Starting phenix.real_space_refine on Sat Feb 24 07:08:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yxx_14368/02_2024/7yxx_14368.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yxx_14368/02_2024/7yxx_14368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yxx_14368/02_2024/7yxx_14368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yxx_14368/02_2024/7yxx_14368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yxx_14368/02_2024/7yxx_14368.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yxx_14368/02_2024/7yxx_14368.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.034 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 288 5.16 5 C 27121 2.51 5 N 7259 2.21 5 O 7689 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 500": "OD1" <-> "OD2" Residue "A ASP 543": "OD1" <-> "OD2" Residue "A ASP 545": "OD1" <-> "OD2" Residue "A ASP 601": "OD1" <-> "OD2" Residue "A PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1503": "OE1" <-> "OE2" Residue "A TYR 1527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2347": "OE1" <-> "OE2" Residue "A TYR 2402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 601": "OD1" <-> "OD2" Residue "B PHE 1358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2167": "OE1" <-> "OE2" Residue "C ASP 470": "OD1" <-> "OD2" Residue "C TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 543": "OD1" <-> "OD2" Residue "C ASP 545": "OD1" <-> "OD2" Residue "C TYR 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1525": "OE1" <-> "OE2" Residue "C GLU 1755": "OE1" <-> "OE2" Residue "C PHE 1800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2291": "OE1" <-> "OE2" Residue "C TYR 2327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2331": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 42357 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 14155 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1754, 14144 Classifications: {'peptide': 1754} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 68, 'TRANS': 1685} Chain breaks: 16 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Conformer: "B" Number of residues, atoms: 1754, 14144 Classifications: {'peptide': 1754} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 68, 'TRANS': 1685} Chain breaks: 16 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 bond proxies already assigned to first conformer: 14438 Chain: "B" Number of atoms: 14155 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1754, 14144 Classifications: {'peptide': 1754} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 68, 'TRANS': 1685} Chain breaks: 16 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Conformer: "B" Number of residues, atoms: 1754, 14144 Classifications: {'peptide': 1754} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 68, 'TRANS': 1685} Chain breaks: 16 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 bond proxies already assigned to first conformer: 14438 Chain: "C" Number of atoms: 14047 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1741, 14036 Classifications: {'peptide': 1741} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 68, 'TRANS': 1672} Chain breaks: 16 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Conformer: "B" Number of residues, atoms: 1741, 14036 Classifications: {'peptide': 1741} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 68, 'TRANS': 1672} Chain breaks: 16 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 bond proxies already assigned to first conformer: 14328 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG A1745 " occ=0.60 ... (20 atoms not shown) pdb=" NH2BARG A1745 " occ=0.40 residue: pdb=" N AARG B1745 " occ=0.60 ... (20 atoms not shown) pdb=" NH2BARG B1745 " occ=0.40 residue: pdb=" N AARG C1745 " occ=0.60 ... (20 atoms not shown) pdb=" NH2BARG C1745 " occ=0.40 Time building chain proxies: 38.89, per 1000 atoms: 0.92 Number of scatterers: 42357 At special positions: 0 Unit cell: (152.256, 213.824, 222.976, 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 288 16.00 O 7689 8.00 N 7259 7.00 C 27121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.22 Conformation dependent library (CDL) restraints added in 15.2 seconds 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10002 Finding SS restraints... Secondary structure from input PDB file: 267 helices and 28 sheets defined 67.4% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.02 Creating SS restraints... Processing helix chain 'A' and resid 325 through 345 Processing helix chain 'A' and resid 347 through 365 Processing helix chain 'A' and resid 384 through 394 removed outlier: 3.540A pdb=" N ASN A 393 " --> pdb=" O TRP A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 403 removed outlier: 3.672A pdb=" N ARG A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASP A 402 " --> pdb=" O ILE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 423 removed outlier: 3.550A pdb=" N LYS A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS A 415 " --> pdb=" O GLU A 411 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A 423 " --> pdb=" O PHE A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 437 Processing helix chain 'A' and resid 442 through 457 removed outlier: 3.646A pdb=" N VAL A 446 " --> pdb=" O HIS A 442 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 479 removed outlier: 3.626A pdb=" N ASN A 478 " --> pdb=" O ALA A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 497 removed outlier: 3.639A pdb=" N ALA A 495 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP A 497 " --> pdb=" O ARG A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 516 removed outlier: 4.056A pdb=" N LYS A 506 " --> pdb=" O VAL A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 539 removed outlier: 3.967A pdb=" N LEU A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 560 removed outlier: 3.962A pdb=" N GLN A 550 " --> pdb=" O THR A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 580 removed outlier: 3.848A pdb=" N LYS A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 576 " --> pdb=" O GLN A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 removed outlier: 4.224A pdb=" N ASN A 604 " --> pdb=" O HIS A 600 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASN A 609 " --> pdb=" O GLN A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 631 removed outlier: 3.668A pdb=" N GLU A 618 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 665 Processing helix chain 'A' and resid 673 through 683 Processing helix chain 'A' and resid 690 through 705 removed outlier: 3.917A pdb=" N ARG A 694 " --> pdb=" O TYR A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 723 removed outlier: 3.546A pdb=" N PHE A 720 " --> pdb=" O ASN A 716 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 751 removed outlier: 3.848A pdb=" N LYS A 738 " --> pdb=" O GLU A 734 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N CYS A 739 " --> pdb=" O ASN A 735 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 780 removed outlier: 3.866A pdb=" N TRP A 775 " --> pdb=" O LEU A 771 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 799 removed outlier: 3.795A pdb=" N ASN A 799 " --> pdb=" O GLU A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 831 removed outlier: 4.052A pdb=" N THR A 829 " --> pdb=" O ALA A 825 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU A 830 " --> pdb=" O SER A 826 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N CYS A 831 " --> pdb=" O TYR A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 866 removed outlier: 3.756A pdb=" N GLU A 859 " --> pdb=" O THR A 855 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS A 864 " --> pdb=" O TYR A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1031 removed outlier: 3.860A pdb=" N LEU A1021 " --> pdb=" O TYR A1017 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A1023 " --> pdb=" O SER A1019 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A1029 " --> pdb=" O ALA A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1046 removed outlier: 3.890A pdb=" N ARG A1037 " --> pdb=" O MET A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1066 removed outlier: 3.509A pdb=" N ARG A1058 " --> pdb=" O ILE A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1081 Processing helix chain 'A' and resid 1084 through 1100 removed outlier: 3.950A pdb=" N VAL A1088 " --> pdb=" O SER A1084 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A1089 " --> pdb=" O ALA A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1121 removed outlier: 4.442A pdb=" N PHE A1115 " --> pdb=" O SER A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1132 Processing helix chain 'A' and resid 1133 through 1136 removed outlier: 4.269A pdb=" N LEU A1136 " --> pdb=" O ASN A1133 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1133 through 1136' Processing helix chain 'A' and resid 1140 through 1164 removed outlier: 3.657A pdb=" N LYS A1153 " --> pdb=" O LEU A1149 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU A1157 " --> pdb=" O LYS A1153 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR A1164 " --> pdb=" O THR A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1250 removed outlier: 3.701A pdb=" N ILE A1239 " --> pdb=" O ASP A1235 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A1241 " --> pdb=" O CYS A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1252 No H-bonds generated for 'chain 'A' and resid 1251 through 1252' Processing helix chain 'A' and resid 1253 through 1257 Processing helix chain 'A' and resid 1261 through 1269 removed outlier: 3.783A pdb=" N THR A1265 " --> pdb=" O ASN A1261 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A1268 " --> pdb=" O ILE A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1299 removed outlier: 3.802A pdb=" N ALA A1288 " --> pdb=" O VAL A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1307 removed outlier: 3.578A pdb=" N ALA A1305 " --> pdb=" O THR A1301 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A1306 " --> pdb=" O ALA A1302 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A1307 " --> pdb=" O LEU A1303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1301 through 1307' Processing helix chain 'A' and resid 1313 through 1321 Processing helix chain 'A' and resid 1326 through 1342 removed outlier: 3.547A pdb=" N MET A1339 " --> pdb=" O GLN A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1359 Processing helix chain 'A' and resid 1364 through 1369 removed outlier: 3.886A pdb=" N ALA A1369 " --> pdb=" O ALA A1365 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1373 removed outlier: 4.072A pdb=" N GLY A1373 " --> pdb=" O LYS A1370 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1370 through 1373' Processing helix chain 'A' and resid 1374 through 1389 Processing helix chain 'A' and resid 1396 through 1417 Processing helix chain 'A' and resid 1423 through 1439 removed outlier: 3.802A pdb=" N LEU A1427 " --> pdb=" O GLU A1423 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A1439 " --> pdb=" O LYS A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1465 Processing helix chain 'A' and resid 1469 through 1479 removed outlier: 3.825A pdb=" N VAL A1473 " --> pdb=" O PRO A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1510 Processing helix chain 'A' and resid 1512 through 1528 removed outlier: 4.815A pdb=" N GLN A1518 " --> pdb=" O