Starting phenix.real_space_refine on Mon Mar 25 17:48:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mu1_9243/03_2024/6mu1_9243_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mu1_9243/03_2024/6mu1_9243.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mu1_9243/03_2024/6mu1_9243_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mu1_9243/03_2024/6mu1_9243_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mu1_9243/03_2024/6mu1_9243_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mu1_9243/03_2024/6mu1_9243.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mu1_9243/03_2024/6mu1_9243.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mu1_9243/03_2024/6mu1_9243_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mu1_9243/03_2024/6mu1_9243_trim_updated.pdb" } resolution = 4.1 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= 0.092 sd= 0.632 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 176 5.16 5 C 29488 2.51 5 N 9968 2.21 5 O 10520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ASP 379": "OD1" <-> "OD2" Residue "A ARG 511": "NH1" <-> "NH2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A ARG 568": "NH1" <-> "NH2" Residue "A ARG 2200": "NH1" <-> "NH2" Residue "A ARG 2203": "NH1" <-> "NH2" Residue "A GLU 2248": "OE1" <-> "OE2" Residue "A PHE 2294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2301": "NH1" <-> "NH2" Residue "A ARG 2343": "NH1" <-> "NH2" Residue "A ARG 2381": "NH1" <-> "NH2" Residue "A GLU 2410": "OE1" <-> "OE2" Residue "A PHE 2411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2423": "NH1" <-> "NH2" Residue "A ARG 2439": "NH1" <-> "NH2" Residue "A GLU 2559": "OE1" <-> "OE2" Residue "A PHE 2586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2618": "NH1" <-> "NH2" Residue "A ASP 2619": "OD1" <-> "OD2" Residue "A ARG 2677": "NH1" <-> "NH2" Residue "A ARG 2679": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C ARG 376": "NH1" <-> "NH2" Residue "C ASP 379": "OD1" <-> "OD2" Residue "C ARG 511": "NH1" <-> "NH2" Residue "C GLU 512": "OE1" <-> "OE2" Residue "C ARG 568": "NH1" <-> "NH2" Residue "C ARG 2200": "NH1" <-> "NH2" Residue "C ARG 2203": "NH1" <-> "NH2" Residue "C GLU 2248": "OE1" <-> "OE2" Residue "C PHE 2294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2301": "NH1" <-> "NH2" Residue "C ARG 2343": "NH1" <-> "NH2" Residue "C ARG 2381": "NH1" <-> "NH2" Residue "C GLU 2410": "OE1" <-> "OE2" Residue "C PHE 2411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2423": "NH1" <-> "NH2" Residue "C ARG 2439": "NH1" <-> "NH2" Residue "C GLU 2559": "OE1" <-> "OE2" Residue "C PHE 2586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2618": "NH1" <-> "NH2" Residue "C ASP 2619": "OD1" <-> "OD2" Residue "C ARG 2677": "NH1" <-> "NH2" Residue "C ARG 2679": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B ASP 379": "OD1" <-> "OD2" Residue "B ARG 511": "NH1" <-> "NH2" Residue "B GLU 512": "OE1" <-> "OE2" Residue "B ARG 568": "NH1" <-> "NH2" Residue "B ARG 2200": "NH1" <-> "NH2" Residue "B ARG 2203": "NH1" <-> "NH2" Residue "B GLU 2248": "OE1" <-> "OE2" Residue "B PHE 2294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2301": "NH1" <-> "NH2" Residue "B ARG 2343": "NH1" <-> "NH2" Residue "B ARG 2381": "NH1" <-> "NH2" Residue "B GLU 2410": "OE1" <-> "OE2" Residue "B PHE 2411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2423": "NH1" <-> "NH2" Residue "B ARG 2439": "NH1" <-> "NH2" Residue "B GLU 2559": "OE1" <-> "OE2" Residue "B PHE 2586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2618": "NH1" <-> "NH2" Residue "B ASP 2619": "OD1" <-> "OD2" Residue "B ARG 2677": "NH1" <-> "NH2" Residue "B ARG 2679": "NH1" <-> "NH2" Residue "D ARG 269": "NH1" <-> "NH2" Residue "D ARG 376": "NH1" <-> "NH2" Residue "D ASP 379": "OD1" <-> "OD2" Residue "D ARG 511": "NH1" <-> "NH2" Residue "D GLU 512": "OE1" <-> "OE2" Residue "D ARG 568": "NH1" <-> "NH2" Residue "D ARG 2200": "NH1" <-> "NH2" Residue "D ARG 2203": "NH1" <-> "NH2" Residue "D GLU 2248": "OE1" <-> "OE2" Residue "D PHE 2294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2301": "NH1" <-> "NH2" Residue "D ARG 2343": "NH1" <-> "NH2" Residue "D ARG 2381": "NH1" <-> "NH2" Residue "D GLU 2410": "OE1" <-> "OE2" Residue "D PHE 2411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2423": "NH1" <-> "NH2" Residue "D ARG 2439": "NH1" <-> "NH2" Residue "D GLU 2559": "OE1" <-> "OE2" Residue "D PHE 2586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2618": "NH1" <-> "NH2" Residue "D ASP 2619": "OD1" <-> "OD2" Residue "D ARG 2677": "NH1" <-> "NH2" Residue "D ARG 2679": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 50164 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 12499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2149, 12499 Classifications: {'peptide': 2149} Incomplete info: {'backbone_only': 1090, 'truncation_to_alanine': 53} Link IDs: {'CIS': 1, 'PTRANS': 60, 'TRANS': 2087} Chain breaks: 19 Unresolved chain link angles: 26 Unresolved non-hydrogen bonds: 5020 Unresolved non-hydrogen angles: 7154 Unresolved non-hydrogen dihedrals: 3211 Unresolved non-hydrogen chiralities: 1447 Planarities with less than four sites: {'GLN:plan1': 68, 'HIS:plan': 34, 'TYR:plan': 36, 'ASN:plan1': 68, 'TRP:plan': 3, 'ASP:plan': 65, 'PHE:plan': 51, 'GLU:plan': 95, 'ARG:plan': 72} Unresolved non-hydrogen planarities: 2413 Chain: "C" Number of atoms: 12499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2149, 12499 Classifications: {'peptide': 2149} Incomplete info: {'backbone_only': 1090, 'truncation_to_alanine': 53} Link IDs: {'CIS': 1, 'PTRANS': 60, 'TRANS': 2087} Chain breaks: 19 Unresolved chain link angles: 26 Unresolved non-hydrogen bonds: 5020 Unresolved non-hydrogen angles: 7154 Unresolved non-hydrogen dihedrals: 3211 Unresolved non-hydrogen chiralities: 1447 Planarities with less than four sites: {'GLN:plan1': 68, 'HIS:plan': 34, 'TYR:plan': 36, 'ASN:plan1': 68, 'TRP:plan': 3, 'ASP:plan': 65, 'PHE:plan': 51, 'GLU:plan': 95, 'ARG:plan': 72} Unresolved non-hydrogen planarities: 2413 Chain: "B" Number of atoms: 12499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2149, 12499 Classifications: {'peptide': 2149} Incomplete info: {'backbone_only': 1090, 'truncation_to_alanine': 53} Link IDs: {'CIS': 1, 'PTRANS': 60, 'TRANS': 2087} Chain breaks: 19 Unresolved chain link angles: 26 Unresolved non-hydrogen bonds: 5020 Unresolved non-hydrogen angles: 7154 Unresolved non-hydrogen dihedrals: 3211 Unresolved non-hydrogen chiralities: 1447 Planarities with less than four sites: {'GLN:plan1': 68, 'HIS:plan': 34, 'TYR:plan': 36, 'ASN:plan1': 68, 'TRP:plan': 3, 'ASP:plan': 65, 'PHE:plan': 51, 'GLU:plan': 95, 'ARG:plan': 72} Unresolved non-hydrogen planarities: 2413 Chain: "D" Number of atoms: 12499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2149, 12499 Classifications: {'peptide': 2149} Incomplete info: {'backbone_only': 1090, 'truncation_to_alanine': 53} Link IDs: {'CIS': 1, 'PTRANS': 60, 'TRANS': 2087} Chain breaks: 19 Unresolved chain link angles: 26 Unresolved non-hydrogen bonds: 5020 Unresolved non-hydrogen angles: 7154 Unresolved non-hydrogen dihedrals: 3211 Unresolved non-hydrogen chiralities: 1447 Planarities with less than four sites: {'GLN:plan1': 68, 'HIS:plan': 34, 'TYR:plan': 36, 'ASN:plan1': 68, 'TRP:plan': 3, 'ASP:plan': 65, 'PHE:plan': 51, 'GLU:plan': 95, 'ARG:plan': 72} Unresolved non-hydrogen planarities: 2413 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'JYP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'JYP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'JYP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'JYP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N PHE A 166 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE A 166 " occ=0.00 residue: pdb=" N PRO A 502 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO A 502 " occ=0.00 residue: pdb=" N PHE C 166 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE C 166 " occ=0.00 residue: pdb=" N PRO C 502 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO C 502 " occ=0.00 residue: pdb=" N PHE B 166 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE B 166 " occ=0.00 residue: pdb=" N PRO B 502 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO B 502 " occ=0.00 residue: pdb=" N PHE D 166 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE D 166 " occ=0.00 residue: pdb=" N PRO D 502 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO D 502 " occ=0.00 Time building chain proxies: 27.19, per 1000 atoms: 0.54 Number of scatterers: 50164 At special positions: 0 Unit cell: (238.14, 238.14, 196.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 176 16.00 P 12 15.00 O 10520 8.00 N 9968 7.00 C 29488 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=20, symmetry=0 Number of additional bonds: simple=20, symmetry=0 Coordination: Other bonds: Time building additional restraints: 24.49 Conformation dependent library (CDL) restraints added in 11.1 seconds 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7688 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 376 helices and 20 sheets defined 55.2% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 22.23 Creating SS restraints... Processing helix chain 'A' and resid 67 through 80 removed outlier: 3.798A pdb=" N ALA A 75 " --> pdb=" O GLN A 71 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS A 77 " --> pdb=" O TRP A 73 " (cutoff:3.500A) Proline residue: A 78 - end of helix Processing helix chain 'A' and resid 86 through 110 removed outlier: 6.011A pdb=" N LYS A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 229 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 437 through 462 Processing helix chain 'A' and resid 468 through 472 Processing helix chain 'A' and resid 477 through 484 removed outlier: 4.378A pdb=" N VAL A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 512 Processing helix chain 'A' and resid 515 through 531 Proline residue: A 526 - end of helix Processing helix chain 'A' and resid 547 through 566 removed outlier: 3.607A pdb=" N LEU A 555 " --> pdb=" O HIS A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 584 removed outlier: 4.241A pdb=" N GLY A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N PHE A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 612 through 625 Processing helix chain 'A' and resid 628 through 635 Processing helix chain 'A' and resid 640 through 646 Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 649 through 661 Proline residue: A 659 - end of helix Processing helix chain 'A' and resid 708 through 722 Processing helix chain 'A' and resid 730 through 741 Processing helix chain 'A' and resid 749 through 755 Processing helix chain 'A' and resid 761 through 770 Processing helix chain 'A' and resid 774 through 793 removed outlier: 3.961A pdb=" N ASP A 793 " --> pdb=" O HIS A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 850 Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 877 through 895 Processing helix chain 'A' and resid 961 through 995 Processing helix chain 'A' and resid 999 through 1005 Processing helix chain 'A' and resid 1029 through 1040 removed outlier: 3.560A pdb=" N ILE A1033 " --> pdb=" O ASP A1029 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU A1038 " --> pdb=" O GLU A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1067 Processing helix chain 'A' and resid 1073 through 1097 removed outlier: 3.622A pdb=" N PHE A1087 " --> pdb=" O LEU A1083 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN A1089 " --> pdb=" O ARG A1085 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG A1090 " --> pdb=" O HIS A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1129 removed outlier: 4.406A pdb=" N GLN A1117 " --> pdb=" O GLN A1114 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP A1118 " --> pdb=" O ILE A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1181 Processing helix chain 'A' and resid 1197 through 1201 Processing helix chain 'A' and resid 1203 through 1208 Processing helix chain 'A' and resid 1229 through 1245 Processing helix chain 'A' and resid 1251 through 1259 Processing helix chain 'A' and resid 1270 through 1276 Processing helix chain 'A' and resid 1281 through 1285 removed outlier: 4.007A pdb=" N SER A1285 " --> pdb=" O GLN