Chi-restraints excluded: chain A residue 2678 SER Chi-restraints excluded: chain A residue 2696 LEU Chi-restraints excluded: chain A residue 2697 ASP Chi-restraints excluded: chain A residue 2712 GLN Chi-restraints excluded: chain B residue 1030 ILE Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1337 LEU Chi-restraints excluded: chain B residue 1341 GLU Chi-restraints excluded: chain B residue 1485 THR Chi-restraints excluded: chain B residue 1511 CYS Chi-restraints excluded: chain B residue 1534 ASP Chi-restraints excluded: chain B residue 1557 ILE Chi-restraints excluded: chain B residue 1609 VAL Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1663 THR Chi-restraints excluded: chain B residue 1691 THR Chi-restraints excluded: chain B residue 1730 SER Chi-restraints excluded: chain B residue 1736 GLU Chi-restraints excluded: chain B residue 1746 VAL Chi-restraints excluded: chain B residue 1769 GLN Chi-restraints excluded: chain B residue 1822 ARG Chi-restraints excluded: chain B residue 1866 LYS Chi-restraints excluded: chain B residue 1935 SER Chi-restraints excluded: chain B residue 2064 ARG Chi-restraints excluded: chain B residue 2112 LEU Chi-restraints excluded: chain B residue 2122 ILE Chi-restraints excluded: chain B residue 2128 HIS Chi-restraints excluded: chain B residue 2263 LYS Chi-restraints excluded: chain B residue 2478 ASP Chi-restraints excluded: chain B residue 2553 ILE Chi-restraints excluded: chain B residue 2559 HIS Chi-restraints excluded: chain B residue 2573 MET Chi-restraints excluded: chain B residue 2622 VAL Chi-restraints excluded: chain B residue 2678 SER Chi-restraints excluded: chain B residue 2696 LEU Chi-restraints excluded: chain B residue 2697 ASP Chi-restraints excluded: chain B residue 2730 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 99 optimal weight: 0.9990 chunk 285 optimal weight: 2.9990 chunk 341 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 338 optimal weight: 0.6980 chunk 343 optimal weight: 5.9990 chunk 173 optimal weight: 0.8980 chunk 238 optimal weight: 0.6980 chunk 185 optimal weight: 0.0980 chunk 189 optimal weight: 2.9990 chunk 302 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1827 GLN A1946 GLN A1962 HIS A2299 GLN A2474 ASN A2550 HIS A2559 HIS A2701 GLN A2732 GLN B1948 GLN B1962 HIS B2233 HIS B2299 GLN B2550 HIS B2701 GLN B2732 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.127864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.101616 restraints weight = 40735.867| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.11 r_work: 0.3212 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28798 Z= 0.117 Angle : 0.571 14.874 39130 Z= 0.291 Chirality : 0.046 0.400 4434 Planarity : 0.004 0.084 4994 Dihedral : 6.078 89.333 4641 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.20 % Favored : 97.77 % Rotamer: Outliers : 2.63 % Allowed : 25.31 % Favored : 72.06 % 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: 0.46 (0.15), residues: 3500 helix: 1.43 (0.35), residues: 224 sheet: 0.98 (0.15), residues: 1190 loop : -0.19 (0.14), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B1912 TYR 0.015 0.001 TYR B2119 PHE 0.023 0.001 PHE A1371 TRP 0.009 0.001 TRP B2296 HIS 0.009 0.001 HIS A2233 Details of bonding type rmsd covalent geometry : bond 0.00261 (28750) covalent geometry : angle 0.55050 (38998) SS BOND : bond 0.00126 ( 12) SS BOND : angle 0.59328 ( 24) hydrogen bonds : bond 0.03310 ( 1065) hydrogen bonds : angle 4.65730 ( 3858) link_ALPHA1-2 : bond 0.01074 ( 2) link_ALPHA1-2 : angle 2.51915 ( 6) link_ALPHA1-3 : bond 0.01122 ( 4) link_ALPHA1-3 : angle 1.56030 ( 12) link_BETA1-4 : bond 0.00522 ( 14) link_BETA1-4 : angle 1.51820 ( 42) link_NAG-ASN : bond 0.00465 ( 16) link_NAG-ASN : angle 4.01489 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 589 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1105 VAL cc_start: 0.8779 (t) cc_final: 0.8510 (p) REVERT: A 1210 ILE cc_start: 0.8571 (pt) cc_final: 0.8334 (mp) REVERT: A 1215 MET cc_start: 0.7812 (tpp) cc_final: 0.7426 (tpp) REVERT: A 1344 CYS cc_start: 0.6974 (m) cc_final: 0.6438 (m) REVERT: A 1356 MET cc_start: 0.5069 (mtp) cc_final: 0.4837 (mtp) REVERT: A 1369 MET cc_start: 0.7848 (tmm) cc_final: 0.7596 (tmm) REVERT: A 1371 PHE cc_start: 0.7837 (p90) cc_final: 0.7554 (p90) REVERT: A 1376 MET cc_start: 0.7142 (mtm) cc_final: 0.6594 (mtm) REVERT: A 1467 LYS cc_start: 0.7936 (mmpt) cc_final: 