ARG A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1578 removed outlier: 4.606A pdb=" N VAL A1571 " --> pdb=" O TYR A1567 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A1577 " --> pdb=" O GLN A1573 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A1578 " --> pdb=" O GLN A1574 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1587 Processing helix chain 'A' and resid 1633 through 1657 Processing helix chain 'A' and resid 1664 through 1671 Processing helix chain 'A' and resid 1685 through 1704 Processing helix chain 'A' and resid 1708 through 1714 Processing helix chain 'A' and resid 1749 through 1760 removed outlier: 3.651A pdb=" N GLN A1756 " --> pdb=" O ASP A1752 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR A1757 " --> pdb=" O SER A1753 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A1758 " --> pdb=" O LEU A1754 " (cutoff:3.500A) Processing helix chain 'A' and resid 1764 through 1768 Processing helix chain 'A' and resid 1825 through 1827 No H-bonds generated for 'chain 'A' and resid 1825 through 1827' Processing helix chain 'A' and resid 1828 through 1837 Processing helix chain 'A' and resid 1912 through 1920 Processing helix chain 'A' and resid 1988 through 2005 removed outlier: 3.567A pdb=" N MET A2003 " --> pdb=" O MET A1999 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A2004 " --> pdb=" O HIS A2000 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A2005 " --> pdb=" O ASN A2001 " (cutoff:3.500A) Processing helix chain 'A' and resid 2006 through 2019 Processing helix chain 'A' and resid 2020 through 2025 removed outlier: 3.918A pdb=" N ASN A2025 " --> pdb=" O VAL A2022 " (cutoff:3.500A) Processing helix chain 'A' and resid 2034 through 2055 removed outlier: 3.526A pdb=" N PHE A2053 " --> pdb=" O ALA A2049 " (cutoff:3.500A) Processing helix chain 'A' and resid 2060 through 2065 Processing helix chain 'A' and resid 2067 through 2079 removed outlier: 3.529A pdb=" N ILE A2076 " --> pdb=" O ASP A2072 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A2077 " --> pdb=" O ALA A2073 " (cutoff:3.500A) Processing helix chain 'A' and resid 2081 through 2093 removed outlier: 3.685A pdb=" N ARG A2085 " --> pdb=" O SER A2081 " (cutoff:3.500A) Processing helix chain 'A' and resid 2098 through 2105 Processing helix chain 'A' and resid 2109 through 2127 Processing helix chain 'A' and resid 2151 through 2163 removed outlier: 3.530A pdb=" N LEU A2163 " --> pdb=" O ALA A2159 " (cutoff:3.500A) Processing helix chain 'A' and resid 2167 through 2171 Processing helix chain 'A' and resid 2175 through 2187 removed outlier: 3.502A pdb=" N PHE A2179 " --> pdb=" O LEU A2175 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE A2182 " --> pdb=" O TYR A2178 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2199 Processing helix chain 'A' and resid 2200 through 2208 Processing helix chain 'A' and resid 2225 through 2238 Processing helix chain 'A' and resid 2241 through 2245 removed outlier: 3.871A pdb=" N MET A2245 " --> pdb=" O SER A2242 " (cutoff:3.500A) Processing helix chain 'A' and resid 2272 through 2280 removed outlier: 3.942A pdb=" N ILE A2278 " --> pdb=" O ASN A2274 " (cutoff:3.500A) Processing helix chain 'A' and resid 2283 through 2292 removed outlier: 3.541A pdb=" N LYS A2287 " --> pdb=" O THR A2283 " (cutoff:3.500A) Processing helix chain 'A' and resid 2296 through 2308 removed outlier: 4.159A pdb=" N VAL A2300 " --> pdb=" O SER A2296 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A2301 " --> pdb=" O GLU A2297 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TRP A2308 " --> pdb=" O ARG A2304 " (cutoff:3.500A) Processing helix chain 'A' and resid 2310 through 2327 Processing helix chain 'A' and resid 2329 through 2332 Processing helix chain 'A' and resid 2333 through 2345 Processing helix chain 'A' and resid 2350 through 2360 Processing helix chain 'A' and resid 2368 through 2376 Processing helix chain 'A' and resid 2380 through 2398 removed outlier: 3.531A pdb=" N ALA A2384 " --> pdb=" O TYR A2380 " (cutoff:3.500A) Processing helix chain 'A' and resid 2399 through 2404 Processing helix chain 'A' and resid 2408 through 2428 removed outlier: 3.539A pdb=" N LYS A2412 " --> pdb=" O ASN A2408 " (cutoff:3.500A) Processing helix chain 'A' and resid 2461 through 2474 removed outlier: 3.502A pdb=" N GLU A2472 " --> pdb=" O ALA A2468 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A2473 " --> pdb=" O LYS A2469 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 345 removed outlier: 3.526A pdb=" N LYS B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 365 Processing helix chain 'B' and resid 382 through 394 removed outlier: 3.825A pdb=" N MET B 386 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 403 removed outlier: 4.499A pdb=" N ASP B 402 " --> pdb=" O ILE B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 423 removed outlier: 3.546A pdb=" N VAL B 410 " --> pdb=" O GLN B 406 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE B 416 " --> pdb=" O LYS B 412 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU B 423 " --> pdb=" O PHE B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 436 Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 442 through 457 Processing helix chain 'B' and resid 458 through 460 No H-bonds generated for 'chain 'B' and resid 458 through 460' Processing helix chain 'B' and resid 461 through 479 removed outlier: 3.672A pdb=" N HIS B 467 " --> pdb=" O GLU B 463 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN B 478 " --> pdb=" O ALA B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 497 Processing helix chain 'B' and resid 502 through 516 removed outlier: 4.117A pdb=" N LYS B 506 " --> pdb=" O VAL B 502 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN B 509 " --> pdb=" O HIS B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 539 removed outlier: 3.706A pdb=" N LEU B 527 " --> pdb=" O ASP B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.515A pdb=" N LEU B 559 " --> pdb=" O PHE B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 580 Processing helix chain 'B' and resid 599 through 609 removed outlier: 3.940A pdb=" N ILE B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN B 604 " --> pdb=" O HIS B 600 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASN B 609 " --> pdb=" O GLN B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 630 removed outlier: 3.724A pdb=" N GLU B 618 " --> pdb=" O THR B 614 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 623 " --> pdb=" O ASN B 619 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER B 626 " --> pdb=" O THR B 622 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 665 Processing helix chain 'B' and resid 673 through 682 removed outlier: 4.162A pdb=" N GLN B 679 " --> pdb=" O PRO B 675 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 680 " --> pdb=" O GLN B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 705 removed outlier: 3.896A pdb=" N ARG B 694 " --> pdb=" O TYR B 690 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET B 705 " --> pdb=" O TYR B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 723 removed outlier: 4.347A pdb=" N GLU B 721 " --> pdb=" O LYS B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 752 removed outlier: 3.752A pdb=" N LYS B 738 " --> pdb=" O GLU B 734 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N CYS B 739 " --> pdb=" O ASN B 735 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG B 750 " --> pdb=" O ALA B 746 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU B 751 " --> pdb=" O VAL B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 780 removed outlier: 3.792A pdb=" N TRP B 775 " --> pdb=" O LEU B 771 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG B 776 " --> pdb=" O ASP B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 798 Processing helix chain 'B' and resid 807 through 831 removed outlier: 3.866A pdb=" N THR B 829 " --> pdb=" O ALA B 825 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 830 " --> pdb=" O SER B 826 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS B 831 " --> pdb=" O TYR B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 866 removed outlier: 3.598A pdb=" N ALA B 847 " --> pdb=" O ALA B 843 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 848 " --> pdb=" O ARG B 844 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 859 " --> pdb=" O THR B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1031 removed outlier: 3.803A pdb=" N LEU B1021 " --> pdb=" O TYR B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1046 removed outlier: 4.534A pdb=" N ARG B1037 " --> pdb=" O MET B1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1065 Processing helix chain 'B' and resid 1077 through 1081 Processing helix chain 'B' and resid 1085 through 1100 removed outlier: 4.120A pdb=" N LEU B1089 " --> pdb=" O ALA B1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 1111 through 1121 removed outlier: 4.552A pdb=" N PHE B1115 " --> pdb=" O SER B1111 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY B1121 " --> pdb=" O PHE B1117 " (cutoff:3.500A) Processing helix chain 'B' and resid 1121 through 1132 removed outlier: 3.593A pdb=" N LEU B1127 " --> pdb=" O LEU B1123 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B1130 " --> pdb=" O VAL B1126 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1163 removed outlier: 3.675A pdb=" N ARG B1145 " --> pdb=" O MET B1141 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B1157 " --> pdb=" O LYS B1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 1235 through 1252 removed outlier: 3.508A pdb=" N ILE B1239 " --> pdb=" O ASP B1235 " (cutoff:3.500A) Processing helix chain 'B' and resid 1253 through 1257 Processing helix chain 'B' and resid 1262 through 1269 removed outlier: 3.657A pdb=" N LYS B1266 " --> pdb=" O GLU B1262 " (cutoff:3.500A) Processing helix chain 'B' and resid 1280 through 1299 removed outlier: 3.573A pdb=" N LEU B1289 " --> pdb=" O CYS B1285 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B1298 " --> pdb=" O LEU B1294 " (cutoff:3.500A) Processing helix chain 'B' and resid 1301 through 1309 removed outlier: 3.751A pdb=" N ALA B1305 " --> pdb=" O THR B1301 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B1306 " --> pdb=" O ALA B1302 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS B1308 " --> pdb=" O ASP B1304 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU B1309 " --> pdb=" O ALA B1305 " (cutoff:3.500A) Processing helix chain 'B' and resid 1313 through 1319 Processing helix chain 'B' and resid 1325 through 1342 removed outlier: 3.643A pdb=" N ARG B1329 " --> pdb=" O SER B1325 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B1334 " --> pdb=" O GLN B1330 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B1335 " --> pdb=" O VAL B1331 " (cutoff:3.500A) Processing helix chain 'B' and resid 1347 through 1358 Processing helix chain 'B' and resid 1364 through 1369 Processing helix chain 'B' and resid 1372 through 1389 removed outlier: 4.241A pdb=" N THR B1377 " --> pdb=" O GLY B1373 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B1378 " --> pdb=" O ASP B1374 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B1379 " --> pdb=" O TYR B1375 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN B1384 " --> pdb=" O ARG B1380 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR B1387 " --> pdb=" O LEU B1383 " (cutoff:3.500A) Processing helix chain 'B' and resid 1397 through 1417 removed outlier: 3.522A pdb=" N ASN B1401 " --> pdb=" O GLU B1397 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE B1410 " --> pdb=" O TRP B1406 " (cutoff:3.500A) Processing helix chain 'B' and resid 1423 through 1438 removed outlier: 3.504A pdb=" N LEU B1427 " --> pdb=" O GLU B1423 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B1436 " --> pdb=" O GLY B1432 " (cutoff:3.500A) Processing helix chain 'B' and resid 1443 through 1448 Processing helix chain 'B' and resid 1457 through 1466 Processing helix chain 'B' and resid 1469 through 1479 Processing helix chain 'B' and resid 1494 through 1510 removed outlier: 3.676A pdb=" N ILE B1498 " --> pdb=" O SER B1494 " (cutoff:3.500A) Processing helix chain 'B' and resid 1512 through 1527 removed outlier: 3.805A pdb=" N LEU B1516 " --> pdb=" O CYS B1512 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN B1518 " --> pdb=" O ARG B1514 " (cutoff:3.500A) Processing helix chain 'B' and resid 1565 through 1578 removed outlier: 3.947A pdb=" N ASN B1569 " --> pdb=" O THR B1565 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL B1571 " --> pdb=" O TYR B1567 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET B1577 " --> pdb=" O GLN B1573 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE B1578 " --> pdb=" O GLN B1574 " (cutoff:3.500A) Processing helix chain 'B' and resid 1578 through 1587 removed outlier: 3.503A pdb=" N LEU B1586 " --> pdb=" O ARG B1582 " (cutoff:3.500A) Processing helix chain 'B' and resid 1633 through 1657 removed outlier: 3.740A pdb=" N ILE B1650 " --> pdb=" O HIS B1646 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B1656 " --> pdb=" O GLY B1652 " (cutoff:3.500A) Processing helix chain 'B' and resid 1664 through 1671 Processing helix chain 'B' and resid 1685 through 1704 Processing helix chain 'B' and resid 1708 through 1714 Processing helix chain 'B' and resid 1749 through 1760 removed outlier: 3.843A pdb=" N TYR B1757 " --> pdb=" O SER B1753 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B1758 " --> pdb=" O LEU B1754 " (cutoff:3.500A) Processing helix chain 'B' and resid 1764 through 1768 Processing helix chain 'B' and resid 1825 through 1827 No H-bonds generated for 'chain 'B' and resid 1825 through 1827' Processing helix chain 'B' and resid 1828 through 1837 Processing helix chain 'B' and resid 1912 through 1920 removed outlier: 4.018A pdb=" N MET B1916 " --> pdb=" O ASP B1912 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS B1917 " --> pdb=" O ASP B1913 " (cutoff:3.500A) Processing helix chain 'B' and resid 1962 through 1966 Processing helix chain 'B' and resid 1988 through 2005 removed outlier: 3.518A pdb=" N TYR B2005 " --> pdb=" O ASN B2001 " (cutoff:3.500A) Processing helix chain 'B' and resid 2006 through 2019 Processing helix chain 'B' and resid 2034 through 2055 Processing helix chain 'B' and resid 2066 through 2079 removed outlier: 3.961A pdb=" N TRP B2070 " --> pdb=" O SER B2066 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B2077 " --> pdb=" O ALA B2073 " (cutoff:3.500A) Processing helix chain 'B' and resid 2081 through 2093 removed outlier: 3.645A pdb=" N ALA B2089 " --> pdb=" O ARG B2085 " (cutoff:3.500A) Processing helix chain 'B' and resid 2098 through 2105 Processing helix chain 'B' and resid 2109 through 2127 Processing helix chain 'B' and resid 2151 through 2163 Processing helix chain 'B' and resid 2167 through 2171 Processing helix chain 'B' and resid 2175 through 2188 removed outlier: 4.227A pdb=" N PHE B2182 " --> pdb=" O TYR B2178 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2199 Processing helix chain 'B' and resid 2200 through 2208 Processing helix chain 'B' and resid 2225 through 2238 removed outlier: 3.576A pdb=" N SER B2230 " --> pdb=" O GLY B2226 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS B2238 " --> pdb=" O GLN B2234 " (cutoff:3.500A) Processing helix chain 'B' and resid 2272 through 2280 removed outlier: 3.535A pdb=" N ILE B2278 " --> pdb=" O ASN B2274 " (cutoff:3.500A) Processing helix chain 'B' and resid 2283 through 2292 removed outlier: 3.563A pdb=" N ILE B2290 " --> pdb=" O VAL B2286 " (cutoff:3.500A) Processing helix chain 'B' and resid 2297 through 2307 Processing helix chain 'B' and resid 2310 through 2327 Processing helix chain 'B' and resid 2333 through 2345 removed outlier: 3.828A pdb=" N GLN B2342 " --> pdb=" O ASP B2338 " (cutoff:3.500A) Processing helix chain 'B' and resid 2350 through 2360 removed outlier: 3.522A pdb=" N ALA B2358 " --> pdb=" O ARG B2354 " (cutoff:3.500A) Processing helix chain 'B' and resid 2368 through 2376 removed outlier: 3.655A pdb=" N GLN B2374 " --> pdb=" O PHE B2370 " (cutoff:3.500A) Processing helix chain 'B' and resid 2380 through 2396 removed outlier: 4.073A pdb=" N ALA B2384 " --> pdb=" O TYR B2380 " (cutoff:3.500A) Processing helix chain 'B' and resid 2398 through 2406 removed outlier: 3.556A pdb=" N ILE B2404 " --> pdb=" O VAL B2400 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B2405 " --> pdb=" O ALA B2401 " (cutoff:3.500A) Processing helix chain 'B' and resid 2409 through 2426 Processing helix chain 'B' and resid 2460 through 2471 Processing helix chain 'C' and resid 325 through 345 removed outlier: 3.537A pdb=" N LYS C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 365 Processing helix chain 'C' and resid 382 through 394 removed outlier: 3.666A pdb=" N MET C 386 " --> pdb=" O THR C 382 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 402 through 405 removed outlier: 3.582A pdb=" N HIS C 405 " --> pdb=" O ASP C 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 402 through 405' Processing helix chain 'C' and resid 406 through 422 removed outlier: 4.159A pdb=" N LYS C 415 " --> pdb=" O GLU C 411 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE C 416 " --> pdb=" O LYS C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 436 Processing helix chain 'C' and resid 437 through 439 No H-bonds generated for 'chain 'C' and resid 437 through 439' Processing helix chain 'C' and resid 442 through 457 Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 461 through 479 removed outlier: 3.562A pdb=" N HIS C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 498 Processing helix chain 'C' and resid 503 through 516 Processing helix chain 'C' and resid 521 through 539 removed outlier: 4.169A pdb=" N ASP C 526 " --> pdb=" O VAL C 522 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU C 527 " --> pdb=" O ASP C 523 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP C 537 " --> pdb=" O ILE C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 559 Processing helix chain 'C' and resid 565 through 580 removed outlier: 3.554A pdb=" N LYS C 571 " --> pdb=" O ILE C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 606 removed outlier: 4.101A pdb=" N ILE C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASN C 604 " --> pdb=" O HIS C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 631 removed outlier: 3.504A pdb=" N MET C 624 " --> pdb=" O LEU C 620 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU C 625 " --> pdb=" O ALA C 621 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER C 626 " --> pdb=" O THR C 622 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET C 627 " --> pdb=" O TYR C 623 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 665 Processing helix chain 'C' and resid 673 through 683 removed outlier: 4.174A pdb=" N GLN C 679 " --> pdb=" O PRO C 675 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE C 680 " --> pdb=" O GLN C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 705 removed outlier: 3.782A pdb=" N ARG C 694 " --> pdb=" O TYR C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 723 removed outlier: 3.661A pdb=" N ASP C 718 " --> pdb=" O ASP C 714 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE C 720 " --> pdb=" O ASN C 716 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU C 721 " --> pdb=" O LYS C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 751 removed outlier: 3.580A pdb=" N LYS C 738 " --> pdb=" O GLU C 734 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS C 739 " --> pdb=" O ASN C 735 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU C 751 " --> pdb=" O VAL C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 780 removed outlier: 3.941A pdb=" N TRP C 775 " --> pdb=" O LEU C 771 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG C 776 " --> pdb=" O ASP C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 798 Processing helix chain 'C' and resid 807 through 831 removed outlier: 3.601A pdb=" N THR C 829 " --> pdb=" O ALA C 825 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU C 830 " --> pdb=" O SER C 826 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS C 831 " --> pdb=" O TYR C 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 866 removed outlier: 3.804A pdb=" N GLU C 859 " --> pdb=" O THR C 855 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN C 862 " --> pdb=" O ARG C 858 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU C 863 " --> pdb=" O GLU C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1032 removed outlier: 3.791A pdb=" N LEU C1021 " --> pdb=" O TYR C1017 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN C1023 " --> pdb=" O SER C1019 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C1029 " --> pdb=" O ALA C1025 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1046 removed outlier: 4.137A pdb=" N ARG C1037 " --> pdb=" O MET C1033 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C1045 " --> pdb=" O ARG C1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1066 removed outlier: 3.720A pdb=" N ILE C1054 " --> pdb=" O ASP C1050 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU C1055 " --> pdb=" O SER C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1077 through 1081 Processing helix chain 'C' and resid 1084 through 1100 removed outlier: 3.983A pdb=" N VAL C1088 " --> pdb=" O SER C1084 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU C1089 " --> pdb=" O ALA C1085 " (cutoff:3.500A) Processing helix chain 'C' and resid 1111 through 1121 removed outlier: 4.392A pdb=" N PHE C1115 " --> pdb=" O SER C1111 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY C1121 " --> pdb=" O PHE C1117 " (cutoff:3.500A) Processing helix chain 'C' and resid 1121 through 1131 removed outlier: 3.564A pdb=" N LEU C1127 " --> pdb=" O LEU C1123 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C1130 " --> pdb=" O VAL C1126 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1164 removed outlier: 3.593A pdb=" N LEU C1157 " --> pdb=" O LYS C1153 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TYR C1164 " --> pdb=" O THR C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1235 through 1251 removed outlier: 3.776A pdb=" N ILE C1239 " --> pdb=" O ASP C1235 " (cutoff:3.500A) Processing helix chain 'C' and resid 1253 through 1257 Processing helix chain 'C' and resid 1262 through 1269 removed outlier: 3.714A pdb=" N LYS C1266 " --> pdb=" O GLU C1262 " (cutoff:3.500A) Processing helix chain 'C' and resid 1280 through 1299 removed outlier: 3.627A pdb=" N MET C1292 " --> pdb=" O ALA C1288 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C1293 " --> pdb=" O LEU C1289 " (cutoff:3.500A) Processing helix chain 'C' and resid 1301 through 1307 removed outlier: 3.595A pdb=" N SER C1307 " --> pdb=" O LEU C1303 " (cutoff:3.500A) Processing helix chain 'C' and resid 1313 through 1321 Processing helix chain 'C' and resid 1326 through 1342 Processing helix chain 'C' and resid 1348 through 1360 removed outlier: 3.622A pdb=" N PHE C1352 " --> pdb=" O ARG C1348 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C1360 " --> pdb=" O LEU C1356 " (cutoff:3.500A) Processing helix chain 'C' and resid 1363 through 1369 removed outlier: 3.924A pdb=" N ALA C1369 " --> pdb=" O ALA C1365 " (cutoff:3.500A) Processing helix chain 'C' and resid 1372 through 1389 removed outlier: 3.544A pdb=" N LEU C1378 " --> pdb=" O ASP C1374 " (cutoff:3.500A) Processing helix chain 'C' and resid 1396 through 1417 removed outlier: 3.629A pdb=" N ASN C1402 " --> pdb=" O VAL C1398 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU C1403 " --> pdb=" O LEU C1399 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C1410 " --> pdb=" O TRP C1406 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C1414 " --> pdb=" O ILE C1410 " (cutoff:3.500A) Processing helix chain 'C' and resid 1423 through 1439 removed outlier: 3.544A pdb=" N LEU C1427 " --> pdb=" O GLU C1423 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU C1436 " --> pdb=" O GLY C1432 " (cutoff:3.500A) Processing helix chain 'C' and resid 1457 through 1465 Processing helix chain 'C' and resid 1469 through 1479 removed outlier: 3.556A pdb=" N VAL C1473 " --> pdb=" O PRO C1469 " (cutoff:3.500A) Processing helix chain 'C' and resid 1494 through 1510 removed outlier: 3.664A pdb=" N PHE C1502 " --> pdb=" O ILE C1498 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C1504 " --> pdb=" O ALA C1500 " (cutoff:3.500A) Processing helix chain 'C' and resid 1512 through 1528 removed outlier: 3.813A pdb=" N GLN C1518 " --> pdb=" O ARG C1514 " (cutoff:3.500A) Processing helix chain 'C' and resid 1565 through 1578 removed outlier: 3.794A pdb=" N VAL C1571 " --> pdb=" O TYR C1567 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET C1577 " --> pdb=" O GLN C1573 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE C1578 " --> pdb=" O GLN C1574 " (cutoff:3.500A) Processing helix chain 'C' and resid 1578 through 1587 Processing helix chain 'C' and resid 1633 through 1657 removed outlier: 3.553A pdb=" N ILE C1650 " --> pdb=" O HIS C1646 " (cutoff:3.500A) Processing helix chain 'C' and resid 1664 through 1671 removed outlier: 3.509A pdb=" N TRP C1668 " --> pdb=" O PRO C1664 " (cutoff:3.500A) Processing helix chain 'C' and resid 1685 through 1704 removed outlier: 3.642A pdb=" N PHE C1689 " --> pdb=" O ASP C1685 " (cutoff:3.500A) Processing helix chain 'C' and resid 1708 through 1714 Processing helix chain 'C' and resid 1749 through 1760 removed outlier: 3.875A pdb=" N TYR C1757 " --> pdb=" O SER C1753 " (cutoff:3.500A) Processing helix chain 'C' and resid 1764 through 1768 Processing helix chain 'C' and resid 1828 through 1837 Processing helix chain 'C' and resid 1912 through 1920 removed outlier: 3.665A pdb=" N MET C1916 " --> pdb=" O ASP C1912 " (cutoff:3.500A) Processing helix chain 'C' and resid 1988 through 2005 removed outlier: 3.541A pdb=" N MET C2003 " --> pdb=" O MET C1999 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN C2004 " --> pdb=" O HIS C2000 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR C2005 " --> pdb=" O ASN C2001 " (cutoff:3.500A) Processing helix chain 'C' and resid 2006 through 2019 Processing helix chain 'C' and resid 2020 through 2024 Processing helix chain 'C' and resid 2034 through 2055 Processing helix chain 'C' and resid 2060 through 2065 Processing helix chain 'C' and resid 2067 through 2079 removed outlier: 3.761A pdb=" N LEU C2077 " --> pdb=" O ALA C2073 " (cutoff:3.500A) Processing helix chain 'C' and resid 2081 through 2093 removed outlier: 3.711A pdb=" N ARG C2085 " --> pdb=" O SER C2081 " (cutoff:3.500A) Processing helix chain 'C' and resid 2098 through 2105 Processing helix chain 'C' and resid 2109 through 2127 Processing helix chain 'C' and resid 2151 through 2162 Processing helix chain 'C' and resid 2163 through 2165 No H-bonds generated for 'chain 'C' and resid 2163 through 2165' Processing helix chain 'C' and resid 2166 through 2171 Processing helix chain 'C' and resid 2175 through 2187 removed outlier: 3.943A pdb=" N LEU C2181 " --> pdb=" O GLN C2177 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE C2182 " --> pdb=" O TYR C2178 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR C2185 " --> pdb=" O LEU C2181 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2199 removed outlier: 3.924A pdb=" N LYS C2193 " --> pdb=" O GLY C2189 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN C2195 " --> pdb=" O ALA C2191 " (cutoff:3.500A) Processing helix chain 'C' and resid 2200 through 2208 removed outlier: 3.705A pdb=" N LEU C2207 " --> pdb=" O ALA C2203 " (cutoff:3.500A) Processing helix chain 'C' and resid 2225 through 2237 removed outlier: 3.719A pdb=" N SER C2230 " --> pdb=" O GLY C2226 " (cutoff:3.500A) Processing helix chain 'C' and resid 2241 through 2245 removed outlier: 3.845A pdb=" N MET C2245 " --> pdb=" O SER C2242 " (cutoff:3.500A) Processing helix chain 'C' and resid 2272 through 2280 Processing helix chain 'C' and resid 2283 through 2292 removed outlier: 3.508A pdb=" N LYS C2287 " --> pdb=" O THR C2283 " (cutoff:3.500A) Processing helix chain 'C' and resid 2297 through 2307 removed outlier: 3.672A pdb=" N LYS C2301 " --> pdb=" O GLU C2297 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C2302 " --> pdb=" O GLU C2298 " (cutoff:3.500A) Processing helix chain 'C' and resid 2310 through 2327 Processing helix chain 'C' and resid 2329 through 2331 No H-bonds generated for 'chain 'C' and resid 2329 through 2331' Processing helix chain 'C' and resid 2332 through 2345 removed outlier: 4.076A pdb=" N TYR C2336 " --> pdb=" O GLU C2332 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN C2342 " --> pdb=" O ASP C2338 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE C2343 " --> pdb=" O LEU C2339 " (cutoff:3.500A) Processing helix chain 'C' and resid 2350 through 2360 Processing helix chain 'C' and resid 2368 through 2377 removed outlier: 3.602A pdb=" N ILE C2373 " --> pdb=" O LEU C2369 " (cutoff:3.500A) Processing helix chain 'C' and resid 2380 through 2398 removed outlier: 3.828A pdb=" N ALA C2384 " --> pdb=" O TYR C2380 " (cutoff:3.500A) Processing helix chain 'C' and resid 2398 through 2406 Processing helix chain 'C' and resid 2408 through 2428 removed outlier: 3.632A pdb=" N TRP C2417 " --> pdb=" O ARG C2413 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU C2420 " --> pdb=" O THR C2416 " (cutoff:3.500A) Processing helix chain 'C' and resid 2461 through 2474 removed outlier: 3.924A pdb=" N MET C2465 " --> pdb=" O HIS C2461 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU C2472 " --> pdb=" O ALA C2468 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C2473 " --> pdb=" O LYS C2469 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 754 through 755 Processing sheet with id=AA2, first strand: chain 'A' and resid 1558 through 1559 removed outlier: 6.401A pdb=" N GLY A1558 " --> pdb=" O TYR A1662 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 1672 through 1673 Processing sheet with id=AA4, first strand: chain 'A' and resid 1730 through 1737 removed outlier: 6.751A pdb=" N SER A1717 " --> pdb=" O LYS A1787 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1740 through 1742 removed outlier: 5.905A pdb=" N LEU A1740 " --> pdb=" O GLN A1796 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N TYR A1949 " --> pdb=" O LEU A1797 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU A1869 " --> pdb=" O TYR A1949 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU A1951 " --> pdb=" O GLY A1867 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY A1867 " --> pdb=" O LEU A1951 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TYR A1953 " --> pdb=" O LEU A1865 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU A1865 " --> pdb=" O TYR A1953 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ARG A1955 " --> pdb=" O TYR A1863 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR A1863 " --> pdb=" O ARG A1955 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1740 through 1742 removed outlier: 5.905A pdb=" N LEU A1740 " --> pdb=" O GLN A1796 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N TYR A1949 " --> pdb=" O LEU A1797 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU A1869 " --> pdb=" O TYR A1949 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU A1951 " --> pdb=" O GLY A1867 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY A1867 " --> pdb=" O LEU A1951 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TYR A1953 " --> pdb=" O LEU A1865 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU A1865 " --> pdb=" O TYR A1953 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ARG A1955 " --> pdb=" O TYR A1863 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR A1863 " --> pdb=" O ARG A1955 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL A1866 " --> pdb=" O ILE A1885 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1769 through 1771 removed outlier: 3.514A pdb=" N LYS A1776 " --> pdb=" O CYS A1771 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1800 through 1803 Processing sheet with id=AA9, first strand: chain 'A' and resid 1924 through 1931 removed outlier: 3.699A pdb=" N ASP A1931 " --> pdb=" O ARG A1936 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 754 through 755 removed outlier: 3.579A pdb=" N VAL B 755 " --> pdb=" O MET B 762 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1558 through 1559 removed outlier: 6.080A pdb=" N GLY B1558 " --> pdb=" O TYR B1662 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 1672 through 1673 Processing sheet with id=AB4, first strand: chain 'B' and resid 1730 through 1737 removed outlier: 6.787A pdb=" N SER B1717 " --> pdb=" O LYS B1787 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1739 through 1743 removed outlier: 6.183A pdb=" N LEU B1740 " --> pdb=" O GLN B1796 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS B1798 " --> pdb=" O LEU B1740 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VAL B1742 " --> pdb=" O LYS B1798 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TYR B1949 " --> pdb=" O LEU B1797 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU B1869 " --> pdb=" O TYR B1949 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU B1951 " --> pdb=" O GLY B1867 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLY B1867 " --> pdb=" O LEU B1951 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TYR B1953 " --> pdb=" O LEU B1865 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B1865 " --> pdb=" O TYR B1953 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG B1955 " --> pdb=" O TYR B1863 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TYR B1863 " --> pdb=" O ARG B1955 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1739 through 1743 removed outlier: 6.183A pdb=" N LEU B1740 " --> pdb=" O GLN B1796 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS B1798 " --> pdb=" O LEU B1740 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VAL B1742 " --> pdb=" O LYS B1798 