A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1298 removed outlier: 3.659A pdb=" N HIS A1297 " --> pdb=" O GLN A1293 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1314 Processing helix chain 'A' and resid 1325 through 1336 Processing helix chain 'A' and resid 1355 through 1358 No H-bonds generated for 'chain 'A' and resid 1355 through 1358' Processing helix chain 'A' and resid 1372 through 1384 Processing helix chain 'A' and resid 1392 through 1403 Proline residue: A1402 - end of helix Processing helix chain 'A' and resid 1406 through 1410 Processing helix chain 'A' and resid 1434 through 1440 Processing helix chain 'A' and resid 1442 through 1445 removed outlier: 4.105A pdb=" N ASN A1445 " --> pdb=" O TYR A1442 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1442 through 1445' Processing helix chain 'A' and resid 1449 through 1453 Processing helix chain 'A' and resid 1477 through 1484 Processing helix chain 'A' and resid 1506 through 1516 Processing helix chain 'A' and resid 1526 through 1537 Processing helix chain 'A' and resid 1600 through 1618 Proline residue: A1617 - end of helix Processing helix chain 'A' and resid 1621 through 1636 Proline residue: A1633 - end of helix Processing helix chain 'A' and resid 1654 through 1665 Processing helix chain 'A' and resid 1670 through 1683 Processing helix chain 'A' and resid 1795 through 1802 Processing helix chain 'A' and resid 1804 through 1813 Processing helix chain 'A' and resid 1818 through 1824 Processing helix chain 'A' and resid 1828 through 1830 No H-bonds generated for 'chain 'A' and resid 1828 through 1830' Processing helix chain 'A' and resid 1837 through 1848 removed outlier: 3.595A pdb=" N CYS A1845 " --> pdb=" O HIS A1841 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A1848 " --> pdb=" O PHE A1844 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1875 Processing helix chain 'A' and resid 1962 through 1978 Proline residue: A1968 - end of helix Processing helix chain 'A' and resid 1983 through 1990 Processing helix chain 'A' and resid 1993 through 1997 Processing helix chain 'A' and resid 2001 through 2012 Processing helix chain 'A' and resid 2022 through 2042 removed outlier: 6.080A pdb=" N LYS A2028 " --> pdb=" O TYR A2024 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASN A2029 " --> pdb=" O ILE A2025 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A2030 " --> pdb=" O ASN A2026 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ALA A2031 " --> pdb=" O GLU A2027 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A2032 " --> pdb=" O LYS A2028 " (cutoff:3.500A) Processing helix chain 'A' and resid 2048 through 2061 Processing helix chain 'A' and resid 2064 through 2071 Processing helix chain 'A' and resid 2081 through 2103 Processing helix chain 'A' and resid 2106 through 2115 Processing helix chain 'A' and resid 2119 through 2136 Processing helix chain 'A' and resid 2149 through 2166 removed outlier: 3.860A pdb=" N HIS A2166 " --> pdb=" O GLN A2162 " (cutoff:3.500A) Processing helix chain 'A' and resid 2168 through 2178 Proline residue: A2176 - end of helix Processing helix chain 'A' and resid 2183 through 2190 Processing helix chain 'A' and resid 2222 through 2229 removed outlier: 3.580A pdb=" N ARG A2226 " --> pdb=" O GLU A2222 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A2228 " --> pdb=" O LYS A2224 " (cutoff:3.500A) Processing helix chain 'A' and resid 2240 through 2262 removed outlier: 3.634A pdb=" N TRP A2256 " --> pdb=" O GLU A2253 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A2262 " --> pdb=" O LYS A2259 " (cutoff:3.500A) Processing helix chain 'A' and resid 2264 through 2293 removed outlier: 3.578A pdb=" N ARG A2271 " --> pdb=" O TYR A2267 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN A2272 " --> pdb=" O TRP A2268 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N SER A2274 " --> pdb=" O ALA A2270 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N PHE A2275 " --> pdb=" O ARG A2271 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU A2290 " --> pdb=" O LEU A2286 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A2291 " --> pdb=" O MET A2287 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA A2292 " --> pdb=" O ASN A2288 " (cutoff:3.500A) Processing helix chain 'A' and resid 2336 through 2346 removed outlier: 3.854A pdb=" N THR A2340 " --> pdb=" O LEU A2336 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2375 Processing helix chain 'A' and resid 2385 through 2406 removed outlier: 4.498A pdb=" N ASP A2389 " --> pdb=" O ALA A2385 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS A2402 " --> pdb=" O TYR A2398 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A2403 " --> pdb=" O LEU A2399 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET A2404 " --> pdb=" O LEU A2400 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A2405 " --> pdb=" O ILE A2401 " (cutoff:3.500A) Processing helix chain 'A' and resid 2413 through 2423 Processing helix chain 'A' and resid 2425 through 2434 removed outlier: 4.039A pdb=" N VAL A2434 " --> pdb=" O VAL A2430 " (cutoff:3.500A) Processing helix chain 'A' and resid 2436 through 2438 No H-bonds generated for 'chain 'A' and resid 2436 through 2438' Processing helix chain 'A' and resid 2442 through 2451 removed outlier: 4.125A pdb=" N ALA A2446 " --> pdb=" O ILE A2442 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A2447 " --> pdb=" O LEU A2443 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA A2448 " --> pdb=" O THR A2444 " (cutoff:3.500A) Processing helix chain 'A' and resid 2453 through 2462 removed outlier: 4.234A pdb=" N ILE A2457 " --> pdb=" O TYR A2453 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE A2462 " --> pdb=" O VAL A2458 " (cutoff:3.500A) Processing helix chain 'A' and resid 2535 through 2542 removed outlier: 3.824A pdb=" N LEU A2539 " --> pdb=" O ILE A2535 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N SER A2540 " --> pdb=" O VAL A2536 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N HIS A2541 " --> pdb=" O THR A2537 " (cutoff:3.500A) Processing helix chain 'A' and resid 2560 through 2598 removed outlier: 3.850A pdb=" N VAL A2581 " --> pdb=" O VAL A2577 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A2588 " --> pdb=" O LEU A2584 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE A2589 " --> pdb=" O ILE A2585 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE A2593 " --> pdb=" O ILE A2589 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG A2597 " --> pdb=" O PHE A2593 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER A2598 " --> pdb=" O ALA A2594 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2605 Processing helix chain 'A' and resid 2619 through 2624 Processing helix chain 'A' and resid 2629 through 2634 removed outlier: 4.152A pdb=" N ILE A2632 " --> pdb=" O GLU A2629 " (cutoff:3.500A) Processing helix chain 'A' and resid 2638 through 2648 Processing helix chain 'A' and resid 2660 through 2669 removed outlier: 3.847A pdb=" N GLU A2665 " --> pdb=" O SER A2661 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A2666 " --> pdb=" O TYR A2662 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ARG A2668 " --> pdb=" O ALA A2664 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU A2669 " --> pdb=" O GLU A2665 " (cutoff:3.500A) Processing helix chain 'A' and resid 2686 through 2692 removed outlier: 3.547A pdb=" N GLY A2690 " --> pdb=" O SER A2686 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU A2691 " --> pdb=" O ASP A2687 " (cutoff:3.500A) Processing helix chain 'A' and resid 2696 through 2712 Processing helix chain 'A' and resid 2714 through 2736 Processing helix chain 'C' and resid 67 through 80 removed outlier: 3.798A pdb=" N ALA C 75 " --> pdb=" O GLN C 71 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA C 76 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS C 77 " --> pdb=" O TRP C 73 " (cutoff:3.500A) Proline residue: C 78 - end of helix Processing helix chain 'C' and resid 86 through 110 removed outlier: 6.011A pdb=" N LYS C 109 " --> pdb=" O THR C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 229 Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 437 through 462 Processing helix chain 'C' and resid 468 through 472 Processing helix chain 'C' and resid 477 through 484 removed outlier: 4.378A pdb=" N VAL C 484 " --> pdb=" O LEU C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 512 Processing helix chain 'C' and resid 515 through 531 Proline residue: C 526 - end of helix Processing helix chain 'C' and resid 547 through 566 removed outlier: 3.608A pdb=" N LEU C 555 " --> pdb=" O HIS C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 584 removed outlier: 4.241A pdb=" N GLY C 579 " --> pdb=" O ALA C 575 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N PHE C 580 " --> pdb=" O LYS C 576 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET C 581 " --> pdb=" O GLN C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 609 Processing helix chain 'C' and resid 612 through 625 Processing helix chain 'C' and resid 628 through 635 Processing helix chain 'C' and resid 640 through 646 Proline residue: C 646 - end of helix Processing helix chain 'C' and resid 649 through 661 Proline residue: C 659 - end of helix Processing helix chain 'C' and resid 708 through 722 Processing helix chain 'C' and resid 730 through 741 Processing helix chain 'C' and resid 749 through 755 Processing helix chain 'C' and resid 761 through 770 Processing helix chain 'C' and resid 774 through 793 removed outlier: 3.961A pdb=" N ASP C 793 " --> pdb=" O HIS C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 850 Processing helix chain 'C' and resid 857 through 873 Processing helix chain 'C' and resid 877 through 895 Processing helix chain 'C' and resid 961 through 995 Processing helix chain 'C' and resid 999 through 1005 Processing helix chain 'C' and resid 1029 through 1040 removed outlier: 3.560A pdb=" N ILE C1033 " --> pdb=" O ASP C1029 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU C1038 " --> pdb=" O GLU C1034 " (cutoff:3.500A) Processing helix chain 'C' and resid 1057 through 1067 Processing helix chain 'C' and resid 1073 through 1097 removed outlier: 3.622A pdb=" N PHE C1087 " --> pdb=" O LEU C1083 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN C1089 " --> pdb=" O ARG C1085 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG C1090 " --> pdb=" O HIS C1086 " (cutoff:3.500A) Processing helix chain 'C' and resid 1107 through 1129 removed outlier: 4.405A pdb=" N GLN C1117 " --> pdb=" O GLN C1114 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP C1118 " --> pdb=" O ILE C1115 " (cutoff:3.500A) Processing helix chain 'C' and resid 1177 through 1181 Processing helix chain 'C' and resid 1197 through 1201 Processing helix chain 'C' and resid 1203 through 1208 Processing helix chain 'C' and resid 1229 through 1245 Processing helix chain 'C' and resid 1251 through 1259 Processing helix chain 'C' and resid 1270 through 1276 Processing helix chain 'C' and resid 1281 through 1285 removed outlier: 4.007A pdb=" N SER C1285 " --> pdb=" O GLN C1282 " (cutoff:3.500A) Processing helix chain 'C' and resid 1291 through 1298 removed outlier: 3.659A pdb=" N HIS C1297 " --> pdb=" O GLN C1293 " (cutoff:3.500A) Processing helix chain 'C' and resid 1309 through 1314 Processing helix chain 'C' and resid 1325 through 1336 Processing helix chain 'C' and resid 1355 through 1358 No H-bonds generated for 'chain 'C' and resid 1355 through 1358' Processing helix chain 'C' and resid 1372 through 1384 Processing helix chain 'C' and resid 1392 through 1403 Proline residue: C1402 - end of helix Processing helix chain 'C' and resid 1406 through 1410 Processing helix chain 'C' and resid 1434 through 1440 Processing helix chain 'C' and resid 1442 through 1445 removed outlier: 4.105A pdb=" N ASN C1445 " --> pdb=" O TYR C1442 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1442 through 1445' Processing helix chain 'C' and resid 1449 through 1453 Processing helix chain 'C' and resid 1477 through 1484 Processing helix chain 'C' and resid 1506 through 1516 Processing helix chain 'C' and resid 1526 through 1537 Processing helix chain 'C' and resid 1600 through 1618 Proline residue: C1617 - end of helix