0.7658 (mmmm) REVERT: A 1488 LEU cc_start: 0.8601 (tp) cc_final: 0.8329 (tt) REVERT: A 1676 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7370 (mm-30) REVERT: A 1742 ASP cc_start: 0.7877 (p0) cc_final: 0.7496 (p0) REVERT: A 1819 ILE cc_start: 0.8824 (mt) cc_final: 0.8578 (tt) REVERT: A 1826 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8291 (mt-10) REVERT: A 1870 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8174 (mtp180) REVERT: A 1917 LYS cc_start: 0.8532 (mmtm) cc_final: 0.8297 (mmtm) REVERT: A 1941 MET cc_start: 0.8559 (ttm) cc_final: 0.8276 (ttp) REVERT: A 2080 SER cc_start: 0.8797 (m) cc_final: 0.8427 (t) REVERT: A 2148 MET cc_start: 0.8921 (ptm) cc_final: 0.8678 (ppp) REVERT: A 2219 ARG cc_start: 0.7968 (ttm110) cc_final: 0.7683 (ttp80) REVERT: A 2272 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: A 2346 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8299 (mt) REVERT: A 2471 ASP cc_start: 0.7918 (t0) cc_final: 0.7646 (t0) REVERT: A 2531 GLU cc_start: 0.8201 (tp30) cc_final: 0.7807 (tp30) REVERT: A 2553 ILE cc_start: 0.8651 (mm) cc_final: 0.8304 (tt) REVERT: A 2657 LEU cc_start: 0.4727 (OUTLIER) cc_final: 0.4381 (tm) REVERT: A 2673 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8601 (t) REVERT: A 2696 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8053 (mp) REVERT: A 2713 GLN cc_start: 0.8496 (tp-100) cc_final: 0.8155 (mm-40) REVERT: B 1105 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8398 (p) REVERT: B 1175 ASN cc_start: 0.8803 (t0) cc_final: 0.8403 (t0) REVERT: B 1210 ILE cc_start: 0.8529 (pt) cc_final: 0.8091 (mm) REVERT: B 1215 MET cc_start: 0.7835 (tpp) cc_final: 0.7623 (tpp) REVERT: B 1260 ARG cc_start: 0.7100 (pmm-80) cc_final: 0.6306 (mtt180) REVERT: B 1376 MET cc_start: 0.6845 (mtm) cc_final: 0.6354 (mtm) REVERT: B 1509 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7390 (pt0) REVERT: B 1542 ILE cc_start: 0.8402 (mt) cc_final: 0.8110 (mp) REVERT: B 1609 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8646 (t) REVERT: B 1742 ASP cc_start: 0.7844 (p0) cc_final: 0.7489 (p0) REVERT: B 1791 GLU cc_start: 0.8053 (mp0) cc_final: 0.7754 (mp0) REVERT: B 1822 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8245 (mtt90) REVERT: B 1875 GLN cc_start: 0.8201 (pm20) cc_final: 0.7906 (pm20) REVERT: B 1954 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8102 (mt-10) REVERT: B 2044 GLU cc_start: 0.8258 (mm-30) cc_final: 0.8029 (mm-30) REVERT: B 2064 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8197 (mtp85) REVERT: B 2080 SER cc_start: 0.8773 (m) cc_final: 0.8431 (t) REVERT: B 2082 GLU cc_start: 0.7868 (tp30) cc_final: 0.7332 (tp30) REVERT: B 2114 VAL cc_start: 0.8542 (p) cc_final: 0.8276 (t) REVERT: B 2127 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7998 (mt-10) REVERT: B 2148 MET cc_start: 0.8887 (ptm) cc_final: 0.8523 (ppp) REVERT: B 2263 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7650 (ttpp) REVERT: B 2471 ASP cc_start: 0.7931 (t0) cc_final: 0.7662 (t0) REVERT: B 2489 GLN cc_start: 0.8609 (mt0) cc_final: 0.8389 (mt0) REVERT: B 2531 GLU cc_start: 0.8369 (tp30) cc_final: 0.7925 (tp30) REVERT: B 2553 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8679 (tt) REVERT: B 2574 PHE cc_start: 0.8743 (t80) cc_final: 0.8519 (t80) REVERT: B 2631 LEU cc_start: 0.8782 (mt) cc_final: 0.8525 (tp) REVERT: B 2690 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8129 (mt-10) REVERT: B 2696 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8350 (mt) REVERT: B 2713 GLN cc_start: 0.8484 (tp40) cc_final: 0.8079 (mm-40) REVERT: B 2730 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7807 (ttmm) REVERT: B 2765 PHE cc_start: 0.8606 (m-80) cc_final: 0.8178 (m-80) outliers start: 80 outliers final: 53 residues processed: 632 average time/residue: 0.6960 time to fit residues: 507.7992 Evaluate side-chains 640 residues out of total 3042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 573 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1115 GLN Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1255 ASP Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1511 CYS Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1591 GLN Chi-restraints excluded: chain A residue 1712 ASN Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1746 VAL Chi-restraints excluded: chain A residue 1834 ILE Chi-restraints excluded: chain A residue 1866 LYS