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TYR B1949 " --> pdb=" O LEU B1797 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU B1869 " --> pdb=" O TYR B1949 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU B1951 " --> pdb=" O GLY B1867 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLY B1867 " --> pdb=" O LEU B1951 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TYR B1953 " --> pdb=" O LEU B1865 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B1865 " --> pdb=" O TYR B1953 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG B1955 " --> pdb=" O TYR B1863 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TYR B1863 " --> pdb=" O ARG B1955 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL B1866 " --> pdb=" O ILE B1885 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1769 through 1771 removed outlier: 3.659A pdb=" N LYS B1776 " --> pdb=" O CYS B1771 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1800 through 1803 Processing sheet with id=AB9, first strand: chain 'B' and resid 1924 through 1931 Processing sheet with id=AC1, first strand: chain 'C' and resid 754 through 755 removed outlier: 3.700A pdb=" N VAL C 755 " --> pdb=" O MET C 762 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1558 through 1559 removed outlier: 6.640A pdb=" N GLY C1558 " --> pdb=" O TYR C1662 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 1672 through 1673 Processing sheet with id=AC4, first strand: chain 'C' and resid 1730 through 1737 removed outlier: 7.076A pdb=" N SER C1717 " --> pdb=" O LYS C1787 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C1780 " --> pdb=" O LEU C1763 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 1740 through 1742 removed outlier: 6.309A pdb=" N LEU C1740 " --> pdb=" O GLN C1796 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N TYR C1949 " --> pdb=" O LEU C1797 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP C1946 " --> pdb=" O SER C1872 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N SER C1872 " --> pdb=" O TRP C1946 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA C1948 " --> pdb=" O VAL C1870 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL C1870 " --> pdb=" O ALA C1948 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE C1950 " --> pdb=" O VAL C1868 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL C1868 " --> pdb=" O ILE C1950 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE C1952 " --> pdb=" O VAL C1866 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR C1863 " --> pdb=" O LEU C1822 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C1822 " --> pdb=" O TYR C1863 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1740 through 1742 removed outlier: 6.309A pdb=" N LEU C1740 " --> pdb=" O GLN C1796 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N TYR C1949 " --> pdb=" O LEU C1797 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP C1946 " --> pdb=" O SER C1872 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N SER C1872 " --> pdb=" O TRP C1946 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA C1948 " --> pdb=" O VAL C1870 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL C1870 " --> pdb=" O ALA C1948 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE C1950 " --> pdb=" O VAL C1868 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL C1868 " --> pdb=" O ILE C1950 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE C1952 " --> pdb=" O VAL C1866 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL C1866 " --> pdb=" O ILE C1885 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1769 through 1771 removed outlier: 3.617A pdb=" N LYS C1776 " --> pdb=" O CYS C1771 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1800 through 1803 Processing sheet with id=AC9, first strand: chain 'C' and resid 1924 through 1931 Processing sheet with id=AD1, first strand: chain 'C' and resid 2239 through 2240 2416 hydrogen bonds defined for protein. 7086 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: 19.86 Time building geometry restraints manager: 18.45 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: 13801 1.34 - 1.46: 8890 1.46 - 1.58: 20159 1.58 - 1.70: 0 1.70 - 1.81: 426 Bond restraints: 43276 Sorted by residual: bond pdb=" N ARG C 544 " pdb=" CA ARG C 544 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.26e-02 6.30e+03 7.78e+00 bond pdb=" N ASP A 543 " pdb=" CA ASP A 543 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.19e-02 7.06e+03 7.45e+00 bond pdb=" N THR B 546 " pdb=" CA THR B 546 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.00e+00 bond pdb=" N ARG B 544 " pdb=" CA ARG B 544 " ideal model delta sigma weight residual 1.458 1.491 -0.032 1.23e-02 6.61e+03 6.80e+00 bond pdb=" N THR C 546 " pdb=" CA THR C 546 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.57e+00 ... (remaining 43271 not shown) Histogram of bond angle deviations from ideal: 98.47 - 105.59: 816 105.59 - 112.71: 22730 112.71 - 119.83: 14419 119.83 - 126.95: 20027 126.95 - 134.07: 546 Bond angle restraints: 58538 Sorted by residual: angle pdb=" N TYR A2402 " pdb=" CA TYR A2402 " pdb=" C TYR A2402 " ideal model delta sigma weight residual 114.62 107.17 7.45 1.14e+00 7.69e-01 4.27e+01 angle pdb=" N ILE C2404 " pdb=" CA ILE C2404 " pdb=" C ILE C2404 " ideal model delta sigma weight residual 111.81 107.16 4.65 8.60e-01 1.35e+00 2.92e+01 angle pdb=" C ASP C1902 " pdb=" CA ASP C1902 " pdb=" CB ASP C1902 " ideal model delta sigma weight residual 116.54 110.37 6.17 1.15e+00 7.56e-01 2.88e+01 angle pdb=" C PHE A1258 " pdb=" N SER A1259 " pdb=" CA SER A1259 " ideal model delta sigma weight residual 121.48 131.86 -10.38 2.04e+00 2.40e-01 2.59e+01 angle pdb=" N ALA B2358 " pdb=" CA ALA B2358 " pdb=" C ALA B2358 " ideal model delta sigma weight residual 114.75 108.70 6.05 1.26e+00 6.30e-01 2.30e+01 ... (remaining 58533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 23567 17.71 - 35.41: 2026 35.41 - 53.12: 344 53.12 - 70.83: 99 70.83 - 88.54: 26 Dihedral angle restraints: 26062 sinusoidal: 10653 harmonic: 15409 Sorted by residual: dihedral pdb=" CA ILE B2362 " pdb=" C ILE B2362 " pdb=" N PRO B2363 " pdb=" CA PRO B2363 " ideal model delta harmonic sigma weight residual -180.00 -155.64 -24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA GLU C1444 " pdb=" C GLU C1444 " pdb=" N LYS C1445 " pdb=" CA LYS C1445 " ideal model delta harmonic sigma weight residual 180.00 156.47 23.53 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA GLU A2170 " pdb=" C GLU A2170 " pdb=" N HIS A2171 " pdb=" CA HIS A2171 " ideal model delta harmonic sigma weight residual -180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 26059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 4800 0.041 - 0.082: 1361 0.082 - 0.124: 278 0.124 - 0.165: 22 0.165 - 0.206: 8 Chirality restraints: 6469 Sorted by residual: chirality pdb=" CB ILE C1299 " pdb=" CA ILE C1299 " pdb=" CG1 ILE C1299 " pdb=" CG2 ILE C1299 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE B1299 " pdb=" CA ILE B1299 " pdb=" CG1 ILE B1299 " pdb=" CG2 ILE B1299 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.73e-01 chirality pdb=" CA ARG A 803 " pdb=" N ARG A 803 " pdb=" C ARG A 803 " pdb=" CB ARG A 803 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.65e-01 ... (remaining 6466 not shown) Planarity restraints: 7485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 541 " -0.016 2.00e-02 2.50e+03 3.29e-02 1.09e+01 pdb=" C SER A 541 " 0.057 2.00e-02 2.50e+03 pdb=" O SER A 541 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN A 542 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A2034 " 0.051 5.00e-02 4.00e+02 7.68e-02 9.45e+00 pdb=" N PRO A2035 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A2035 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A2035 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B 541 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C SER B 541 " -0.049 2.00e-02 2.50e+03 pdb=" O SER B 541 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN B 542 " 0.016 2.00e-02 2.50e+03 ... (remaining 7482 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3137 2.74 - 3.28: 45538 3.28 - 3.82: 71463 3.82 - 4.36: 87259 4.36 - 4.90: 143025 Nonbonded interactions: 350422 Sorted by model distance: nonbonded pdb=" O VAL B2160 " pdb=" OH TYR B2178 " model vdw 2.196 2.440 nonbonded pdb=" NZ LYS A1811 " pdb=" O TRP A1945 " model vdw 2.198 2.520 nonbonded pdb=" O LYS A1446 " pdb=" ND2 ASN A1515 " model vdw 2.203 2.520 nonbonded pdb=" NH2 ARG B2304 " pdb=" OE1 GLN B2342 " model vdw 2.206 2.520 nonbonded pdb=" O GLN C2324 " pdb=" OG SER C2328 " model vdw 2.206 2.440 ... (remaining 350417 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 321 through 1744 or resid 1746 through 2428 or resid 2460 \ through 2475)) selection = (chain 'B' and (resid 321 through 1744 or resid 1746 through 2428 or resid 2460 \ through 2475)) selection = (chain 'C' and (resid 321 through 1744 or resid 1746 through 2475)) } 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=0.40 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: 5.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 20.630 Check model and map are aligned: 0.620 Set scattering table: 0.370 Process input model: 142.200 Find NCS groups from input model: 3.570 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43276 Z= 0.209 Angle : 0.627 10.379 58538 Z= 0.363 Chirality : 0.039 0.206 6469 Planarity : 0.004 0.077 7485 Dihedral : 14.011 88.536 16060 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.13 % Favored : 94.68 % Rotamer: Outliers : 0.26 % Allowed : 0.32 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.12), residues: 5156 helix: -0.17 (0.09), residues: 3161 sheet: 0.36 (0.33), residues: 275 loop : -1.52 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B 565 HIS 0.006 0.001 HIS B2032 PHE 0.023 0.001 PHE A1651 TYR 0.019 0.001 TYR C2329 ARG 0.010 0.000 ARG C1665 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 254 time to evaluate : 4.663 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: symmetry clash revert: symmetry clash REVERT: A 542 GLN cc_start: 0.6157 (OUTLIER) cc_final: 0.5121 (pm20) REVERT: A 663 PHE cc_start: 0.9225 (t80) cc_final: 0.8984 (t80) REVERT: A 700 TRP cc_start: 0.9454 (t60) cc_final: 0.9092 (t60) REVERT: A 705 MET cc_start: 0.8424 (mpp) cc_final: 0.7977 (mpp) REVERT: A 785 ILE cc_start: 0.8715 (mm) cc_final: 0.8363 (mm) REVERT: A 1718 PHE cc_start: 0.8442 (m-80) cc_final: 0.7931 (m-80) REVERT: A 1934 MET cc_start: 0.6119 (tpt) cc_final: 0.5684 (tpp) REVERT: A 1937 MET cc_start: 0.6913 (mmp) cc_final: 0.6573 (tpt) REVERT: B 705 MET cc_start: -0.0218 (ptt) cc_final: -0.0502 (ppp) REVERT: B 1047 MET cc_start: 0.4507 (ppp) cc_final: 0.2168 (mmt) REVERT: B 1916 MET cc_start: 0.6744 (mpp) cc_final: 0.6176 (mpp) REVERT: C 525 MET cc_start: -0.1284 (ptm) cc_final: -0.1509 (ptm) REVERT: C 627 MET cc_start: 0.0168 (mtt) cc_final: -0.0456 (ptt) REVERT: C 1116 HIS cc_start: 0.8871 (m-70) cc_final: 0.8575 (m-70) REVERT: C 1339 MET cc_start: 0.8014 (ptt) cc_final: 0.7676 (ppp) outliers start: 12 outliers final: 5 residues processed: 266 average time/residue: 0.5318 time to fit residues: 238.4733 Evaluate side-chains 196 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 190 time to evaluate : 4.