Processing helix chain 'C' and resid 1621 through 1636 Proline residue: C1633 - end of helix Processing helix chain 'C' and resid 1654 through 1665 Processing helix chain 'C' and resid 1670 through 1683 Processing helix chain 'C' and resid 1795 through 1802 Processing helix chain 'C' and resid 1804 through 1813 Processing helix chain 'C' and resid 1818 through 1824 Processing helix chain 'C' and resid 1828 through 1830 No H-bonds generated for 'chain 'C' and resid 1828 through 1830' Processing helix chain 'C' and resid 1837 through 1848 removed outlier: 3.596A pdb=" N CYS C1845 " --> pdb=" O HIS C1841 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR C1848 " --> pdb=" O PHE C1844 " (cutoff:3.500A) Processing helix chain 'C' and resid 1852 through 1875 Processing helix chain 'C' and resid 1962 through 1978 Proline residue: C1968 - end of helix Processing helix chain 'C' and resid 1983 through 1990 Processing helix chain 'C' and resid 1993 through 1997 Processing helix chain 'C' and resid 2001 through 2012 Processing helix chain 'C' and resid 2022 through 2042 removed outlier: 6.080A pdb=" N LYS C2028 " --> pdb=" O TYR C2024 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASN C2029 " --> pdb=" O ILE C2025 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C2030 " --> pdb=" O ASN C2026 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ALA C2031 " --> pdb=" O GLU C2027 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU C2032 " --> pdb=" O LYS C2028 " (cutoff:3.500A) Processing helix chain 'C' and resid 2048 through 2061 Processing helix chain 'C' and resid 2064 through 2071 Processing helix chain 'C' and resid 2081 through 2103 Processing helix chain 'C' and resid 2106 through 2115 Processing helix chain 'C' and resid 2119 through 2136 Processing helix chain 'C' and resid 2149 through 2166 removed outlier: 3.860A pdb=" N HIS C2166 " --> pdb=" O GLN C2162 " (cutoff:3.500A) Processing helix chain 'C' and resid 2168 through 2178 Proline residue: C2176 - end of helix Processing helix chain 'C' and resid 2183 through 2190 Processing helix chain 'C' and resid 2222 through 2229 removed outlier: 3.580A pdb=" N ARG C2226 " --> pdb=" O GLU C2222 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR C2228 " --> pdb=" O LYS C2224 " (cutoff:3.500A) Processing helix chain 'C' and resid 2240 through 2262 removed outlier: 3.634A pdb=" N TRP C2256 " --> pdb=" O GLU C2253 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C2262 " --> pdb=" O LYS C2259 " (cutoff:3.500A) Processing helix chain 'C' and resid 2264 through 2293 removed outlier: 3.579A pdb=" N ARG C2271 " --> pdb=" O TYR C2267 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN C2272 " --> pdb=" O TRP C2268 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N SER C2274 " --> pdb=" O ALA C2270 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N PHE C2275 " --> pdb=" O ARG C2271 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU C2290 " --> pdb=" O LEU C2286 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C2291 " --> pdb=" O MET C2287 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA C2292 " --> pdb=" O ASN C2288 " (cutoff:3.500A) Processing helix chain 'C' and resid 2336 through 2346 removed outlier: 3.853A pdb=" N THR C2340 " --> pdb=" O LEU C2336 " (cutoff:3.500A) Processing helix chain 'C' and resid 2352 through 2375 Processing helix chain 'C' and resid 2385 through 2406 removed outlier: 4.497A pdb=" N ASP C2389 " --> pdb=" O ALA C2385 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS C2402 " --> pdb=" O TYR C2398 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA C2403 " --> pdb=" O LEU C2399 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET C2404 " --> pdb=" O LEU C2400 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY C2405 " --> pdb=" O ILE C2401 " (cutoff:3.500A) Processing helix chain 'C' and resid 2413 through 2423 Processing helix chain 'C' and resid 2425 through 2434 removed outlier: 4.039A pdb=" N VAL C2434 " --> pdb=" O VAL C2430 " (cutoff:3.500A) Processing helix chain 'C' and resid 2436 through 2438 No H-bonds generated for 'chain 'C' and resid 2436 through 2438' Processing helix chain 'C' and resid 2442 through 2451 removed outlier: 4.125A pdb=" N ALA C2446 " --> pdb=" O ILE C2442 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C2447 " --> pdb=" O LEU C2443 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA C2448 " --> pdb=" O THR C2444 " (cutoff:3.500A) Processing helix chain 'C' and resid 2453 through 2462 removed outlier: 4.234A pdb=" N ILE C2457 " --> pdb=" O TYR C2453 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE C2462 " --> pdb=" O VAL C2458 " (cutoff:3.500A) Processing helix chain 'C' and resid 2535 through 2542 removed outlier: 3.824A pdb=" N LEU C2539 " --> pdb=" O ILE C2535 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N SER C2540 " --> pdb=" O VAL C2536 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N HIS C2541 " --> pdb=" O THR C2537 " (cutoff:3.500A) Processing helix chain 'C' and resid 2560 through 2598 removed outlier: 3.850A pdb=" N VAL C2581 " --> pdb=" O VAL C2577 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL C2588 " --> pdb=" O LEU C2584 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE C2589 " --> pdb=" O ILE C2585 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE C2593 " --> pdb=" O ILE C2589 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG C2597 " --> pdb=" O PHE C2593 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER C2598 " --> pdb=" O ALA C2594 " (cutoff:3.500A) Processing helix chain 'C' and resid 2600 through 2608 removed outlier: 3.506A pdb=" N ILE C2606 " --> pdb=" O LYS C2602 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU C2607 " --> pdb=" O LYS C2603 " (cutoff:3.500A) Processing helix chain 'C' and resid 2619 through 2624 Processing helix chain 'C' and resid 2629 through 2634 removed outlier: 4.153A pdb=" N ILE C2632 " --> pdb=" O GLU C2629 " (cutoff:3.500A) Processing helix chain 'C' and resid 2638 through 2648 Processing helix chain 'C' and resid 2660 through 2669 removed outlier: 3.847A pdb=" N GLU C2665 " --> pdb=" O SER C2661 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET C2666 " --> pdb=" O TYR C2662 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ARG C2668 " --> pdb=" O ALA C2664 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU C2669 " --> pdb=" O GLU C2665 " (cutoff:3.500A) Processing helix chain 'C' and resid 2686 through 2692 removed outlier: 3.547A pdb=" N GLY C2690 " --> pdb=" O SER C2686 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU C2691 " --> pdb=" O ASP C2687 " (cutoff:3.500A) Processing helix chain 'C' and resid 2696 through 2712 Processing helix chain 'C' and resid 2714 through 2736 Processing helix chain 'B' and resid 67 through 80 removed outlier: 3.797A pdb=" N ALA B 75 " --> pdb=" O GLN B 71 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA B 76 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS B 77 " --> pdb=" O TRP B 73 " (cutoff:3.500A) Proline residue: B 78 - end of helix Processing helix chain 'B' and resid 86 through 110 removed outlier: 6.011A pdb=" N LYS B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 229 Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 437 through 462 Processing helix chain 'B' and resid 468 through 472 Processing helix chain 'B' and resid 477 through 484 removed outlier: 4.379A pdb=" N VAL B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 512 Processing helix chain 'B' and resid 515 through 531 Proline residue: B 526 - end of helix Processing helix chain 'B' and resid 547 through 566 removed outlier: 3.607A pdb=" N LEU B 555 " --> pdb=" O HIS B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 584 removed outlier: 4.241A pdb=" N GLY B 579 " --> pdb=" O ALA B 575 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N PHE B 580 " --> pdb=" O LYS B 576 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 609 Processing helix chain 'B' and resid 612 through 625 Processing helix chain 'B' and resid 628 through 635 Processing helix chain 'B' and resid 640 through 646 Proline residue: B 646 - end of helix Processing helix chain 'B' and resid 649 through 661 Proline residue: B 659 - end of helix Processing helix chain 'B' and resid 708 through 722 Processing helix chain 'B' and resid 730 through 741 Processing helix chain 'B' and resid 749 through 755 Processing helix chain 'B' and resid 761 through 770 Processing helix chain 'B' and resid 774 through 793 removed outlier: 3.960A pdb=" N ASP B 793 " --> pdb=" O HIS B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 850 Processing helix chain 'B' and resid 857 through 873 Processing helix chain 'B' and resid 877 through 895 Processing helix chain 'B' and resid 961 through 995 Processing helix chain 'B' and resid 999 through 1005 Processing helix chain 'B' and resid 1029 through 1040 removed outlier: 3.560A pdb=" N ILE B1033 " --> pdb=" O ASP B1029 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU B1038 " --> pdb=" O GLU B1034 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1067 Processing helix chain 'B' and resid 1073 through 1097 removed outlier: 3.621A pdb=" N PHE B1087 " --> pdb=" O LEU B1083 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN B1089 " --> pdb=" O ARG B1085 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG B1090 " --> pdb=" O HIS B1086 " (cutoff:3.500A) Processing helix chain 'B' and resid 1107 through 1129 removed outlier: 4.406A pdb=" N GLN B1117 " --> pdb=" O GLN B1114 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP B1118 " --> pdb=" O ILE B1115 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1181 Processing helix chain 'B' and resid 1197 through 1201 Processing helix chain 'B' and resid 1203 through 1208 Processing helix chain 'B' and resid 1229 through 1245 Processing helix chain 'B' and resid 1251 through 1259 Processing helix chain 'B' and resid 1270 through 1276 Processing helix chain 'B' and resid 1281 through 1285 removed outlier: 4.006A pdb=" N SER B1285 " --> pdb=" O GLN B1282 " (cutoff:3.500A) Processing helix chain 'B' and resid 1291 through 1298 removed outlier: 3.658A pdb=" N HIS B1297 " --> pdb=" O GLN B1293 " (cutoff:3.500A) Processing helix chain 'B' and resid 1309 through 1314 Processing helix chain 'B' and resid 1325 through 1336 Processing helix chain 'B' and resid 1355 through 1358 No H-bonds generated for 'chain 'B' and resid 1355 through 1358' Processing helix chain 'B' and resid 1372 through 1384 Processing helix chain 'B' and resid 1392 through 1403 Proline residue: B1402 - end of helix Processing helix chain 'B' and resid 1406 through 1410 Processing helix chain 'B' and resid 1434 through 1440 Processing helix chain 'B' and resid 1442 through 1445 removed outlier: 4.105A pdb=" N ASN B1445 " --> pdb=" O TYR B1442 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1442 through 1445' Processing helix chain 'B' and resid 1449 through 1453 Processing helix chain 'B' and resid 1477 through 1484 Processing helix chain 'B' and resid 1506 through 1516 Processing helix chain 'B' and resid 1526 through 1537 Processing helix chain 'B' and resid 1600 through 1618 Proline residue: B1617 - end of helix Processing helix chain 'B' and resid 1621 through 1636 Proline residue: B1633 - end of helix Processing helix chain 'B' and resid 1654 through 1665 Processing helix chain 'B' and resid 1670 through 1683 Processing helix chain 'B' and resid 1795 through 1802 Processing helix chain 'B' and resid 1804 through 1813 Processing helix chain 'B' and resid 1818 through 1824 Processing helix chain 'B' and resid 1828 through 1830 No H-bonds generated for 'chain 'B' and resid 1828 through 1830' Processing helix chain 'B' and resid 1837 through 1848 removed outlier: 3.595A pdb=" N CYS B1845 " --> pdb=" O HIS B1841 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR B1848 " --> pdb=" O PHE B1844 " (cutoff:3.500A) Processing helix chain 'B' and resid 1852 through 1875 Processing helix chain 'B' and resid 1962 through 1978 Proline residue: B1968 - end of helix Processing helix chain 'B' and resid 1983 through 1990 Processing helix chain 'B' and resid 1993 through 1997 Processing helix chain 'B' and resid 2001 through 2012 Processing helix chain 