Chi-restraints excluded: chain A residue 1868 THR Chi-restraints excluded: chain A residue 1870 ARG Chi-restraints excluded: chain A residue 1909 MET Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2112 LEU Chi-restraints excluded: chain A residue 2122 ILE Chi-restraints excluded: chain A residue 2126 VAL Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2272 GLN Chi-restraints excluded: chain A residue 2346 LEU Chi-restraints excluded: chain A residue 2412 HIS Chi-restraints excluded: chain A residue 2427 GLN Chi-restraints excluded: chain A residue 2448 VAL Chi-restraints excluded: chain A residue 2657 LEU Chi-restraints excluded: chain A residue 2673 SER Chi-restraints excluded: chain A residue 2676 LEU Chi-restraints excluded: chain A residue 2678 SER Chi-restraints excluded: chain A residue 2696 LEU Chi-restraints excluded: chain A residue 2712 GLN Chi-restraints excluded: chain B residue 1030 ILE Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1341 GLU Chi-restraints excluded: chain B residue 1485 THR Chi-restraints excluded: chain B residue 1511 CYS Chi-restraints excluded: chain B residue 1557 ILE Chi-restraints excluded: chain B residue 1609 VAL Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1663 THR Chi-restraints excluded: chain B residue 1691 THR Chi-restraints excluded: chain B residue 1730 SER Chi-restraints excluded: chain B residue 1736 GLU Chi-restraints excluded: chain B residue 1746 VAL Chi-restraints excluded: chain B residue 1769 GLN Chi-restraints excluded: chain B residue 1822 ARG Chi-restraints excluded: chain B residue 1866 LYS Chi-restraints excluded: chain B residue 1935 SER Chi-restraints excluded: chain B residue 2064 ARG Chi-restraints excluded: chain B residue 2112 LEU Chi-restraints excluded: chain B residue 2122 ILE Chi-restraints excluded: chain B residue 2128 HIS Chi-restraints excluded: chain B residue 2263 LYS Chi-restraints excluded: chain B residue 2345 SER Chi-restraints excluded: chain B residue 2478 ASP Chi-restraints excluded: chain B residue 2553 ILE Chi-restraints excluded: chain B residue 2559 HIS Chi-restraints excluded: chain B residue 2573 MET Chi-restraints excluded: chain B residue 2622 VAL Chi-restraints excluded: chain B residue 2678 SER Chi-restraints excluded: chain B residue 2696 LEU Chi-restraints excluded: chain B residue 2697 ASP Chi-restraints excluded: chain B residue 2730 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 73 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 244 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 chunk 85 optimal weight: 0.1980 chunk 153 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 214 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1827 GLN A1946 GLN A1962 HIS A2299 GLN A2468 ASN A2474 ASN A2550 HIS A2559 HIS A2701 GLN A2732 GLN B1111 GLN B1962 HIS B2233 HIS B2299 GLN B2550 HIS B2701 GLN B2732 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.127510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.101359 restraints weight = 41074.746| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.11 r_work: 0.3207 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28798 Z= 0.124 Angle : 0.569 14.911 39130 Z= 0.290 Chirality : 0.046 0.397 4434 Planarity : 0.004 0.084 4994 Dihedral : 5.976 87.339 4641 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.43 % Favored : 97.54 % Rotamer: Outliers : 2.33 % Allowed : 25.61 % Favored : 72.06 % 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: 0.47 (0.15), residues: 3500 helix: 1.43 (0.35), residues: 224 sheet: 1.00 (0.15), residues: 1190 loop : -0.18 (0.14), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B1912 TYR 0.014 0.001 TYR B2119 PHE 0.022 0.001 PHE A1371 TRP 0.009 0.001 TRP B2296 HIS 0.009 0.001 HIS A2233 Details of bonding type rmsd covalent geometry : bond 0.00281 (28750) covalent geometry : angle 0.54828 (38998) SS BOND : bond 0.00130 ( 12) SS BOND : angle 0.59252 ( 24) hydrogen bonds : bond 0.03316 ( 1065) hydrogen bonds : angle 4.63118 ( 3858) link_ALPHA1-2 : bond 0.01142 ( 2) link_ALPHA1-2 : angle 2.54024 ( 6) link_ALPHA1-3 : bond 0.01127 ( 4) link_ALPHA1-3 : angle 1.52284 ( 12) link_BETA1-4 : bond 0.00524 ( 14) link_BETA1-4 : angle 1.51762 ( 42) link_NAG-ASN : bond 0.00464 ( 16) link_NAG-ASN : angle 4.02205 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13043.03 seconds wall clock time: 222 minutes 9.32 seconds (13329.32 seconds total)