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 1356 LEU Chi-restraints excluded: chain C residue 1357 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 442 optimal weight: 2.9990 chunk 397 optimal weight: 10.0000 chunk 220 optimal weight: 30.0000 chunk 135 optimal weight: 0.6980 chunk 267 optimal weight: 0.9980 chunk 212 optimal weight: 30.0000 chunk 410 optimal weight: 0.4980 chunk 158 optimal weight: 3.9990 chunk 249 optimal weight: 0.8980 chunk 305 optimal weight: 4.9990 chunk 475 optimal weight: 40.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A 650 HIS A1335 GLN A1746 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 GLN B 817 GLN B1330 GLN ** B1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1684 HIS ** B1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN ** C1330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 43276 Z= 0.211 Angle : 0.669 14.446 58538 Z= 0.344 Chirality : 0.041 0.229 6469 Planarity : 0.005 0.081 7485 Dihedral : 4.966 74.378 5705 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.54 % Favored : 94.31 % Rotamer: Outliers : 0.35 % Allowed : 4.42 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.12), residues: 5156 helix: 0.51 (0.09), residues: 3269 sheet: 0.41 (0.33), residues: 262 loop : -1.48 (0.16), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 435 HIS 0.010 0.001 HIS A 610 PHE 0.031 0.002 PHE C1336 TYR 0.022 0.001 TYR B1661 ARG 0.006 0.000 ARG C1145 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 207 time to evaluate : 4.723 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: symmetry clash REVERT: A 542 GLN cc_start: 0.6291 (OUTLIER) cc_final: 0.5120 (pm20) REVERT: A 570 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7711 (pp) REVERT: A 663 PHE cc_start: 0.9290 (t80) cc_final: 0.9047 (t80) REVERT: A 700 TRP cc_start: 0.9444 (t60) cc_final: 0.9055 (t60) REVERT: A 705 MET cc_start: 0.8411 (mpp) cc_final: 0.7897 (mpp) REVERT: A 850 MET cc_start: 0.8326 (mpp) cc_final: 0.7696 (mpp) REVERT: A 1577 MET cc_start: 0.7681 (mmm) cc_final: 0.7235 (tmm) REVERT: A 1718 PHE cc_start: 0.8529 (m-80) cc_final: 0.7867 (m-80) REVERT: A 1934 MET cc_start: 0.5835 (tpt) cc_final: 0.5527 (tpp) REVERT: B 392 GLN cc_start: -0.0291 (OUTLIER) cc_final: -0.0735 (mp-120) REVERT: B 1033 MET cc_start: 0.6640 (pmm) cc_final: 0.6280 (pmm) REVERT: B 1047 MET cc_start: 0.4484 (ppp) cc_final: 0.4193 (ppp) REVERT: B 1141 MET cc_start: 0.5017 (tpt) cc_final: 0.4606 (tpt) REVERT: B 1910 MET cc_start: -0.2432 (tpp) cc_final: -0.2716 (tpp) REVERT: B 1916 MET cc_start: 0.6212 (mpp) cc_final: 0.5987 (mpp) REVERT: C 763 MET cc_start: 0.3057 (mtm) cc_final: 0.2517 (mmt) REVERT: C 1116 HIS cc_start: 0.8991 (m-70) cc_final: 0.8655 (m-70) REVERT: C 1339 MET cc_start: 0.8389 (ptt) cc_final: 0.8109 (ppp) REVERT: C 1354 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8764 (mp) REVERT: C 1926 MET cc_start: 0.5799 (ppp) cc_final: 0.5182 (tmm) outliers start: 16 outliers final: 8 residues processed: 218 average time/residue: 0.5009 time to fit residues: 189.5194 Evaluate side-chains 202 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 190 time to evaluate : 4.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 1735 GLU Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1812 PHE Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1709 MET Chi-restraints excluded: chain C residue 1354 ILE Chi-restraints excluded: chain C residue 1356 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 264 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 396 optimal weight: 9.9990 chunk 324 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 476 optimal weight: 0.4980 chunk 514 optimal weight: 2.9990 chunk 424 optimal weight: 30.0000 chunk 472 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 382 optimal weight: 20.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 542 GLN A 610 HIS A1116 HIS ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 GLN ** B1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2080 HIS ** C 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN ** C1330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1371 HIS C2155 HIS ** C2176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43276 Z= 0.200 Angle : 0.616 13.005 58538 Z= 0.311 Chirality : 0.040 0.187 6469 Planarity : 0.004 0.060 7485 Dihedral : 4.759 67.485 5698 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.30 % Favored : 94.54 % Rotamer: Outliers : 0.61 % Allowed : 6.23 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.12), residues: 5156 helix: 0.72 (0.09), residues: 3281 sheet: 0.35 (0.32), residues: 262 loop : -1.46 (0.16), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 512 HIS 0.005 0.001 HIS A1871 PHE 0.033 0.002 PHE C1336 TYR 0.018 0.001 TYR A1268 ARG 0.005 0.000 ARG C1681 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 199 time to evaluate : 4.508 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: symmetry clash revert: symmetry clash REVERT: A 542 GLN cc_start: 0.6343 (OUTLIER) cc_final: 0.5266 (pm20) REVERT: A 570 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7659 (pp) REVERT: A 663 PHE cc_start: 0.9283 (t80) cc_final: 0.9016 (t80) REVERT: A 680 ILE cc_start: 0.8190 (pt) cc_final: 0.7925 (pt) REVERT: A 700 TRP cc_start: 0.9414 (t60) cc_final: 0.8965 (t60) REVERT: A 850 MET cc_start: 0.8326 (mpp) cc_final: 0.7864 (mpp) REVERT: A 1044 MET cc_start: 0.9129 (mtm) cc_final: 0.8730 (mtm) REVERT: A 1577 MET cc_start: 0.7675 (mmm) cc_final: 0.7310 (tmm) REVERT: A 1718 PHE cc_start: 0.8508 (m-80) cc_final: 0.7877 (m-80) REVERT: B 392 GLN cc_start: -0.0170 (OUTLIER) cc_final: -0.0633 (mp-120) REVERT: B 543 ASP cc_start: 0.2731 (OUTLIER) cc_final: 0.2497 (t0) REVERT: B 705 MET cc_start: -0.0579 (ppp) cc_final: -0.0896 (ppp) REVERT: B 1047 MET cc_start: 0.4458 (ppp) cc_final: 0.4236 (ppp) REVERT: B 1100 MET cc_start: 0.3797 (ppp) cc_final: 0.3261 (ptt) REVERT: B 1141 MET cc_start: 0.5007 (tpt) cc_final: 0.4582 (tpt) REVERT: B 1910 MET cc_start: -0.1986 (tpp) cc_final: -0.2320 (tpt) REVERT: B 1916 MET cc_start: 0.6349 (mpp) cc_final: 0.6128 (mpp) REVERT: C 763 MET cc_start: 0.2970 (mtm) cc_final: 0.2493 (mmt) REVERT: C 1100 MET cc_start: 0.6682 (ppp) cc_final: 0.5881 (ptp) REVERT: C 1116 HIS cc_start: 0.9006 (m-70) cc_final: 0.8660 (m-70) REVERT: C 1354 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8623 (mp) REVERT: C 1577 MET cc_start: 0.6406 (tpp) cc_final: 0.6111 (tpt) REVERT: C 1926 MET cc_start: 0.5818 (ppp) cc_final: 0.5308 (tmm) outliers start: 28 outliers final: 12 residues processed: 215 average time/residue: 0.4896 time to fit residues: 186.1915 Evaluate side-chains 208 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 191 time to evaluate : 4.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 1116 HIS Chi-restraints excluded: chain A residue 1568 MET Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1709 MET Chi-restraints excluded: chain B residue 2055 THR Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 1354 ILE Chi-restraints excluded: chain C residue 1647 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 470 optimal weight: 20.0000 chunk 358 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 227 optimal weight: 8.9990 chunk 320 optimal weight: 0.8980 chunk 478 optimal weight: 30.0000 chunk 506 optimal weight: 1.9990 chunk 249 optimal weight: 0.0470 chunk 453 optimal weight: 1.9990 chunk 136 optimal weight: 0.0570 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2221 GLN ** C 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1330 GLN ** C2176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 43276 Z= 0.157 Angle : 0.585 20.330 58538 Z= 0.293 Chirality : 0.039 0.174 6469 Planarity : 0.004 0.057 7485 Dihedral : 4.627 65.222 5696 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.93 % Favored : 94.93 % Rotamer: Outliers : 0.58 % Allowed : 7.10 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.12), residues: 5156 helix: 0.89 (0.09), residues: 3279 sheet: 0.28 (0.31), residues: 268 loop : -1.40 (0.16), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B1945 HIS 0.029 0.001 HIS A1116 PHE 0.023 0.001 PHE C1336 TYR 0.019 0.001 TYR A 623 ARG 0.004 0.000 ARG C1681 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 197 time to evaluate : 4.780 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 542 GLN cc_start: 0.6364 (OUTLIER) cc_final: 0.5468 (pm20) REVERT: A 570 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7615 (pp) REVERT: A 663 PHE cc_start: 0.9283 (t80) cc_final: 0.9017 (t80) REVERT: A 700 TRP cc_start: 0.9388 (t60) cc_final: 0.8900 (t60) REVERT: A 850 MET cc_start: 0.8289 (mpp) cc_final: 0.7806 (mpp) REVERT: A 1577 MET cc_start: 0.7609 (mmm) cc_final: 0.7309 (tmm) REVERT: A 1718 PHE cc_start: 0.8446 (m-80) cc_final: 0.7924 (m-80) REVERT: A 1933 MET cc_start: 0.3043 (mpp) cc_final: 0.1592 (mtm) REVERT: B 392 GLN cc_start: 0.0023 (OUTLIER) cc_final: -0.0520 (mp-120) REVERT: B 543 ASP cc_start: 0.3171 (OUTLIER) cc_final: 0.2784 (t0) REVERT: B 705 MET cc_start: -0.0611 (ppp) cc_final: -0.0908 (ppp) REVERT: B 762 MET cc_start: 0.6608 (pmm) cc_final: 0.6320 (pmm) REVERT: B 1047 MET cc_start: 0.4452 (ppp) cc_final: 0.4196 (ppp) REVERT: B 1100 MET cc_start: 0.3867 (ppp) cc_final: 0.3405 (ptt) REVERT: B 1141 MET cc_start: 0.4952 (tpt) cc_final: 0.4613 (tpt) REVERT: C 763 MET cc_start: 0.2979 (mtm) cc_final: 0.2364 (mmt) REVERT: C 1116 HIS cc_start: 0.9004 (m-70) cc_final: 0.8656 (m-70) REVERT: C 1254 LEU cc_start: 0.5010 (OUTLIER) cc_final: 0.4495 (mp) REVERT: C 1577 MET cc_start: 0.6552 (tpp) cc_final: 0.6307 (tpt) REVERT: C 1926 MET cc_start: 0.5815 (ppp) cc_final: 0.5347 (tmm) REVERT: C 2188 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8264 (mp) outliers start: 27 outliers final: 13 residues processed: 213 average time/residue: 0.4838 time to fit residues: 182.1896 Evaluate side-chains 209 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 190 time to evaluate : 4.