'B' and resid 2022 through 2042 removed outlier: 6.080A pdb=" N LYS B2028 " --> pdb=" O TYR B2024 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASN B2029 " --> pdb=" O ILE B2025 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B2030 " --> pdb=" O ASN B2026 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ALA B2031 " --> pdb=" O GLU B2027 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU B2032 " --> pdb=" O LYS B2028 " (cutoff:3.500A) Processing helix chain 'B' and resid 2048 through 2061 Processing helix chain 'B' and resid 2064 through 2071 Processing helix chain 'B' and resid 2081 through 2103 Processing helix chain 'B' and resid 2106 through 2115 Processing helix chain 'B' and resid 2119 through 2136 Processing helix chain 'B' and resid 2149 through 2166 removed outlier: 3.860A pdb=" N HIS B2166 " --> pdb=" O GLN B2162 " (cutoff:3.500A) Processing helix chain 'B' and resid 2168 through 2178 Proline residue: B2176 - end of helix Processing helix chain 'B' and resid 2183 through 2190 Processing helix chain 'B' and resid 2222 through 2229 removed outlier: 3.580A pdb=" N ARG B2226 " --> pdb=" O GLU B2222 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR B2228 " --> pdb=" O LYS B2224 " (cutoff:3.500A) Processing helix chain 'B' and resid 2240 through 2262 removed outlier: 3.633A pdb=" N TRP B2256 " --> pdb=" O GLU B2253 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B2262 " --> pdb=" O LYS B2259 " (cutoff:3.500A) Processing helix chain 'B' and resid 2264 through 2293 removed outlier: 3.578A pdb=" N ARG B2271 " --> pdb=" O TYR B2267 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN B2272 " --> pdb=" O TRP B2268 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N SER B2274 " --> pdb=" O ALA B2270 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N PHE B2275 " --> pdb=" O ARG B2271 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LEU B2290 " --> pdb=" O LEU B2286 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B2291 " --> pdb=" O MET B2287 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA B2292 " --> pdb=" O ASN B2288 " (cutoff:3.500A) Processing helix chain 'B' and resid 2336 through 2346 removed outlier: 3.854A pdb=" N THR B2340 " --> pdb=" O LEU B2336 " (cutoff:3.500A) Processing helix chain 'B' and resid 2352 through 2375 Processing helix chain 'B' and resid 2385 through 2406 removed outlier: 4.498A pdb=" N ASP B2389 " --> pdb=" O ALA B2385 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS B2402 " --> pdb=" O TYR B2398 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA B2403 " --> pdb=" O LEU B2399 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET B2404 " --> pdb=" O LEU B2400 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY B2405 " --> pdb=" O ILE B2401 " (cutoff:3.500A) Processing helix chain 'B' and resid 2413 through 2423 Processing helix chain 'B' and resid 2425 through 2434 removed outlier: 4.038A pdb=" N VAL B2434 " --> pdb=" O VAL B2430 " (cutoff:3.500A) Processing helix chain 'B' and resid 2436 through 2438 No H-bonds generated for 'chain 'B' and resid 2436 through 2438' Processing helix chain 'B' and resid 2442 through 2451 removed outlier: 4.124A pdb=" N ALA B2446 " --> pdb=" O ILE B2442 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B2447 " --> pdb=" O LEU B2443 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA B2448 " --> pdb=" O THR B2444 " (cutoff:3.500A) Processing helix chain 'B' and resid 2453 through 2462 removed outlier: 4.234A pdb=" N ILE B2457 " --> pdb=" O TYR B2453 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE B2462 " --> pdb=" O VAL B2458 " (cutoff:3.500A) Processing helix chain 'B' and resid 2535 through 2542 removed outlier: 3.825A pdb=" N LEU B2539 " --> pdb=" O ILE B2535 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N SER B2540 " --> pdb=" O VAL B2536 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N HIS B2541 " --> pdb=" O THR B2537 " (cutoff:3.500A) Processing helix chain 'B' and resid 2560 through 2598 removed outlier: 3.850A pdb=" N VAL B2581 " --> pdb=" O VAL B2577 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL B2588 " --> pdb=" O LEU B2584 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE B2589 " --> pdb=" O ILE B2585 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE B2593 " --> pdb=" O ILE B2589 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG B2597 " --> pdb=" O PHE B2593 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER B2598 " --> pdb=" O ALA B2594 " (cutoff:3.500A) Processing helix chain 'B' and resid 2600 through 2608 removed outlier: 3.506A pdb=" N ILE B2606 " --> pdb=" O LYS B2602 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B2607 " --> pdb=" O LYS B2603 " (cutoff:3.500A) Processing helix chain 'B' and resid 2619 through 2624 Processing helix chain 'B' and resid 2629 through 2634 removed outlier: 4.153A pdb=" N ILE B2632 " --> pdb=" O GLU B2629 " (cutoff:3.500A) Processing helix chain 'B' and resid 2638 through 2648 Processing helix chain 'B' and resid 2660 through 2669 removed outlier: 3.846A pdb=" N GLU B2665 " --> pdb=" O SER B2661 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET B2666 " --> pdb=" O TYR B2662 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ARG B2668 " --> pdb=" O ALA B2664 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU B2669 " --> pdb=" O GLU B2665 " (cutoff:3.500A) Processing helix chain 'B' and resid 2686 through 2692 removed outlier: 3.547A pdb=" N GLY B2690 " --> pdb=" O SER B2686 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU B2691 " --> pdb=" O ASP B2687 " (cutoff:3.500A) Processing helix chain 'B' and resid 2696 through 2712 Processing helix chain 'B' and resid 2714 through 2736 Processing helix chain 'D' and resid 67 through 80 removed outlier: 3.798A pdb=" N ALA D 75 " --> pdb=" O GLN D 71 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA D 76 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS D 77 " --> pdb=" O TRP D 73 " (cutoff:3.500A) Proline residue: D 78 - end of helix Processing helix chain 'D' and resid 86 through 110 removed outlier: 6.011A pdb=" N LYS D 109 " --> pdb=" O THR D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 229 Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 437 through 462 Processing helix chain 'D' and resid 468 through 472 Processing helix chain 'D' and resid 477 through 484 removed outlier: 4.378A pdb=" N VAL D 484 " --> pdb=" O LEU D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 512 Processing helix chain 'D' and resid 515 through 531 Proline residue: D 526 - end of helix Processing helix chain 'D' and resid 547 through 566 removed outlier: 3.607A pdb=" N LEU D 555 " --> pdb=" O HIS D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 584 removed outlier: 4.240A pdb=" N GLY D 579 " --> pdb=" O ALA D 575 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N PHE D 580 " --> pdb=" O LYS D 576 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 609 Processing helix chain 'D' and resid 612 through 625 Processing helix chain 'D' and resid 628 through 635 Processing helix chain 'D' and resid 640 through 646 Proline residue: D 646 - end of helix Processing helix chain 'D' and resid 649 through 661 Proline residue: D 659 - end of helix Processing helix chain 'D' and resid 708 through 722 Processing helix chain 'D' and resid 730 through 741 Processing helix chain 'D' and resid 749 through 755 Processing helix chain 'D' and resid 761 through 770 Processing helix chain 'D' and resid 774 through 793 removed outlier: 3.961A pdb=" N ASP D 793 " --> pdb=" O HIS D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 826 through 850 Processing helix chain 'D' and resid 857 through 873 Processing helix chain 'D' and resid 877 through 895 Processing helix chain 'D' and resid 961 through 995 Processing helix chain 'D' and resid 999 through 1005 Processing helix chain 'D' and resid 1029 through 1040 removed outlier: 3.559A pdb=" N ILE D1033 " --> pdb=" O ASP D1029 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU D1038 " --> pdb=" O GLU D1034 " (cutoff:3.500A) Processing helix chain 'D' and resid 1057 through 1067 Processing helix chain 'D' and resid 1073 through 1097 removed outlier: 3.622A pdb=" N PHE D1087 " --> pdb=" O LEU D1083 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN D1089 " --> pdb=" O ARG D1085 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG D1090 " --> pdb=" O HIS D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1107 through 1129 removed outlier: 4.406A pdb=" N GLN D1117 " --> pdb=" O GLN D1114 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP D1118 " --> pdb=" O ILE D1115 " (cutoff:3.500A) Processing helix chain 'D' and resid 1177 through 1181 Processing helix chain 'D' and resid 1197 through 1201 Processing helix chain 'D' and resid 1203 through 1208 Processing helix chain 'D' and resid 1229 through 1245 Processing helix chain 'D' and resid 1251 through 1259 Processing helix chain 'D' and resid 1270 through 1276 Processing helix chain 'D' and resid 1281 through 1285 removed outlier: 4.007A pdb=" N SER D1285 " --> pdb=" O GLN D1282 " (cutoff:3.500A) Processing helix chain 'D' and resid 1291 through 1298 removed outlier: 3.658A pdb=" N HIS D1297 " --> pdb=" O GLN D1293 " (cutoff:3.500A) Processing helix chain 'D' and resid 1309 through 1314 Processing helix chain 'D' and resid 1325 through 1336 Processing helix chain 'D' and resid 1355 through 1358 No H-bonds generated for 'chain 'D' and resid 1355 through 1358' Processing helix chain 'D' and resid 1372 through 1384 Processing helix chain 'D' and resid 1392 through 1403 Proline residue: D1402 - end of helix Processing helix chain 'D' and resid 1406 through 1410 Processing helix chain 'D' and resid 1434 through 1440 Processing helix chain 'D' and resid 1442 through 1445 removed outlier: 4.105A pdb=" N ASN D1445 " --> pdb=" O TYR D1442 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1442 through 1445' Processing helix chain 'D' and resid 1449 through 1453 Processing helix chain 'D' and resid 1477 through 1484 Processing helix chain 'D' and resid 1506 through 1516 Processing helix chain 'D' and resid 1526 through 1537 Processing helix chain 'D' and resid 1600 through 1618 Proline residue: D1617 - end of helix Processing helix chain 'D' and resid 1621 through 1636 Proline residue: D1633 - end of helix Processing helix chain 'D' and resid 1654 through 1665 Processing helix chain 'D' and resid 1670 through 1683 Processing helix chain 'D' and resid 1795 through 1802 Processing helix chain 'D' and resid 1804 through 1813 Processing helix chain 'D' and resid 1818 through 1824 Processing helix chain 'D' and resid 1828 through 1830 No H-bonds generated for 'chain 'D' and resid 1828 through 1830' Processing helix chain 'D' and resid 1837 through 1848 removed outlier: 3.595A pdb=" N CYS D1845 " --> pdb=" O HIS D1841 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR D1848 " --> pdb=" O PHE D1844 " (cutoff:3.500A) Processing helix chain 'D' and resid 1852 through 1875 Processing helix chain 'D' and resid 1962 through 1978 Proline residue: D1968 - end of helix Processing helix chain 'D' and resid 1983 through 1990 Processing helix chain 'D' and resid 1993 through 1997 Processing helix chain 'D' and resid 2001 through 2012 Processing helix chain 'D' and resid 2022 through 2042 removed outlier: 6.080A pdb=" N LYS D2028 " --> pdb=" O TYR D2024 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASN D2029 " --> pdb=" O ILE D2025 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL D2030 " --> pdb=" O ASN D2026 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ALA D2031 " --> pdb=" O GLU D2027 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU D2032 " --> pdb=" O LYS D2028 " (cutoff:3.500A) Processing helix chain 'D' and resid 2048 through 2061 Processing helix chain 'D' and resid 2064 through 2071 Processing helix chain 'D' and resid 2081 through 2103 Processing helix chain 'D' and resid 2106 through 2115 Processing helix chain 'D' and resid 2119 through 2136 Processing helix chain 'D' and resid 2149 through 2166 removed outlier: 3.860A pdb=" N HIS D2166 " --> pdb=" O GLN D2162 " (cutoff:3.500A) Processing helix chain 'D' and resid 2168 through 2178 Proline residue: D2176 - end of helix Processing helix chain 'D' and resid 2183 through 2190 Processing helix chain 'D' and resid 2222 through 2229 removed outlier: 3.580A pdb=" N ARG D2226 " --> pdb=" O GLU D2222 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR D2228 " --> pdb=" O LYS D2224 " (cutoff:3.500A) Processing helix chain 'D' and resid 2240 through 2262 removed outlier: 3.633A pdb=" N TRP D2256 " --> pdb=" O GLU D2253 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D2262 " --> pdb=" O LYS D2259 " (cutoff:3.500A) Processing helix chain 'D' and resid 2264 through 2293 removed outlier: 3.578A pdb=" N ARG D2271 " --> pdb=" O TYR D2267 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN D2272 " --> pdb=" O TRP D2268 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N SER D2274 " --> pdb=" O ALA D2270 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N PHE D2275 " --> pdb=" O ARG D2271 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU D2290 " --> pdb=" O LEU D2286 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL D2291 " --> pdb=" O MET D2287 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA D2292 " --> pdb=" O ASN D2288 " (cutoff:3.500A) Processing helix chain 'D' and resid 2336 through 2346 removed outlier: 3.854A pdb=" N THR D2340 " --> pdb=" O LEU D2336 " (cutoff:3.500A) Processing helix chain 'D' and resid 2352 through 2375 Processing helix chain 'D' and resid 2385 through 2406 removed outlier: 4.497A pdb=" N ASP D2389 " --> pdb=" O ALA D2385 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS D2402 " --> pdb=" O TYR D2398 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA D2403 " --> pdb=" O LEU D2399 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET D2404 " --> pdb=" O LEU D2400 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY D2405 " --> pdb=" O ILE D2401 " (cutoff:3.500A) Processing helix chain 'D' and resid 2413 through 2423 Processing helix chain 'D' and resid 2425 through 2434 removed outlier: 4.039A pdb=" N VAL D2434 " --> pdb=" O VAL D2430 " (cutoff:3.500A) Processing helix chain 'D' and resid 2436 through 2438 No H-bonds generated for 'chain 'D' and resid 2436 through 2438' Processing helix chain 'D' and resid 2442 through 2451 removed outlier: 4.125A pdb=" N ALA D2446 " --> pdb=" O ILE D2442 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU D2447 " --> pdb=" O LEU D2443 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA D2448 " --> pdb=" O THR D2444 " (cutoff:3.500A) Processing helix chain 'D' and resid 2453 through 2462 removed outlier: 4.234A pdb=" N ILE D2457 " --> pdb=" O TYR D2453 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE D2462 " --> pdb=" O VAL D2458 " (cutoff:3.500A) Processing helix chain 'D' and resid 2535 through 2542 removed outlier: 3.824A pdb=" N LEU D2539 " --> pdb=" O ILE D2535 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N SER D2540 " --> pdb=" O VAL D2536 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N HIS D2541 " --> pdb=" O THR D2537 " (cutoff:3.500A) Processing helix chain 'D' and resid 2560 through 2598 removed outlier: 3.850A pdb=" N VAL D2581 " --> pdb=" O VAL D2577 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL D2588 " --> pdb=" O LEU D2584 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE D2589 " --> pdb=" O ILE D2585 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE D2593 " --> pdb=" O ILE D2589 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG D2597 " --> pdb=" O PHE D2593 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER D2598 " --> pdb=" O ALA D2594 " (cutoff:3.500A) Processing helix chain 'D' and resid 2600 through 2605 Processing helix chain 'D' and resid 2619 through 2624 Processing helix chain 'D' and resid 2629 through 2634 removed outlier: 4.152A pdb=" N ILE D2632 " --> pdb=" O GLU D2629 " (cutoff:3.500A) Processing helix chain 'D' and resid 2638 through 2648 Processing helix chain 'D' and resid 2660 through 2669 removed outlier: 3.846A pdb=" N GLU D2665 " --> pdb=" O SER D2661 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET D2666 " --> pdb=" O TYR D2662 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ARG D2668 " --> pdb=" O ALA D2664 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU D2669 " --> pdb=" O GLU D2665 " (cutoff:3.500A) Processing helix chain 'D' and resid 2686 through 2692 removed outlier: 3.547A pdb=" N GLY D2690 " --> pdb=" O SER D2686 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU D2691 " --> pdb=" O ASP D2687 " (cutoff:3.500A) Processing helix chain 'D' and resid 2696 through 2712 Processing helix chain 'D' and resid 2714 through 2736 Processing sheet with id= A, first strand: chain 'A' and resid 193 through 196 Processing sheet with id= B, first strand: chain 'A' and resid 242 through 244 removed outlier: 4.418A pdb=" N PHE A 243 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 431 " --> pdb=" O PHE A 243 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 251 through 255 Processing sheet with id= D, first strand: chain 'A' and resid 283 through 286 Processing sheet with id= E, first strand: chain 'A' and resid 14 through 17 removed outlier: 5.267A pdb=" N SER A 16 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LEU A 222 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 193 through 196 Processing sheet with id= G, first strand: chain 'C' and resid 242 through 244 removed outlier: 4.418A pdb=" N PHE C 243 " --> pdb=" O ALA C 431 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA C 431 " --> pdb=" O PHE C 243 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 251 through 255 Processing sheet with id= I, first strand: chain 'C' and resid 283 through 286 Processing sheet with id= J, first strand: chain 'C' and resid 14 through 17 removed outlier: 5.267A pdb=" N SER C 16 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LEU C 222 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 193 through 196 Processing sheet with id= L, first strand: chain 'B' and resid 242 through 244 removed outlier: 4.419A pdb=" N PHE B 243 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B 431 " --> pdb=" O PHE B 243 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'B' and resid 251 through 255 Processing sheet with id= N, first strand: chain 'B' and resid 283 through 286 Processing sheet with id= O, first strand: chain 'B' and resid 14 through 17 removed outlier: 5.267A pdb=" N SER B 16 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LEU B 222 " --> pdb=" O SER B 16 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 193 through 196 Processing sheet with id= Q, first strand: chain 'D' and resid 242 through 244 removed outlier: 4.418A pdb=" N PHE D 243 " --> pdb=" O ALA D 431 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA D 431 " --> pdb=" O PHE D 243 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'D' and resid 251 through 255 Processing sheet with id= S, first strand: chain 'D' and resid 283 through 286 Processing sheet with id= T, first strand: chain 'D' and resid 14 through 17 removed outlier: 5.267A pdb=" N SER D 16 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LEU D 222 " --> pdb=" O SER D 16 " (cutoff:3.500A) 2974 hydrogen bonds defined for protein. 8322 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: 23.13 Time building geometry restraints manager: 25.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 9849 1.28 - 1.42: 12866 1.42 - 1.55: 27538 1.55 - 1.69: 252 1.69 - 1.83: 267 Bond restraints: 50772 Sorted by residual: bond pdb=" C GLN B1201 " pdb=" N GLN B1202 " ideal model delta sigma weight residual 1.332 1.576 -0.244 1.40e-02 5.10e+03 3.04e+02 bond pdb=" C GLN C1201 " pdb=" N GLN C1202 " ideal model delta sigma weight residual 1.332 1.576 -0.243 1.40e-02 5.10e+03 3.03e+02 bond pdb=" C GLN A1201 " pdb=" N GLN A1202 " ideal model delta sigma weight residual 1.332 1.576 -0.243 1.40e-02 5.10e+03 3.02e+02 bond pdb=" C GLN D1201 " pdb=" N GLN D1202 " ideal model delta sigma weight residual 1.332 1.575 -0.243 1.40e-02 5.10e+03 3.01e+02 bond pdb=" CA ILE C2579 " pdb=" C ILE C2579 " ideal model delta sigma weight residual 1.523 1.369 0.154 1.37e-02 5.33e+03 1.26e+02 ... (remaining 50767 not shown) Histogram of bond angle deviations from ideal: 84.85 - 98.33: 64 98.33 - 111.81: 17942 111.81 - 125.29: 47698 125.29 - 138.77: 1120 138.77 - 152.24: 16 Bond angle restraints: 66840 Sorted by residual: angle pdb=" N LYS C1389 " pdb=" CA LYS C1389 " pdb=" C LYS C1389 " ideal model delta sigma weight residual 111.07 135.64 -24.57 1.07e+00 8.73e-01 5.27e+02 angle pdb=" N LYS D1389 " pdb=" CA LYS D1389 " pdb=" C LYS D1389 " ideal model delta sigma weight residual 111.07 135.64 -24.57 1.07e+00 8.73e-01 5.27e+02 angle pdb=" N LYS A1389 " pdb=" CA LYS A1389 " pdb=" C LYS A1389 " ideal model delta sigma weight residual 111.07 135.62 -24.55 1.07e+00 8.73e-01 5.26e+02 angle pdb=" N LYS B1389 " pdb=" CA LYS B1389 " pdb=" C LYS B1389 " ideal model delta sigma weight residual 111.07 135.57 -24.50 1.07e+00 8.73e-01 5.24e+02 angle pdb=" N ILE D2240 " pdb=" CA ILE D2240 " pdb=" C ILE D2240 " ideal model delta sigma weight residual 110.62 135.60 -24.98 1.14e+00 7.69e-01 4.80e+02 ... (remaining 66835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.18: 22083 23.18 - 46.36: 1599 46.36 - 69.55: 262 69.55 - 92.73: 32 92.73 - 115.91: 8 Dihedral angle restraints: 23984 sinusoidal: 7672 harmonic: 16312 Sorted by residual: dihedral pdb=" CA GLY B1650 " pdb=" C GLY B1650 " pdb=" N GLY B1651 " pdb=" CA GLY B1651 " ideal model delta harmonic sigma weight residual 180.00 83.75 96.25 0 5.00e+00 4.00e-02 3.71e+02 dihedral pdb=" CA GLY C1650 " pdb=" C GLY C1650 " pdb=" N GLY C1651 " pdb=" CA GLY C1651 " ideal model delta harmonic sigma weight residual 180.00 83.77 96.23 0 5.00e+00 4.00e-02 3.70e+02 dihedral pdb=" CA GLY D1650 " pdb=" C GLY D1650 " pdb=" N GLY D1651 " pdb=" CA GLY D1651 " ideal model delta harmonic sigma weight residual 180.00 83.80 96.20 0 5.00e+00 4.00e-02 3.70e+02 ... (remaining 23981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.231: 4534 0.231 - 0.462: 402 0.462 - 0.693: 92 0.693 - 0.925: 12 0.925 - 1.156: 24 Chirality restraints: 5064 Sorted by residual: chirality pdb=" CA ASP B2419 " pdb=" N ASP B2419 " pdb=" C ASP B2419 " pdb=" CB ASP B2419 " both_signs ideal model delta sigma weight residual False 2.51 1.35 1.16 2.00e-01 2.50e+01 3.34e+01 chirality pdb=" CA ASP A2419 " pdb=" N ASP A2419 " pdb=" C ASP A2419 " pdb=" CB ASP A2419 " both_signs ideal model delta sigma weight residual False 2.51 1.36 1.15 2.00e-01 2.50e+01 3.31e+01 chirality pdb=" CA ASP C2419 " pdb=" N ASP C2419 " pdb=" C ASP C2419 " pdb=" CB ASP C2419 " both_signs ideal model delta sigma weight residual False 2.51 1.36 1.15 2.00e-01 2.50e+01 3.31e+01 ... (remaining 5061 not shown) Planarity restraints: 10144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 JYP C2801 " -0.027 2.00e-02 2.50e+03 1.31e-01 4.73e+02 pdb=" C2 JYP C2801 " 0.189 2.00e-02 2.50e+03 pdb=" C3 JYP C2801 " 0.084 2.00e-02 2.50e+03 pdb=" C4 JYP C2801 " -0.073 2.00e-02 2.50e+03 pdb=" C5 JYP C2801 " 0.024 2.00e-02 2.50e+03 pdb=" C6 JYP C2801 " -0.294 2.00e-02 2.50e+03 pdb=" N1 JYP C2801 " 0.138 2.00e-02 2.50e+03 pdb=" N2 JYP C2801 " -0.112 2.00e-02 2.50e+03 pdb=" N3 JYP C2801 " -0.033 2.00e-02 2.50e+03 pdb=" N4 JYP C2801 " -0.034 2.00e-02 2.50e+03 pdb=" N5 JYP C2801 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 JYP D2801 " -0.028 2.00e-02 2.50e+03 1.31e-01 4.72e+02 pdb=" C2 JYP D2801 " 0.189 2.00e-02 2.50e+03 pdb=" C3 JYP D2801 " 0.084 2.00e-02 2.50e+03 pdb=" C4 JYP D2801 " -0.073 2.00e-02 2.50e+03 pdb=" C5 JYP D2801 " 0.024 2.00e-02 2.50e+03 pdb=" C6 JYP D2801 " -0.294 2.00e-02 2.50e+03 pdb=" N1 JYP D2801 " 0.138 2.00e-02 2.50e+03 pdb=" N2 JYP D2801 " -0.112 2.00e-02 2.50e+03 pdb=" N3 JYP D2801 " -0.034 2.00e-02 2.50e+03 pdb=" N4 JYP D2801 " -0.035 2.00e-02 2.50e+03 pdb=" N5 JYP D2801 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 JYP B2801 " -0.027 2.00e-02 2.50e+03 1.31e-01 4.72e+02 pdb=" C2 JYP B2801 " 0.190 2.00e-02 2.50e+03 pdb=" C3 JYP B2801 " 0.083 2.00e-02 2.50e+03 pdb=" C4 JYP B2801 " -0.073 2.00e-02 2.50e+03 pdb=" C5 JYP B2801 " 0.024 2.00e-02 2.50e+03 pdb=" C6 JYP B2801 " -0.294 2.00e-02 2.50e+03 pdb=" N1 JYP B2801 " 0.137 2.00e-02 2.50e+03 pdb=" N2 JYP B2801 " -0.112 2.00e-02 2.50e+03 