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 1568 MET Chi-restraints excluded: chain A residue 1934 MET Chi-restraints excluded: chain A residue 1937 MET Chi-restraints excluded: chain A residue 2184 MET Chi-restraints excluded: chain A residue 2420 GLU Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1709 MET Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain C residue 1345 MET Chi-restraints excluded: chain C residue 1647 LEU Chi-restraints excluded: chain C residue 2188 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 421 optimal weight: 5.9990 chunk 287 optimal weight: 50.0000 chunk 7 optimal weight: 10.0000 chunk 377 optimal weight: 7.9990 chunk 208 optimal weight: 20.0000 chunk 432 optimal weight: 2.9990 chunk 350 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 258 optimal weight: 0.6980 chunk 454 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 HIS A1116 HIS ** A1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1347 HIS ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1430 HIS ** B1472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2221 GLN ** C 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2221 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 43276 Z= 0.449 Angle : 0.716 13.824 58538 Z= 0.361 Chirality : 0.043 0.250 6469 Planarity : 0.005 0.061 7485 Dihedral : 4.833 63.487 5694 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.08 % Favored : 93.78 % Rotamer: Outliers : 0.82 % Allowed : 7.75 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.12), residues: 5156 helix: 0.64 (0.09), residues: 3283 sheet: 0.21 (0.32), residues: 264 loop : -1.50 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 512 HIS 0.009 0.002 HIS B 516 PHE 0.041 0.002 PHE A 580 TYR 0.027 0.002 TYR A1375 ARG 0.009 0.001 ARG C2113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 191 time to evaluate : 4.791 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 GLN cc_start: 0.6318 (OUTLIER) cc_final: 0.5426 (pm20) REVERT: A 570 LEU cc_start: 0.7886 (tt) cc_final: 0.7608 (pp) REVERT: A 663 PHE cc_start: 0.9292 (t80) cc_final: 0.9028 (t80) REVERT: A 700 TRP cc_start: 0.9412 (t60) cc_final: 0.9058 (t60) REVERT: A 705 MET cc_start: 0.8358 (mpp) cc_final: 0.7782 (mpp) REVERT: A 763 MET cc_start: -0.2464 (tmm) cc_final: -0.5181 (ptm) REVERT: A 1718 PHE cc_start: 0.8504 (m-80) cc_final: 0.7978 (m-80) REVERT: A 1933 MET cc_start: 0.3061 (mpp) cc_final: 0.1680 (mtm) REVERT: B 392 GLN cc_start: -0.0010 (OUTLIER) cc_final: -0.0553 (mp-120) REVERT: B 705 MET cc_start: -0.0462 (ppp) cc_final: -0.0731 (ppp) REVERT: B 1047 MET cc_start: 0.4549 (ppp) cc_final: 0.4283 (ppp) REVERT: B 1100 MET cc_start: 0.4015 (ppp) cc_final: 0.3549 (ptt) REVERT: B 1141 MET cc_start: 0.4824 (tpt) cc_final: 0.4409 (tpt) REVERT: B 1824 MET cc_start: 0.7440 (tpp) cc_final: 0.5274 (mtp) REVERT: C 763 MET cc_start: 0.3072 (mtm) cc_final: 0.2441 (mmt) REVERT: C 1047 MET cc_start: -0.2325 (tpt) cc_final: -0.2584 (tpt) REVERT: C 1254 LEU cc_start: 0.5198 (OUTLIER) cc_final: 0.4673 (mp) REVERT: C 1345 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7104 (ptt) REVERT: C 1577 MET cc_start: 0.6493 (tpp) cc_final: 0.6250 (tpp) REVERT: C 1926 MET cc_start: 0.5931 (ppp) cc_final: 0.5397 (tmm) outliers start: 38 outliers final: 23 residues processed: 217 average time/residue: 0.4899 time to fit residues: 187.5719 Evaluate side-chains 210 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 183 time to evaluate : 4.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 1116 HIS Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1568 MET Chi-restraints excluded: chain A residue 1735 GLU Chi-restraints excluded: chain A residue 1934 MET Chi-restraints excluded: chain A residue 1937 MET Chi-restraints excluded: chain A residue 2420 GLU Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1290 GLU Chi-restraints excluded: chain B residue 1709 MET Chi-restraints excluded: chain B residue 2055 THR Chi-restraints excluded: chain B residue 2245 MET Chi-restraints excluded: chain B residue 2362 ILE Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 1245 ILE Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain C residue 1345 MET Chi-restraints excluded: chain C residue 1643 VAL Chi-restraints excluded: chain C residue 1647 LEU Chi-restraints excluded: chain C residue 2283 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 170 optimal weight: 0.7980 chunk 456 optimal weight: 20.0000 chunk 100 optimal weight: 0.9990 chunk 297 optimal weight: 20.0000 chunk 125 optimal weight: 40.0000 chunk 506 optimal weight: 0.9990 chunk 420 optimal weight: 9.9990 chunk 234 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 167 optimal weight: 0.9990 chunk 266 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 HIS ** A1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2221 GLN ** C 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 43276 Z= 0.185 Angle : 0.607 14.229 58538 Z= 0.303 Chirality : 0.039 0.231 6469 Planarity : 0.004 0.053 7485 Dihedral : 4.640 61.961 5694 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.15 % Favored : 94.72 % Rotamer: Outliers : 0.63 % Allowed : 8.70 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.12), residues: 5156 helix: 0.88 (0.09), residues: 3285 sheet: 0.16 (0.31), residues: 270 loop : -1.41 (0.16), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 512 HIS 0.037 0.001 HIS A1116 PHE 0.035 0.001 PHE C1353 TYR 0.019 0.001 TYR A 623 ARG 0.004 0.000 ARG C1681 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 189 time to evaluate : 4.814 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: symmetry clash REVERT: A 542 GLN cc_start: 0.6421 (OUTLIER) cc_final: 0.5525 (pm20) REVERT: A 570 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7635 (pp) REVERT: A 663 PHE cc_start: 0.9277 (t80) cc_final: 0.9007 (t80) REVERT: A 700 TRP cc_start: 0.9398 (t60) cc_final: 0.9013 (t60) REVERT: A 705 MET cc_start: 0.8484 (mpp) cc_final: 0.7865 (mpp) REVERT: A 763 MET cc_start: -0.2399 (tmm) cc_final: -0.5082 (ptm) REVERT: A 850 MET cc_start: 0.8301 (mpp) cc_final: 0.7831 (mpp) REVERT: A 1718 PHE cc_start: 0.8508 (m-80) cc_final: 0.7978 (m-80) REVERT: A 1933 MET cc_start: 0.3519 (mpp) cc_final: 0.2259 (mtm) REVERT: B 392 GLN cc_start: -0.0048 (OUTLIER) cc_final: -0.0594 (mp-120) REVERT: B 705 MET cc_start: -0.0387 (ppp) cc_final: -0.0643 (ppp) REVERT: B 762 MET cc_start: 0.6694 (pmm) cc_final: 0.6329 (pmm) REVERT: B 1047 MET cc_start: 0.4561 (ppp) cc_final: 0.4295 (ppp) REVERT: B 1100 MET cc_start: 0.3945 (ppp) cc_final: 0.3526 (ptt) REVERT: B 1141 MET cc_start: 0.4661 (tpt) cc_final: 0.4269 (tpt) REVERT: B 1824 MET cc_start: 0.7647 (tpp) cc_final: 0.5502 (mtp) REVERT: C 763 MET cc_start: 0.3077 (mtm) cc_final: 0.2443 (mmt) REVERT: C 1116 HIS cc_start: 0.8996 (m-70) cc_final: 0.8625 (m170) REVERT: C 1254 LEU cc_start: 0.5261 (OUTLIER) cc_final: 0.4784 (mp) REVERT: C 1345 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7072 (ptt) REVERT: C 1577 MET cc_start: 0.6839 (tpp) cc_final: 0.6606 (tpp) REVERT: C 1926 MET cc_start: 0.5998 (ppp) cc_final: 0.5462 (tmm) outliers start: 29 outliers final: 15 residues processed: 207 average time/residue: 0.4838 time to fit residues: 176.1756 Evaluate side-chains 206 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 4.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 1116 HIS Chi-restraints excluded: chain A residue 1568 MET Chi-restraints excluded: chain A residue 1735 GLU Chi-restraints excluded: chain A residue 1934 MET Chi-restraints excluded: chain A residue 1937 MET Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1709 MET Chi-restraints excluded: chain B residue 2055 THR Chi-restraints excluded: chain B residue 2245 MET Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain C residue 1345 MET Chi-restraints excluded: chain C residue 1647 LEU Chi-restraints excluded: chain C residue 2283 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 488 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 288 optimal weight: 9.9990 chunk 370 optimal weight: 50.0000 chunk 286 optimal weight: 8.9990 chunk 426 optimal weight: 0.4980 chunk 283 optimal weight: 10.0000 chunk 505 optimal weight: 0.0040 chunk 316 optimal weight: 0.0170 chunk 307 optimal weight: 2.9990 chunk 233 optimal weight: 40.0000 overall best weight: 0.4632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 HIS A1116 HIS ** A1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 862 ASN ** B1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 43276 Z= 0.149 Angle : 0.589 15.705 58538 Z= 0.293 Chirality : 0.038 0.232 6469 Planarity : 0.004 0.054 7485 Dihedral : 4.464 61.361 5694 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.11 % Favored : 94.79 % Rotamer: Outliers : 0.61 % Allowed : 8.94 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.12), residues: 5156 helix: 1.08 (0.09), residues: 3273 sheet: 0.28 (0.32), residues: 264 loop : -1.39 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B1945 HIS 0.029 0.001 HIS A1116 PHE 0.031 0.001 PHE C1353 TYR 0.017 0.001 TYR A2222 ARG 0.006 0.000 ARG C2366 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 190 time to evaluate : 4.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.7877 (ptp) cc_final: 0.7624 (pmm) REVERT: A 542 GLN cc_start: 0.6590 (OUTLIER) cc_final: 0.5775 (pm20) REVERT: A 570 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7593 (pp) REVERT: A 663 PHE cc_start: 0.9272 (t80) cc_final: 0.8999 (t80) REVERT: A 700 TRP cc_start: 0.9369 (t60) cc_final: 0.8875 (t60) REVERT: A 705 MET cc_start: 0.8473 (mpp) cc_final: 0.7904 (mpp) REVERT: A 763 MET cc_start: -0.2489 (tmm) cc_final: -0.5054 (ptm) REVERT: A 850 MET cc_start: 0.8177 (mpp) cc_final: 0.7741 (mpp) REVERT: A 1116 HIS cc_start: 0.7965 (OUTLIER) cc_final: 0.7482 (m90) REVERT: A 1687 LEU cc_start: 0.8508 (mm) cc_final: 0.8291 (tp) REVERT: A 1718 PHE cc_start: 0.8470 (m-80) cc_final: 0.7939 (m-80) REVERT: A 1933 MET cc_start: 0.3601 (mpp) cc_final: 0.2349 (mtm) REVERT: B 392 GLN cc_start: -0.0140 (OUTLIER) cc_final: -0.0631 (mp-120) REVERT: B 705 MET cc_start: -0.0399 (ppp) cc_final: -0.0650 (ppp) REVERT: B 1047 MET cc_start: 0.4611 (ppp) cc_final: 0.4325 (ppp) REVERT: B 1100 MET cc_start: 0.3978 (ppp) cc_final: 0.3639 (ptt) REVERT: B 1141 MET cc_start: 0.4690 (tpt) cc_final: 0.4305 (tpt) REVERT: B 1824 MET cc_start: 0.7733 (tpp) cc_final: 0.6429 (ttm) REVERT: C 763 MET cc_start: 0.3161 (mtm) cc_final: 0.2542 (mmt) REVERT: C 1116 HIS cc_start: 0.8935 (m-70) cc_final: 0.8590 (m170) REVERT: C 1254 LEU cc_start: 0.5292 (OUTLIER) cc_final: 0.4819 (mp) REVERT: C 1345 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7036 (ptt) REVERT: C 1718 PHE cc_start: 0.8079 (m-80) cc_final: 0.7777 (m-80) REVERT: C 1824 MET cc_start: 0.7201 (tmm) cc_final: 0.5079 (pmm) REVERT: C 1926 MET cc_start: 0.6196 (ppp) cc_final: 0.5698 (tmm) outliers start: 28 outliers final: 13 residues processed: 205 average time/residue: 0.5012 time to fit residues: 181.7665 Evaluate side-chains 207 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 188 time to evaluate : 4.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 782 ASN Chi-restraints excluded: chain A residue 1116 HIS Chi-restraints excluded: chain A residue 1568 MET Chi-restraints excluded: chain A residue 1934 MET Chi-restraints excluded: chain A residue 1937 MET Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1709 MET Chi-restraints excluded: chain B residue 2362 ILE Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain C residue 1345 MET Chi-restraints excluded: chain C residue 1647 LEU Chi-restraints excluded: chain C residue 2283 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 312 optimal weight: 1.9990 chunk 201 optimal weight: 20.0000 chunk 301 optimal weight: 20.0000 chunk 152 optimal weight: 0.8980 chunk 99 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 321 optimal weight: 1.9990 chunk 344 optimal weight: 0.8980 chunk 249 optimal weight: 0.0970 chunk 47 optimal weight: 0.3980 chunk 396 optimal weight: 20.