pdb=" N3 JYP B2801 " -0.033 2.00e-02 2.50e+03 pdb=" N4 JYP B2801 " -0.034 2.00e-02 2.50e+03 pdb=" N5 JYP B2801 " 0.139 2.00e-02 2.50e+03 ... (remaining 10141 not shown) Histogram of nonbonded interaction distances: 1.07 - 1.83: 380 1.83 - 2.60: 2971 2.60 - 3.37: 78760 3.37 - 4.13: 115973 4.13 - 4.90: 185048 Nonbonded interactions: 383132 Sorted by model distance: nonbonded pdb=" CE2 TYR D2398 " pdb=" CD1 LEU D2416 " model vdw 1.066 3.760 nonbonded pdb=" CE2 TYR C2398 " pdb=" CD1 LEU C2416 " model vdw 1.066 3.760 nonbonded pdb=" CE2 TYR B2398 " pdb=" CD1 LEU B2416 " model vdw 1.066 3.760 nonbonded pdb=" CE2 TYR A2398 " pdb=" CD1 LEU A2416 " model vdw 1.066 3.760 nonbonded pdb=" O LEU B 895 " pdb=" N CYS B 897 " model vdw 1.075 2.520 ... (remaining 383127 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.450 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: 0.060 Extract box with map and model: 5.340 Check model and map are aligned: 0.800 Set scattering table: 0.470 Process input model: 145.320 Find NCS groups from input model: 3.930 Set up NCS constraints: 0.360 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:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 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 : 0.013 0.244 50772 Z= 0.927 Angle : 2.215 32.990 66840 Z= 1.484 Chirality : 0.162 1.156 5064 Planarity : 0.014 0.218 10144 Dihedral : 14.966 115.909 16296 Min Nonbonded Distance : 1.066 Molprobity Statistics. All-atom Clashscore : 78.96 Ramachandran Plot: Outliers : 2.89 % Allowed : 12.11 % Favored : 84.99 % Rotamer: Outliers : 16.69 % Allowed : 12.02 % Favored : 71.30 % Cbeta Deviations : 3.80 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 3.39 % Twisted General : 0.39 % 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: -0.62 (0.10), residues: 8436 helix: 2.01 (0.08), residues: 4772 sheet: -3.02 (0.30), residues: 244 loop : -4.09 (0.08), residues: 3420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP C 282 HIS 0.018 0.004 HIS C 94 PHE 0.113 0.006 PHE A2575 TYR 0.057 0.005 TYR C2398 ARG 0.029 0.002 ARG B2679 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1732 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 572 poor density : 1160 time to evaluate : 6.301 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASP cc_start: 0.8732 (m-30) cc_final: 0.8432 (t70) REVERT: A 81 ASN cc_start: 0.7492 (OUTLIER) cc_final: 0.6981 (p0) REVERT: A 120 VAL cc_start: 0.7767 (t) cc_final: 0.5970 (t) REVERT: A 125 HIS cc_start: 0.7496 (t-170) cc_final: 0.6992 (t70) REVERT: A 137 ARG cc_start: 0.8424 (ptp-170) cc_final: 0.8151 (ptm160) REVERT: A 162 TYR cc_start: 0.8869 (m-80) cc_final: 0.8332 (m-80) REVERT: A 247 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8144 (tp40) REVERT: A 430 PHE cc_start: 0.8514 (m-80) cc_final: 0.8186 (m-80) REVERT: A 516 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.7526 (tp) REVERT: A 517 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.6341 (tttp) REVERT: A 519 ILE cc_start: 0.9495 (OUTLIER) cc_final: 0.9291 (mp) REVERT: A 582 GLN cc_start: 0.9345 (OUTLIER) cc_final: 0.9094 (tm-30) REVERT: A 2187 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8286 (pt0) REVERT: A 2198 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.6969 (tp) REVERT: A 2206 GLU cc_start: 0.9319 (tm-30) cc_final: 0.8945 (tm-30) REVERT: A 2250 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9284 (tm) REVERT: A 2254 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.9089 (ppp) REVERT: A 2401 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7570 (pp) REVERT: A 2524 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8417 (mmtt) REVERT: A 2533 MET cc_start: 0.7357 (tpt) cc_final: 0.7112 (pmm) REVERT: A 2534 CYS cc_start: 0.8527 (t) cc_final: 0.8072 (t) REVERT: A 2605 GLU cc_start: 0.9162 (tp30) cc_final: 0.8676 (tp30) REVERT: A 2609 THR cc_start: 0.9116 (m) cc_final: 0.7819 (m) REVERT: A 2670 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8711 (mtm-85) REVERT: A 2698 LEU cc_start: 0.5509 (OUTLIER) cc_final: 0.4647 (tp) REVERT: A 2712 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8398 (pp) REVERT: A 2721 ASP cc_start: 0.9421 (t0) cc_final: 0.9150 (p0) REVERT: A 2723 MET cc_start: 0.9647 (tmm) cc_final: 0.9259 (tmm) REVERT: A 2724 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8809 (p) REVERT: C 45 ASP cc_start: 0.8787 (m-30) cc_final: 0.8531 (t70) REVERT: C 81 ASN cc_start: 0.7154 (OUTLIER) cc_final: 0.6757 (p0) REVERT: C 97 ASP cc_start: 0.9290 (OUTLIER) cc_final: 0.9046 (m-30) REVERT: C 120 VAL cc_start: 0.7742 (t) cc_final: 0.5988 (t) REVERT: C 125 HIS cc_start: 0.7482 (t-170) cc_final: 0.7241 (t70) REVERT: C 137 ARG cc_start: 0.8793 (ptp-170) cc_final: 0.7991 (ttt90) REVERT: C 162 TYR cc_start: 0.8917 (m-80) cc_final: 0.8646 (m-80) REVERT: C 181 LYS cc_start: 0.7849 (mttt) cc_final: 0.7215 (mppt) REVERT: C 206 CYS cc_start: 0.7795 (m) cc_final: 0.5665 (m) REVERT: C 247 GLN cc_start: 0.8916 (mm-40) cc_final: 0.7935 (tm-30) REVERT: C 430 PHE cc_start: 0.8509 (m-80) cc_final: 0.8241 (m-80) REVERT: C 516 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.7699 (tp) REVERT: C 518 GLN cc_start: 0.9316 (tm-30) cc_final: 0.9111 (tm-30) REVERT: C 582 GLN cc_start: 0.9313 (OUTLIER) cc_final: 0.8999 (tm-30) REVERT: C 2184 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8402 (mm-30) REVERT: C 2206 GLU cc_start: 0.9264 (tm-30) cc_final: 0.8981 (tm-30) REVERT: C 2218 PHE cc_start: 0.8771 (m-80) cc_final: 0.8246 (m-80) REVERT: C 2241 ASN cc_start: 0.9053 (OUTLIER) cc_final: 0.8795 (p0) REVERT: C 2253 GLU cc_start: 0.9711 (pp20) cc_final: 0.9468 (pp20) REVERT: C 2254 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8921 (ppp) REVERT: C 2401 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7883 (pp) REVERT: C 2408 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8434 (m) REVERT: C 2524 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8118 (mmtt) REVERT: C 2540 SER cc_start: 0.8957 (m) cc_final: 0.8649 (p) REVERT: C 2605 GLU cc_start: 0.9143 (tp30) cc_final: 0.8642 (tp30) REVERT: C 2616 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7230 (tt) REVERT: C 2641 TYR cc_start: 0.9165 (m-80) cc_final: 0.8488 (m-80) REVERT: C 2649 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8192 (mmmt) REVERT: C 2670 ARG cc_start: 0.9231 (OUTLIER) cc_final: 0.8860 (mtm110) REVERT: C 2674 TRP cc_start: 0.8249 (m-90) cc_final: 0.7894 (m-90) REVERT: C 2712 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8636 (pp) REVERT: C 2723 MET cc_start: 0.9631 (tmm) cc_final: 0.9278 (tmm) REVERT: C 2724 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8752 (p) REVERT: B 81 ASN cc_start: 0.5375 (OUTLIER) cc_final: 0.4804 (p0) REVERT: B 121 ILE cc_start: 0.8353 (pp) cc_final: 0.8076 (pp) REVERT: B 137 ARG cc_start: 0.8927 (ptp-170) cc_final: 0.8722 (ptm160) REVERT: B 181 LYS cc_start: 0.7953 (mttt) cc_final: 0.7353 (mmtm) REVERT: B 247 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8319 (tm-30) REVERT: B 371 ASP cc_start: 0.8860 (t0) cc_final: 0.8593 (p0) REVERT: B 430 PHE cc_start: 0.8209 (m-80) cc_final: 0.7980 (m-80) REVERT: B 516 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7829 (tp) REVERT: B 526 PRO cc_start: 0.7487 (OUTLIER) cc_final: 0.7262 (Cg_endo) REVERT: B 2184 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8374 (mm-30) REVERT: B 2206 GLU cc_start: 0.9275 (tm-30) cc_final: 0.8921 (tm-30) REVERT: B 2218 PHE cc_start: 0.8736 (m-80) cc_final: 0.8197 (m-80) REVERT: B 2250 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9051 (tm) REVERT: B 2395 HIS cc_start: 0.7671 (m170) cc_final: 0.7394 (m170) REVERT: B 2401 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8124 (pp) REVERT: B 2408 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8587 (m) REVERT: B 2524 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7890 (mmtt) REVERT: B 2540 SER cc_start: 0.8965 (m) cc_final: 0.8614 (p) REVERT: B 2605 GLU cc_start: 0.9080 (tp30) cc_final: 0.8862 (tp30) REVERT: B 2649 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7677 (mmmt) REVERT: B 2668 ARG cc_start: 0.9522 (mmt90) cc_final: 0.9299 (mmp80) REVERT: B 2670 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.8842 (mtm110) REVERT: B 2674 TRP cc_start: 0.8073 (m-90) cc_final: 0.7802 (m-90) REVERT: B 2698 LEU cc_start: 0.4552 (OUTLIER) cc_final: 0.3777 (tp) REVERT: B 2723 MET cc_start: 0.9510 (tmm) cc_final: 0.9252 (tmm) REVERT: B 2724 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8930 (p) REVERT: D 45 ASP cc_start: 0.8938 (m-30) cc_final: 0.8672 (t70) REVERT: D 81 ASN cc_start: 0.7554 (OUTLIER) cc_final: 0.7154 (p0) REVERT: D 120 VAL cc_start: 0.7580 (t) cc_final: 0.5838 (t) REVERT: D 125 HIS cc_start: 0.7630 (t-170) cc_final: 0.7152 (t70) REVERT: D 137 ARG cc_start: 0.8803 (ptp-170) cc_final: 0.8341 (ptm160) REVERT: D 162 TYR cc_start: 0.8862 (m-80) cc_final: 0.8656 (m-80) REVERT: D 181 LYS cc_start: 0.7785 (mttt) cc_final: 0.7078 (mmtm) REVERT: D 206 CYS cc_start: 0.7951 (m) cc_final: 0.5901 (m) REVERT: D 218 TRP cc_start: 0.8119 (m100) cc_final: 0.7896 (m-90) REVERT: D 247 GLN cc_start: 0.8830 (mm-40) cc_final: 0.7877 (tm-30) REVERT: D 430 PHE cc_start: 0.7940 (m-80) cc_final: 0.7704 (m-80) REVERT: D 516 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7759 (tp) REVERT: D 2206 GLU cc_start: 0.9256 (tm-30) cc_final: 0.8839 (tm-30) REVERT: D 2241 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8790 (p0) REVERT: D 2250 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9189 (tm) REVERT: D 2401 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7874 (pp) REVERT: D 2533 MET cc_start: 0.7120 (tpt) cc_final: 0.6898 (pmm) REVERT: D 2534 CYS cc_start: 0.8564 (t) cc_final: 0.8272 (t) REVERT: D 2599 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7774 (tm-30) REVERT: D 2600 LYS cc_start: 0.8677 (tppt) cc_final: 0.8295 (mmmt) REVERT: D 2609 THR cc_start: 0.9146 (m) cc_final: 0.8744 (m) REVERT: D 2649 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8072 (mmmm) REVERT: D 2668 ARG cc_start: 0.9428 (mmt90) cc_final: 0.9180 (mmp80) REVERT: D 2670 ARG cc_start: 0.9261 (OUTLIER) cc_final: 0.8843 (mtm-85) REVERT: D 2674 TRP cc_start: 0.8151 (m-90) cc_final: 0.7935 (m-90) REVERT: D 2698 LEU cc_start: 0.6737 (OUTLIER) cc_final: 0.5888 (tp) REVERT: D 2712 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8697 (pp) REVERT: D 2723 MET cc_start: 0.9581 (tmm) cc_final: 0.9340 (tmm) outliers start: 572 outliers final: 340 residues processed: 1604 average time/residue: 0.6117 time to fit residues: 1598.4535 Evaluate side-chains 1311 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 391 poor density : 920 time to evaluate : 4.