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 HIS ** A1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 605 GLN ** C1994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 43276 Z= 0.156 Angle : 0.585 13.356 58538 Z= 0.290 Chirality : 0.038 0.206 6469 Planarity : 0.004 0.054 7485 Dihedral : 4.396 62.190 5694 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.97 % Favored : 94.93 % Rotamer: Outliers : 0.52 % Allowed : 9.16 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.12), residues: 5156 helix: 1.17 (0.09), residues: 3273 sheet: 0.29 (0.32), residues: 264 loop : -1.38 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B1945 HIS 0.027 0.001 HIS A1116 PHE 0.019 0.001 PHE B1689 TYR 0.017 0.001 TYR A2222 ARG 0.003 0.000 ARG C1145 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 192 time to evaluate : 4.739 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 542 GLN cc_start: 0.6569 (OUTLIER) cc_final: 0.5817 (pm20) REVERT: A 570 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7559 (pp) REVERT: A 663 PHE cc_start: 0.9260 (t80) cc_final: 0.8993 (t80) REVERT: A 700 TRP cc_start: 0.9365 (t60) cc_final: 0.8869 (t60) REVERT: A 705 MET cc_start: 0.8406 (mpp) cc_final: 0.7864 (mpp) REVERT: A 763 MET cc_start: -0.2589 (tmm) cc_final: -0.5131 (ptm) REVERT: A 850 MET cc_start: 0.8141 (mpp) cc_final: 0.7712 (mpp) REVERT: A 1116 HIS cc_start: 0.8080 (OUTLIER) cc_final: 0.7424 (m-70) REVERT: A 1718 PHE cc_start: 0.8471 (m-80) cc_final: 0.7930 (m-80) REVERT: A 1933 MET cc_start: 0.3573 (mpp) cc_final: 0.2339 (mtm) REVERT: B 392 GLN cc_start: -0.0105 (OUTLIER) cc_final: -0.0598 (mp-120) REVERT: B 705 MET cc_start: -0.0291 (ppp) cc_final: -0.0533 (ppp) REVERT: B 762 MET cc_start: 0.6767 (pmm) cc_final: 0.6369 (pmm) REVERT: B 1047 MET cc_start: 0.4671 (ppp) cc_final: 0.4223 (ppp) REVERT: B 1100 MET cc_start: 0.4004 (ppp) cc_final: 0.3660 (ptt) REVERT: B 1141 MET cc_start: 0.4681 (tpt) cc_final: 0.4296 (tpt) REVERT: B 1824 MET cc_start: 0.7771 (tpp) cc_final: 0.6554 (ttm) REVERT: C 763 MET cc_start: 0.3035 (mtm) cc_final: 0.2421 (mmt) REVERT: C 1116 HIS cc_start: 0.8955 (m-70) cc_final: 0.8620 (m170) REVERT: C 1254 LEU cc_start: 0.5185 (OUTLIER) cc_final: 0.4707 (mp) REVERT: C 1345 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.6997 (ptt) REVERT: C 1577 MET cc_start: 0.6533 (tpp) cc_final: 0.6194 (tpp) REVERT: C 1718 PHE cc_start: 0.8025 (m-80) cc_final: 0.7783 (m-80) REVERT: C 1926 MET cc_start: 0.6227 (ppp) cc_final: 0.5730 (tmm) outliers start: 24 outliers final: 17 residues processed: 204 average time/residue: 0.4940 time to fit residues: 177.7539 Evaluate side-chains 209 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 186 time to evaluate : 5.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 782 ASN Chi-restraints excluded: chain A residue 1116 HIS Chi-restraints excluded: chain A residue 1568 MET Chi-restraints excluded: chain A residue 1735 GLU Chi-restraints excluded: chain A residue 1934 MET Chi-restraints excluded: chain A residue 1937 MET Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1709 MET Chi-restraints excluded: chain B residue 2188 LEU Chi-restraints excluded: chain B residue 2362 ILE Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain C residue 1345 MET Chi-restraints excluded: chain C residue 1647 LEU Chi-restraints excluded: chain C residue 2283 THR Chi-restraints excluded: chain C residue 2465 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 459 optimal weight: 5.9990 chunk 483 optimal weight: 2.9990 chunk 441 optimal weight: 2.9990 chunk 470 optimal weight: 0.5980 chunk 283 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 369 optimal weight: 8.9990 chunk 144 optimal weight: 1.9990 chunk 425 optimal weight: 0.7980 chunk 445 optimal weight: 8.9990 chunk 469 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 HIS ** A1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 43276 Z= 0.200 Angle : 0.605 15.884 58538 Z= 0.299 Chirality : 0.039 0.207 6469 Planarity : 0.004 0.053 7485 Dihedral : 4.402 63.055 5694 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.19 % Favored : 94.72 % Rotamer: Outliers : 0.58 % Allowed : 9.33 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.12), residues: 5156 helix: 1.17 (0.09), residues: 3279 sheet: 0.24 (0.32), residues: 264 loop : -1.40 (0.16), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP A 476 HIS 0.012 0.001 HIS A 610 PHE 0.019 0.001 PHE B1689 TYR 0.017 0.001 TYR A2222 ARG 0.004 0.000 ARG A1041 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 191 time to evaluate : 4.805 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 542 GLN cc_start: 0.6642 (OUTLIER) cc_final: 0.5922 (pm20) REVERT: A 570 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7565 (pp) REVERT: A 663 PHE cc_start: 0.9259 (t80) cc_final: 0.8991 (t80) REVERT: A 700 TRP cc_start: 0.9364 (t60) cc_final: 0.8872 (t60) REVERT: A 705 MET cc_start: 0.8429 (mpp) cc_final: 0.7879 (mpp) REVERT: A 763 MET cc_start: -0.2455 (tmm) cc_final: -0.5077 (ptm) REVERT: A 850 MET cc_start: 0.8150 (mpp) cc_final: 0.7762 (mpp) REVERT: A 1116 HIS cc_start: 0.8301 (m-70) cc_final: 0.8020 (t-90) REVERT: A 1718 PHE cc_start: 0.8493 (m-80) cc_final: 0.7741 (m-80) REVERT: A 1933 MET cc_start: 0.3555 (mpp) cc_final: 0.2328 (mtm) REVERT: B 392 GLN cc_start: -0.0102 (OUTLIER) cc_final: -0.0598 (mp-120) REVERT: B 705 MET cc_start: -0.0252 (ppp) cc_final: -0.0499 (ppp) REVERT: B 762 MET cc_start: 0.6736 (pmm) cc_final: 0.6342 (pmm) REVERT: B 1047 MET cc_start: 0.4703 (ppp) cc_final: 0.4240 (ppp) REVERT: B 1100 MET cc_start: 0.3990 (ppp) cc_final: 0.3654 (ptt) REVERT: B 1141 MET cc_start: 0.4550 (tpt) cc_final: 0.4179 (tpt) REVERT: B 1824 MET cc_start: 0.7792 (tpp) cc_final: 0.5863 (mtp) REVERT: B 1910 MET cc_start: -0.2794 (tpp) cc_final: -0.3073 (tpt) REVERT: C 763 MET cc_start: 0.3003 (mtm) cc_final: 0.2398 (mmt) REVERT: C 1116 HIS cc_start: 0.8955 (m-70) cc_final: 0.8641 (m-70) REVERT: C 1254 LEU cc_start: 0.5133 (OUTLIER) cc_final: 0.4525 (mt) REVERT: C 1345 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7018 (ptt) REVERT: C 1577 MET cc_start: 0.6584 (tpp) cc_final: 0.6241 (tpp) REVERT: C 1824 MET cc_start: 0.7175 (tmm) cc_final: 0.4849 (pmm) REVERT: C 1926 MET cc_start: 0.6262 (ppp) cc_final: 0.5778 (tmm) outliers start: 27 outliers final: 14 residues processed: 206 average time/residue: 0.5070 time to fit residues: 183.1665 Evaluate side-chains 206 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 187 time to evaluate : 5.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 782 ASN Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1568 MET Chi-restraints excluded: chain A residue 1934 MET Chi-restraints excluded: chain A residue 1937 MET Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 2362 ILE Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain C residue 1345 MET Chi-restraints excluded: chain C residue 1647 LEU Chi-restraints excluded: chain C residue 2283 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 309 optimal weight: 0.8980 chunk 497 optimal weight: 0.9990 chunk 303 optimal weight: 6.9990 chunk 236 optimal weight: 7.9990 chunk 345 optimal weight: 4.9990 chunk 522 optimal weight: 1.9990 chunk 480 optimal weight: 0.8980 chunk 415 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 321 optimal weight: 0.6980 chunk 254 optimal weight: 20.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 HIS ** A1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 HIS ** B1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 43276 Z= 0.165 Angle : 0.601 18.696 58538 Z= 0.296 Chirality : 0.038 0.206 6469 Planarity : 0.004 0.053 7485 Dihedral : 4.379 63.861 5694 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.99 % Favored : 94.91 % Rotamer: Outliers : 0.43 % Allowed : 9.65 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.12), residues: 5156 helix: 1.24 (0.09), residues: 3271 sheet: 0.25 (0.32), residues: 264 loop : -1.38 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP C 512 HIS 0.012 0.001 HIS A 610 PHE 0.025 0.001 PHE C1718 TYR 0.021 0.001 TYR B1661 ARG 0.003 0.000 ARG A 628 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 185 time to evaluate : 5.070 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 542 GLN cc_start: 0.6755 (OUTLIER) cc_final: 0.5963 (pm20) REVERT: A 570 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7479 (pp) REVERT: A 663 PHE cc_start: 0.9262 (t80) cc_final: 0.8996 (t80) REVERT: A 700 TRP cc_start: 0.9357 (t60) cc_final: 0.8858 (t60) REVERT: A 705 MET cc_start: 0.8416 (mpp) cc_final: 0.7882 (mpp) REVERT: A 763 MET cc_start: -0.2361 (tmm) cc_final: -0.4976 (ptm) REVERT: A 850 MET cc_start: 0.8114 (mpp) cc_final: 0.7650 (mpp) REVERT: A 1116 HIS cc_start: 0.8291 (m-70) cc_final: 0.7950 (t-90) REVERT: A 1577 MET cc_start: 0.7918 (mmm) cc_final: 0.7286 (tpp) REVERT: A 1718 PHE cc_start: 0.8372 (m-80) cc_final: 0.7816 (m-80) REVERT: A 1933 MET cc_start: 0.3648 (mpp) cc_final: 0.2427 (mtm) REVERT: B 392 GLN cc_start: -0.0024 (OUTLIER) cc_final: -0.0554 (mp-120) REVERT: B 705 MET cc_start: -0.0259 (ppp) cc_final: -0.0513 (ppp) REVERT: B 762 MET cc_start: 0.6714 (pmm) cc_final: 0.6330 (pmm) REVERT: B 1047 MET cc_start: 0.4788 (ppp) cc_final: 0.4291 (ppp) REVERT: B 1100 MET cc_start: 0.3986 (ppp) cc_final: 0.3628 (ptt) REVERT: B 1141 MET cc_start: 0.4582 (tpt) cc_final: 0.4203 (tpt) REVERT: B 1824 MET cc_start: 0.7775 (tpp) cc_final: 0.5870 (mtp) REVERT: B 1910 MET cc_start: -0.2594 (tpp) cc_final: -0.2834 (tpt) REVERT: C 763 MET cc_start: 0.2994 (mtm) cc_final: 0.2395 (mmt) REVERT: C 1116 HIS cc_start: 0.8948 (m-70) cc_final: 0.8636 (m-70) REVERT: C 1254 LEU cc_start: 0.5116 (OUTLIER) cc_final: 0.4510 (mt) REVERT: C 1345 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.6990 (ptt) REVERT: C 1577 MET cc_start: 0.6657 (tpp) cc_final: 0.6298 (tpp) REVERT: C 1824 MET cc_start: 0.7146 (tmm) cc_final: 0.4920 (pmm) REVERT: C 1926 MET cc_start: 0.6299 (ppp) cc_final: 0.5800 (tmm) outliers start: 20 outliers final: 11 residues processed: 196 average time/residue: 0.4932 time to fit residues: 170.3938 Evaluate side-chains 201 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 185 time to evaluate : 4.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 610 HIS Chi-restraints excluded: chain A residue 1568 MET Chi-restraints excluded: chain A residue 1934 MET Chi-restraints excluded: chain A residue 1937 MET Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 2362 ILE Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain C residue 1345 MET Chi-restraints excluded: chain C residue 2283 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 330 optimal weight: 1.9990 chunk 442 optimal weight: 0.6980 chunk 127 optimal weight: 20.0000 chunk 383 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 115 optimal weight: 30.0000 chunk 416 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 427 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1947 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2221 GLN ** C 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.139245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.109733 restraints weight = 347516.909| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 8.21 r_work: 0.3273 rms_B_bonded: 7.96 restraints_weight: 2.0000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43276 Z= 0.219 Angle : 0.607 13.769 58538 Z= 0.301 Chirality : 0.039 0.200 6469 Planarity : 0.004 0.052 7485 Dihedral : 4.391 64.760 5694 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.21 % Favored : 94.68 % Rotamer: Outliers : 0.41 % Allowed : 9.70 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.12), residues: 5156 helix: 1.20 (0.09), residues: 3286 sheet: 0.28 (0.32), residues: 264 loop : -1.39 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP C 512 HIS 0.017 0.001 HIS A 610 PHE 0.030 0.001 PHE C1718 TYR 0.016 0.001 TYR A2222 ARG 0.004 0.000 ARG C2113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9607.08 seconds wall clock time: 175 minutes 49.04 seconds (10549.04 seconds total)