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 722 optimal weight: 7.9990 chunk 648 optimal weight: 4.9990 chunk 360 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 437 optimal weight: 10.0000 chunk 346 optimal weight: 10.0000 chunk 670 optimal weight: 5.9990 chunk 259 optimal weight: 30.0000 chunk 407 optimal weight: 7.9990 chunk 499 optimal weight: 7.9990 chunk 777 optimal weight: 0.1980 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN A 156 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 HIS A 198 HIS A 203 ASN A 261 HIS ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 GLN A 584 GLN A2195 GLN ** A2236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2409 HIS ** A2640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2715 GLN ** A2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2729 GLN ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS C 198 HIS C 203 ASN C 261 HIS ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 GLN C 584 GLN C2195 GLN ** C2236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2409 HIS ** C2640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2715 GLN ** C2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 HIS B 198 HIS B 203 ASN B 261 HIS ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 GLN ** B 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2195 GLN B2236 GLN ** B2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2409 HIS ** B2640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2715 GLN ** B2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2729 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 HIS D 198 HIS D 203 ASN D 261 HIS ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 565 GLN D 584 GLN D2195 GLN ** D2236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2409 HIS ** D2640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2715 GLN ** D2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2729 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 50772 Z= 0.312 Angle : 0.937 10.354 66840 Z= 0.503 Chirality : 0.055 0.276 5064 Planarity : 0.007 0.088 10144 Dihedral : 8.786 102.749 8876 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 25.05 Ramachandran Plot: Outliers : 0.71 % Allowed : 12.71 % Favored : 86.58 % Rotamer: Outliers : 0.20 % Allowed : 6.30 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 3.39 % Twisted General : 0.39 % 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: -1.98 (0.09), residues: 8436 helix: 0.42 (0.07), residues: 4856 sheet: -2.66 (0.32), residues: 236 loop : -4.04 (0.09), residues: 3344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 218 HIS 0.015 0.002 HIS B 562 PHE 0.048 0.003 PHE A2368 TYR 0.042 0.003 TYR A 567 ARG 0.014 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1157 time to evaluate : 5.781 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9313 (pt0) cc_final: 0.9037 (pt0) REVERT: A 45 ASP cc_start: 0.8941 (m-30) cc_final: 0.8635 (t70) REVERT: A 52 LYS cc_start: 0.9311 (pttt) cc_final: 0.9006 (ptmt) REVERT: A 69 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8056 (tm-30) REVERT: A 97 ASP cc_start: 0.9113 (m-30) cc_final: 0.8802 (m-30) REVERT: A 125 HIS cc_start: 0.7462 (t-170) cc_final: 0.6542 (t70) REVERT: A 137 ARG cc_start: 0.8351 (ptp-170) cc_final: 0.7737 (ttt90) REVERT: A 157 GLU cc_start: 0.9213 (mp0) cc_final: 0.8967 (mp0) REVERT: A 161 PHE cc_start: 0.7485 (m-80) cc_final: 0.7098 (m-80) REVERT: A 162 TYR cc_start: 0.8702 (m-80) cc_final: 0.8128 (m-80) REVERT: A 247 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8423 (tp40) REVERT: A 430 PHE cc_start: 0.8503 (m-80) cc_final: 0.8178 (m-80) REVERT: A 2197 GLU cc_start: 0.8867 (tp30) cc_final: 0.8586 (tp30) REVERT: A 2232 GLU cc_start: 0.6744 (tm-30) cc_final: 0.6355 (tm-30) REVERT: A 2254 MET cc_start: 0.9050 (ppp) cc_final: 0.8689 (ppp) REVERT: A 2258 LYS cc_start: 0.9600 (mmtm) cc_final: 0.9388 (mmtt) REVERT: A 2274 SER cc_start: 0.9509 (p) cc_final: 0.9150 (p) REVERT: A 2395 HIS cc_start: 0.8897 (m90) cc_final: 0.8639 (m90) REVERT: A 2541 HIS cc_start: 0.7969 (t-90) cc_final: 0.7728 (t-90) REVERT: A 2599 GLU cc_start: 0.8511 (tm-30) cc_final: 0.7860 (tm-30) REVERT: A 2605 GLU cc_start: 0.8625 (tp30) cc_final: 0.8377 (tp30) REVERT: A 2641 TYR cc_start: 0.9177 (m-80) cc_final: 0.8740 (m-80) REVERT: A 2670 ARG cc_start: 0.9342 (ptt-90) cc_final: 0.9020 (mtm-85) REVERT: C 45 ASP cc_start: 0.8910 (m-30) cc_final: 0.8678 (t70) REVERT: C 52 LYS cc_start: 0.9328 (pttt) cc_final: 0.9049 (ptmt) REVERT: C 69 GLN cc_start: 0.8819 (tm-30) cc_final: 0.7605 (tm-30) REVERT: C 100 LYS cc_start: 0.9525 (mmtt) cc_final: 0.9217 (mmtt) REVERT: C 125 HIS cc_start: 0.7364 (t-170) cc_final: 0.6826 (t70) REVERT: C 137 ARG cc_start: 0.8704 (ptp-170) cc_final: 0.8000 (ttt90) REVERT: C 157 GLU cc_start: 0.9179 (mp0) cc_final: 0.8923 (mp0) REVERT: C 161 PHE cc_start: 0.7133 (m-80) cc_final: 0.6890 (m-80) REVERT: C 162 TYR cc_start: 0.8775 (m-80) cc_final: 0.8292 (m-80) REVERT: C 247 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8157 (tm-30) REVERT: C 430 PHE cc_start: 0.8613 (m-80) cc_final: 0.8315 (m-80) REVERT: C 2197 GLU cc_start: 0.8797 (tp30) cc_final: 0.8316 (tp30) REVERT: C 2203 ARG cc_start: 0.9053 (pmt170) cc_final: 0.8618 (ptp90) REVERT: C 2218 PHE cc_start: 0.8567 (m-80) cc_final: 0.8102 (m-80) REVERT: C 2254 MET cc_start: 0.8946 (ppp) cc_final: 0.8668 (ppp) REVERT: C 2259 LYS cc_start: 0.9559 (tmtt) cc_final: 0.9356 (mmtp) REVERT: C 2274 SER cc_start: 0.9435 (p) cc_final: 0.9147 (p) REVERT: C 2281 PHE cc_start: 0.9082 (t80) cc_final: 0.8810 (t80) REVERT: C 2394 TYR cc_start: 0.7508 (m-80) cc_final: 0.7279 (m-10) REVERT: C 2540 SER cc_start: 0.8999 (m) cc_final: 0.8756 (p) REVERT: C 2599 GLU cc_start: 0.8619 (tm-30) cc_final: 0.7946 (tm-30) REVERT: C 2630 GLU cc_start: 0.9002 (mp0) cc_final: 0.8767 (pm20) REVERT: C 2641 TYR cc_start: 0.8944 (m-80) cc_final: 0.8113 (m-80) REVERT: C 2670 ARG cc_start: 0.9346 (ptt-90) cc_final: 0.9005 (mtm-85) REVERT: B 69 GLN cc_start: 0.8908 (tm-30) cc_final: 0.7541 (tm-30) REVERT: B 100 LYS cc_start: 0.9556 (mmtt) cc_final: 0.9246 (mmtt) REVERT: B 125 HIS cc_start: 0.7638 (t-170) cc_final: 0.7155 (t-90) REVERT: B 137 ARG cc_start: 0.8800 (ptp-170) cc_final: 0.8142 (ttt90) REVERT: B 247 GLN cc_start: 0.9309 (mm-40) cc_final: 0.8459 (tm-30) REVERT: B 430 PHE cc_start: 0.8169 (m-80) cc_final: 0.7876 (m-80) REVERT: B 2203 ARG cc_start: 0.8868 (pmt170) cc_final: 0.8562 (ptp90) REVERT: B 2218 PHE cc_start: 0.8635 (m-80) cc_final: 0.8117 (m-80) REVERT: B 2274 SER cc_start: 0.9364 (p) cc_final: 0.9027 (p) REVERT: B 2281 PHE cc_start: 0.9100 (t80) cc_final: 0.8768 (t80) REVERT: B 2395 HIS cc_start: 0.8458 (m170) cc_final: 0.8194 (m170) REVERT: B 2522 GLN cc_start: 0.9102 (pm20) cc_final: 0.8836 (pm20) REVERT: B 2524 LYS cc_start: 0.8618 (mmpt) cc_final: 0.8368 (mmtt) REVERT: B 2599 GLU cc_start: 0.8563 (tm-30) cc_final: 0.7741 (tm-30) REVERT: B 2605 GLU cc_start: 0.8564 (tp30) cc_final: 0.8270 (tp30) REVERT: B 2612 PHE cc_start: 0.8147 (t80) cc_final: 0.7919 (t80) REVERT: B 2630 GLU cc_start: 0.9117 (mp0) cc_final: 0.8912 (pm20) REVERT: B 2665 GLU cc_start: 0.9588 (tp30) cc_final: 0.9312 (tp30) REVERT: B 2668 ARG cc_start: 0.9577 (mmt90) cc_final: 0.9329 (ttm110) REVERT: B 2670 ARG cc_start: 0.9270 (ptt-90) cc_final: 0.8898 (mtm110) REVERT: D 17 LEU cc_start: 0.7596 (tp) cc_final: 0.7347 (tp) REVERT: D 42 GLU cc_start: 0.9287 (pt0) cc_final: 0.9032 (pt0) REVERT: D 69 GLN cc_start: 0.8796 (tm-30) cc_final: 0.7960 (tm-30) REVERT: D 97 ASP cc_start: 0.9199 (m-30) cc_final: 0.8878 (m-30) REVERT: D 137 ARG cc_start: 0.8708 (ptp-170) cc_final: 0.7985 (ttt90) REVERT: D 156 ASN cc_start: 0.9024 (m-40) cc_final: 0.8725 (m-40) REVERT: D 157 GLU cc_start: 0.9119 (mp0) cc_final: 0.8913 (mp0) REVERT: D 161 PHE cc_start: 0.6954 (m-80) cc_final: 0.6641 (m-80) REVERT: D 162 TYR cc_start: 0.8918 (m-80) cc_final: 0.8577 (m-80) REVERT: D 210 ASN cc_start: 0.8299 (p0) cc_final: 0.8070 (p0) REVERT: D 247 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8235 (tm-30) REVERT: D 387 TYR cc_start: 0.8471 (m-10) cc_final: 0.8133 (t80) REVERT: D 430 PHE cc_start: 0.8162 (m-80) cc_final: 0.7874 (m-80) REVERT: D 2188 PHE cc_start: 0.8417 (m-10) cc_final: 0.8003 (m-80) REVERT: D 2197 GLU cc_start: 0.8927 (tp30) cc_final: 0.8572 (tp30) REVERT: D 2203 ARG cc_start: 0.9106 (pmt170) cc_final: 0.8659 (ptp90) REVERT: D 2232 GLU cc_start: 0.6708 (tm-30) cc_final: 0.6387 (tm-30) REVERT: D 2246 ARG cc_start: 0.9101 (mmt90) cc_final: 0.8413 (mtt180) REVERT: D 2281 PHE cc_start: 0.8956 (t80) cc_final: 0.8599 (t80) REVERT: D 2394 TYR cc_start: 0.7889 (m-80) cc_final: 0.7646 (m-10) REVERT: D 2413 TYR cc_start: 0.7665 (m-80) cc_final: 0.7257 (m-80) REVERT: D 2524 LYS cc_start: 0.8619 (mptt) cc_final: 0.8189 (mmtm) REVERT: D 2600 LYS cc_start: 0.9159 (tppt) cc_final: 0.8507 (tppt) REVERT: D 2601 GLN cc_start: 0.8757 (pm20) cc_final: 0.8481 (pm20) REVERT: D 2603 LYS cc_start: 0.9662 (pttt) cc_final: 0.9111 (pttp) REVERT: D 2612 PHE cc_start: 0.8344 (t80) cc_final: 0.8121 (t80) REVERT: D 2630 GLU cc_start: 0.9140 (mp0) cc_final: 0.8921 (pm20) REVERT: D 2665 GLU cc_start: 0.9614 (tp30) cc_final: 0.9282 (tp30) REVERT: D 2668 ARG cc_start: 0.9487 (mmt90) cc_final: 0.9182 (ttm110) REVERT: D 2670 ARG cc_start: 0.9303 (ptt-90) cc_final: 0.8914 (mtm-85) REVERT: D 2679 ARG cc_start: 0.7872 (ttp80) cc_final: 0.7399 (tmm-80) outliers start: 7 outliers final: 2 residues processed: 1162 average time/residue: 0.6099 time to fit residues: 1175.0305 Evaluate side-chains 881 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 879 time to evaluate : 5.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 432 optimal weight: 2.9990 chunk 241 optimal weight: 9.9990 chunk 646 optimal weight: 0.0070 chunk 529 optimal weight: 50.0000 chunk 214 optimal weight: 20.0000 chunk 778 optimal weight: 40.0000 chunk 841 optimal weight: 0.6980 chunk 693 optimal weight: 7.9990 chunk 772 optimal weight: 0.6980 chunk 265 optimal weight: 9.9990 chunk 624 optimal weight: 0.0030 overall best weight: 0.8810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 ASN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 GLN ** A2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 GLN ** C2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 GLN ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 GLN D 156 ASN D 203 ASN ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 GLN ** D2640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 50772 Z= 0.206 Angle : 0.791 10.607 66840 Z= 0.417 Chirality : 0.048 0.204 5064 Planarity : 0.006 0.098 10144 Dihedral : 7.717 97.733 8876 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.83 % Allowed : 11.58 % Favored : 87.59 % Rotamer: Outliers : 0.61 % Allowed : 7.58 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 3.39 % Twisted General : 0.14 % 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: -1.66 (0.09), residues: 8436 helix: 0.61 (0.08), residues: 4888 sheet: -2.64 (0.33), residues: 248 loop : -3.81 (0.09), residues: 3300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 73 HIS 0.014 0.002 HIS C2395 PHE 0.040 0.002 PHE A2281 TYR 0.056 0.002 TYR C2189 ARG 0.013 0.001 ARG D 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1142 time to evaluate : 6.678 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: 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: 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: 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: 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 14 ILE cc_start: 0.8379 (mp) cc_final: 0.8113 (mp) REVERT: A 17 LEU cc_start: 0.7640 (tp) cc_final: 0.7370 (tp) REVERT: A 45 ASP cc_start: 0.8889 (m-30) cc_final: 0.8568 (t70) REVERT: A 66 TYR cc_start: 0.7258 (m-80) cc_final: 0.6941 (m-80) REVERT: A 97 ASP cc_start: 0.9046 (m-30) cc_final: 0.8720 (m-30) REVERT: A 121 ILE cc_start: 0.8207 (tp) cc_final: 0.7939 (tp) REVERT: A 124 LEU cc_start: 0.8008 (tp) cc_final: 0.7705 (tt) REVERT: A 125 HIS cc_start: 0.7614 (t-170) cc_final: 0.6904 (t70) REVERT: A 137 ARG cc_start: 0.8231 (ptp-170) cc_final: 0.8022 (ptm160) REVERT: A 157 GLU cc_start: 0.9091 (mp0) cc_final: 0.8350 (mp0) REVERT: A 161 PHE cc_start: 0.6725 (m-80) cc_final: 0.6524 (m-80) REVERT: A 162 TYR cc_start: 0.8613 (m-80) cc_final: 0.8095 (m-80) REVERT: A 242 LEU cc_start: 0.8672 (mt) cc_final: 0.8397 (mt) REVERT: A 247 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8006 (tm-30) REVERT: A 251 LEU cc_start: 0.7610 (tp) cc_final: 0.7094 (tp) REVERT: A 313 TYR cc_start: 0.8405 (m-80) cc_final: 0.7996 (m-80) REVERT: A 430 PHE cc_start: 0.8400 (m-80) cc_final: 0.8129 (m-80) REVERT: A 505 GLU cc_start: 0.9400 (pt0) cc_final: 0.9024 (pm20) REVERT: A 573 TYR cc_start: 0.8902 (t80) cc_final: 0.8594 (t80) REVERT: A 581 MET cc_start: 0.9474 (tmm) cc_final: 0.9178 (ppp) REVERT: A 2184 GLU cc_start: 0.8332 (tt0) cc_final: 0.7871 (tt0) REVERT: A 2188 PHE cc_start: 0.8057 (m-10) cc_final: 0.7530 (m-80) REVERT: A 2205 MET cc_start: 0.8363 (mmt) cc_final: 0.8129 (tpt) REVERT: A 2232 GLU cc_start: 0.6599 (tm-30) cc_final: 0.6160 (tp30) REVERT: A 2242 ASP cc_start: 0.8420 (t70) cc_final: 0.8180 (t0) REVERT: A 2246 ARG cc_start: 0.9202 (mmt90) cc_final: 0.8418 (mtt180) REVERT: A 2248 GLU cc_start: 0.9190 (pm20) cc_final: 0.8880 (pm20) REVERT: A 2252 ASN cc_start: 0.9528 (m-40) cc_final: 0.9236 (m-40) REVERT: A 2258 LYS cc_start: 0.9471 (mmtm) cc_final: 0.9264 (mmmt) REVERT: A 2589 ILE cc_start: 0.8732 (mm) cc_final: 0.8412 (mt) REVERT: A 2641 TYR cc_start: 0.9107 (m-80) cc_final: 0.8749 (m-80) REVERT: A 2670 ARG cc_start: 0.9191 (ptt-90) cc_final: 0.8820 (mtm-85) REVERT: A 2681 MET cc_start: 0.8137 (tmm) cc_final: 0.7780 (tmm) REVERT: C 45 ASP cc_start: 0.8805 (m-30) cc_final: 0.8571 (t70) REVERT: C 66 TYR cc_start: 0.7129 (m-80) cc_final: 0.6843 (m-10) REVERT: C 69 GLN cc_start: 0.8904 (tm-30) cc_final: 0.7919 (tm-30) REVERT: C 100 LYS cc_start: 0.9478 (mmtt) cc_final: 0.9199 (mmtt) REVERT: C 125 HIS cc_start: 0.7072 (t-170) cc_final: 0.6815 (t70) REVERT: C 137 ARG cc_start: 0.8605 (ptp-170) cc_final: 0.7944 (ttt90) REVERT: C 157 GLU cc_start: 0.9069 (mp0) cc_final: 0.8836 (mp0) REVERT: C 162 TYR cc_start: 0.8642 (m-80) cc_final: 0.8047 (m-80) REVERT: C 242 LEU cc_start: 0.8593 (mt) cc_final: 0.8342 (mt) REVERT: C 247 GLN cc_start: 0.9090 (mm-40) cc_final: 0.8147 (tm-30) REVERT: C 251 LEU cc_start: 0.7812 (tp) cc_final: 0.7274 (tp) REVERT: C 313 TYR cc_start: 0.8425 (m-80) cc_final: 0.7838 (m-80) REVERT: C 430 PHE cc_start: 0.8606 (m-80) cc_final: 0.8374 (m-80) REVERT: C 573 TYR cc_start: 0.9034 (t80) cc_final: 0.8751 (t80) REVERT: C 2197 GLU cc_start: 0.8857 (tp30) cc_final: 0.8561 (tp30) REVERT: C 2205 MET cc_start: 0.8726 (mmt) cc_final: 0.8196 (tpt) REVERT: C 2218 PHE cc_start: 0.8370 (m-80) cc_final: 0.7926 (m-80) REVERT: C 2242 ASP cc_start: 0.8439 (t70) cc_final: 0.8221 (t0) REVERT: C 2248 GLU cc_start: 0.9094 (pm20) cc_final: 0.8827 (pm20) REVERT: C 2281 PHE cc_start: 0.8886 (t80) cc_final: 0.8605 (t80) REVERT: C 2395 HIS cc_start: 0.8282 (m-70) cc_final: 0.7715 (m-70) REVERT: C 2401 ILE cc_start: 0.5325 (pt) cc_final: 0.4285 (mt) REVERT: C 2582 LEU cc_start: 0.7810 (mt) cc_final: 0.7511 (mt) REVERT: C 2624 LYS cc_start: 0.9302 (mmpt) cc_final: 0.8979 (mmmt) REVERT: C 2630 GLU cc_start: 0.9020 (mp0) cc_final: 0.8739 (pm20) REVERT: C 2670 ARG cc_start: 0.9202 (ptt-90) cc_final: 0.8850 (mtm-85) REVERT: C 2681 MET cc_start: 0.8238 (tmm) cc_final: 0.7883 (tmm) REVERT: B 52 LYS cc_start: 0.8812 (tmtt) cc_final: 0.8526 (tptp) REVERT: B 69 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8279 (tm-30) REVERT: B 97 ASP cc_start: 0.9040 (m-30) cc_final: 0.8776 (m-30) REVERT: B 121 ILE cc_start: 0.8607 (pt) cc_final: 0.8379 (tt) REVERT: B 125 HIS cc_start: 0.7489 (t-170) cc_final: 0.7109 (t-90) REVERT: B 137 ARG cc_start: 0.8872 (ptp-170) cc_final: 0.8246 (ttt90) REVERT: B 157 GLU cc_start: 0.9152 (mp0) cc_final: 0.8950 (mp0) REVERT: B 242 LEU cc_start: 0.8583 (mt) cc_final: 0.8294 (mt) REVERT: B 247 GLN cc_start: 0.9291 (mm-40) cc_final: 0.8387 (tm-30) REVERT: B 251 LEU cc_start: 0.7947 (tp) cc_final: 0.7557 (tp) REVERT: B 387 TYR cc_start: 0.8662 (m-10) cc_final: 0.8202 (t80) REVERT: B 388 VAL cc_start: 0.7928 (m) cc_final: 0.7669 (p) REVERT: B 430 PHE cc_start: 0.8105 (m-80) cc_final: 0.7846 (m-80) REVERT: B 505 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8836 (mp0) REVERT: B 2197 GLU cc_start: 0.8985 (tp30) cc_final: 0.8555 (tp30) REVERT: B 2205 MET cc_start: 0.7477 (tpt) cc_final: 0.6941 (mmm) REVERT: B 2248 GLU cc_start: 0.9214 (pm20) cc_final: 0.8819 (pm20) REVERT: B 2281 PHE cc_start: 0.9060 (t80) cc_final: 0.8807 (t80) REVERT: B 2395 HIS cc_start: 0.8333 (m170) cc_final: 0.8128 (m170) REVERT: B 2522 GLN cc_start: 0.9062 (pm20) cc_final: 0.8719 (pm20) REVERT: B 2524 LYS cc_start: 0.8582 (mmpt) cc_final: 0.8345 (mmtt) REVERT: B 2531 LEU cc_start: 0.8932 (pt) cc_final: 0.8425 (pt) REVERT: B 2540 SER cc_start: 0.9034 (m) cc_final: 0.8682 (p) REVERT: B 2582 LEU cc_start: 0.7880 (mt) cc_final: 0.7533 (mt) REVERT: B 2599 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8079 (tm-30) REVERT: B 2600 LYS cc_start: 0.8849 (mmpt) cc_final: 0.8304 (mmmt) REVERT: B 2601 GLN cc_start: 0.8556 (pm20) cc_final: 0.8191 (pm20) REVERT: B 2609 THR cc_start: 0.8953 (m) cc_final: 0.8687 (m) REVERT: B 2630 GLU cc_start: 0.9075 (mp0) cc_final: 0.8844 (pm20) REVERT: B 2666 MET cc_start: 0.8852 (mtp) cc_final: 0.8580 (ttm) REVERT: B 2668 ARG cc_start: 0.9499 (mmt90) cc_final: 0.9052 (ttm110) REVERT: B 2670 ARG cc_start: 0.9184 (ptt-90) cc_final: 0.8708 (mtm-85) REVERT: D 45 ASP cc_start: 0.9018 (m-30) cc_final: 0.8760 (t70) REVERT: D 63 MET cc_start: 0.9190 (tpt) cc_final: 0.8923 (tpp) REVERT: D 69 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8229 (tm-30) REVERT: D 97 ASP cc_start: 0.9147 (m-30) cc_final: 0.8721 (m-30) REVERT: D 120 VAL cc_start: 0.7771 (t) cc_final: 0.7152 (t) REVERT: D 125 HIS cc_start: 0.7459 (t-170) cc_final: 0.6941 (t-90) REVERT: D 137 ARG cc_start: 0.8710 (ptp-170) cc_final: 0.8374 (ptm160) REVERT: D 157 GLU cc_start: 0.9077 (mp0) cc_final: 0.8238 (mp0) REVERT: D 162 TYR cc_start: 0.8748 (m-80) cc_final: 0.8173 (m-80) REVERT: D 242 LEU cc_start: 0.8563 (mt) cc_final: 0.8325 (mt) REVERT: D 247 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8198 (tm-30) REVERT: D 251 LEU cc_start: 0.7909 (tp) cc_final: 0.7594 (tp) REVERT: D 387 TYR cc_start: 0.8351 (m-10) cc_final: 0.8097 (t80) REVERT: D 388 VAL cc_start: 0.8285 (m) cc_final: 0.7997 (p) REVERT: D 430 PHE cc_start: 0.7888 (m-80) cc_final: 0.7653 (m-80) REVERT: D 581 MET cc_start: 0.9381 (tmm) cc_final: 0.9112 (ppp) REVERT: D 2187 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8567 (pp20) REVERT: D 2197 GLU cc_start: 0.8799 (tp30) cc_final: 0.8458 (tp30) REVERT: D 2205 MET cc_start: 0.8365 (mmp) cc_final: 0.8016 (tpt) REVERT: D 2218 PHE cc_start: 0.9002 (m-80) cc_final: 0.8777 (m-10) REVERT: D 2281 PHE cc_start: 0.8801 (t80) cc_final: 0.8555 (t80) REVERT: D 2294 PHE cc_start: 0.8834 (m-80) cc_final: 0.8178 (m-80) REVERT: D 2524 LYS cc_start: 0.8678 (mptt) cc_final: 0.8393 (mmtt) REVERT: D 2582 LEU cc_start: 0.7716 (mt) cc_final: 0.7330 (mt) REVERT: D 2600 LYS cc_start: 0.8961 (tppt) cc_final: 0.8735 (tppt) REVERT: D 2603 LYS cc_start: 0.9624 (pttt) cc_final: 0.9188 (ptmm) REVERT: D 2604 GLU cc_start: 0.8925 (mp0) cc_final: 0.8697 (mp0) REVERT: D 2605 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8210 (tm-30) REVERT: D 2630 GLU cc_start: 0.9059 (mp0) cc_final: 0.8851 (pm20) REVERT: D 2665 GLU cc_start: 0.9636 (tp30) cc_final: 0.9376 (tp30) REVERT: D 2670 ARG cc_start: 0.9280 (ptt-90) cc_final: 0.8844 (mtm-85) outliers start: 21 outliers final: 2 residues processed: 1158 average time/residue: 0.5673 time to fit residues: 1102.0980 Evaluate side-chains 937 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 934 time to evaluate : 5.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 769 optimal weight: 8.9990 chunk 585 optimal weight: 5.9990 chunk 404 optimal weight: 0.9990 chunk 86 optimal weight: 50.0000 chunk 371 optimal weight: 5.9990 chunk 522 optimal weight: 30.0000 chunk 781 optimal weight: 40.0000 chunk 827 optimal weight: 20.0000 chunk 408 optimal weight: 7.9990 chunk 740 optimal weight: 0.3980 chunk 222 optimal weight: 9.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 ASN A 312 HIS A 584 GLN ** A2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 ASN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN C 312 HIS ** C2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2715 GLN ** B2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 ASN D 135 ASN ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 GLN ** D2395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 50772 Z= 0.227 Angle : 0.752 9.646 66840 Z= 0.401 Chirality : 0.047 0.229 5064 Planarity : 0.005 0.094 10144 Dihedral : 7.510 97.080 8876 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 21.61 Ramachandran Plot: Outliers : 0.76 % Allowed : 11.84 % Favored : 87.40 % Rotamer: Outliers : 0.15 % Allowed : 5.28 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 3.39 % Twisted General : 0.18 % 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: -1.33 (0.09), residues: 8436 helix: 0.87 (0.08), residues: 4924 sheet: -2.38 (0.37), residues: 228 loop : -3.71 (0.09), residues: 3284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 73 HIS 0.014 0.002 HIS C 93 PHE 0.040 0.003 PHE B 223 TYR 0.031 0.002 TYR D 131 ARG 0.007 0.001 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1092 time to evaluate : 6.027 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASP cc_start: 0.9154 (m-30) cc_final: 0.8791 (t70) REVERT: A 54 ARG cc_start: 0.8229 (ptp90) cc_final: 0.7976 (ttp-110) REVERT: A 63 MET cc_start: 0.8589 (mmp) cc_final: 0.8158 (tpp) REVERT: A 66 TYR cc_start: 0.7467 (m-80) cc_final: 0.6476 (m-10) REVERT: A 97 ASP cc_start: 0.9081 (m-30) cc_final: 0.8692 (m-30) REVERT: A 125 HIS cc_start: 0.7523 (t-170) cc_final: 0.7091 (t70) REVERT: A 131 TYR cc_start: 0.7497 (m-80) cc_final: 0.7265 (m-80) REVERT: A 137 ARG cc_start: 0.8329 (ptp-170) cc_final: 0.8014 (ptm160) REVERT: A 157 GLU cc_start: 0.9089 (mp0) cc_final: 0.8427 (mp0) REVERT: A 162 TYR cc_start: 0.8751 (m-80) cc_final: 0.8212 (m-80) REVERT: A 224 MET cc_start: 0.8249 (mpp) cc_final: 0.7864 (mmt) REVERT: A 242 LEU cc_start: 0.8744 (mt) cc_final: 0.8445 (mt) REVERT: A 247 GLN cc_start: 0.9163 (mm-40) cc_final: 0.8391 (tp40) REVERT: A 251 LEU cc_start: 0.7993 (tp) cc_final: 0.7537 (tp) REVERT: A 430 PHE cc_start: 0.8348 (m-80) cc_final: 0.8007 (m-80) REVERT: A 505 GLU cc_start: 0.9401 (pt0) cc_final: 0.9038 (pm20) REVERT: A 581 MET cc_start: 0.9455 (tmm) cc_final: 0.9168 (ppp) REVERT: A 2232 GLU cc_start: 0.6860 (tm-30) cc_final: 0.6089 (tp30) REVERT: A 2252 ASN cc_start: 0.9548 (m-40) cc_final: 0.9233 (m-40) REVERT: A 2258 LYS cc_start: 0.9500 (mmtm) cc_final: 0.9217 (mmmt) REVERT: A 2294 PHE cc_start: 0.8998 (m-80) cc_final: 0.8408 (m-80) REVERT: A 2524 LYS cc_start: 0.8760 (mmpt) cc_final: 0.8440 (mmtt) REVERT: A 2589 ILE cc_start: 0.8847 (mm) cc_final: 0.8523 (mt) REVERT: A 2605 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8101 (tm-30) REVERT: A 2641 TYR cc_start: 0.9075 (m-80) cc_final: 0.8694 (m-80) REVERT: A 2665 GLU cc_start: 0.9600 (tp30) cc_final: 0.9396 (tp30) REVERT: A 2668 ARG cc_start: 0.9512 (mmt90) cc_final: 0.9041 (ttm110) REVERT: A 2670 ARG cc_start: 0.9226 (ptt-90) cc_final: 0.8885 (mtm-85) REVERT: C 45 ASP cc_start: 0.8988 (m-30) cc_final: 0.8694 (t70) REVERT: C 57 LEU cc_start: 0.8851 (mt) cc_final: 0.8644 (mt) REVERT: C 66 TYR cc_start: 0.7955 (m-80) cc_final: 0.7235 (m-10) REVERT: C 125 HIS cc_start: 0.7193 (t-170) cc_final: 0.6986 (t70) REVERT: C 131 TYR cc_start: 0.7814 (m-80) cc_final: 0.7412 (m-80) REVERT: C 137 ARG cc_start: 0.8670 (ptp-170) cc_final: 0.7986 (ttt90) REVERT: C 162 TYR cc_start: 0.8701 (m-80) cc_final: 0.8136 (m-80) REVERT: C 228 ASP cc_start: 0.8986 (m-30) cc_final: 0.8774 (t0) REVERT: C 242 LEU cc_start: 0.8736 (mt) cc_final: 0.8475 (mt) REVERT: C 247 GLN cc_start: 0.9111 (mm-40) cc_final: 0.8113 (tm-30) REVERT: C 251 LEU cc_start: 0.8023 (tp) cc_final: 0.7526 (tp) REVERT: C 430 PHE cc_start: 0.8427 (m-80) cc_final: 0.8137 (m-80) REVERT: C 505 GLU cc_start: 0.9387 (pt0) cc_final: 0.9092 (pm20) REVERT: C 2218 PHE cc_start: 0.8505 (m-80) cc_final: 0.8067 (m-80) REVERT: C 2242 ASP cc_start: 0.8596 (t70) cc_final: 0.8165 (t0) REVERT: C 2248 GLU cc_start: 0.9440 (pm20) cc_final: 0.9145 (pm20) REVERT: C 2281 PHE cc_start: 0.8915 (t80) cc_final: 0.8667 (t80) REVERT: C 2395 HIS cc_start: 0.8139 (m-70) cc_final: 0.7791 (m-70) REVERT: C 2451 LEU cc_start: 0.8048 (mt) cc_final: 0.7811 (mt) REVERT: C 2589 ILE cc_start: 0.8866 (mm) cc_final: 0.8534 (mt) REVERT: C 2624 LYS cc_start: 0.9157 (mmpt) cc_final: 0.8887 (mmmt) REVERT: C 2630 GLU cc_start: 0.9068 (mp0) cc_final: 0.8778 (pm20) REVERT: C 2670 ARG cc_start: 0.9160 (ptt-90) cc_final: 0.8685 (mtm-85) REVERT: B 69 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8124 (tm-30) REVERT: B 100 LYS cc_start: 0.9508 (mmtt) cc_final: 0.9306 (mmtt) REVERT: B 121 ILE cc_start: 0.8530 (pt) cc_final: 0.8282 (tt) REVERT: B 125 HIS cc_start: 0.7776 (t-170) cc_final: 0.7357 (t-90) REVERT: B 137 ARG cc_start: 0.8918 (ptp-170) cc_final: 0.8643 (ptm160) REVERT: B 157 GLU cc_start: 0.9258 (mp0) cc_final: 0.8941 (mp0) REVERT: B 242 LEU cc_start: 0.8675 (mt) cc_final: 0.8284 (mt) REVERT: B 247 GLN cc_start: 0.9313 (mm-40) cc_final: 0.8343 (tm-30) REVERT: B 251 LEU cc_start: 0.8301 (tp) cc_final: 0.7959 (tp) REVERT: B 430 PHE cc_start: 0.8089 (m-80) cc_final: 0.7789 (m-80) REVERT: B 505 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8784 (mp0) REVERT: B 573 TYR cc_start: 0.9010 (t80) cc_final: 0.8747 (t80) REVERT: B 2197 GLU cc_start: 0.8999 (tp30) cc_final: 0.8484 (tp30) REVERT: B 2205 MET cc_start: 0.7848 (tpt) cc_final: 0.7186 (mmm) REVERT: B 2242 ASP cc_start: 0.8477 (t0) cc_final: 0.8183 (t0) REVERT: B 2248 GLU cc_start: 0.9596 (pm20) cc_final: 0.9371 (pm20) REVERT: B 2252 ASN cc_start: 0.9560 (m110) cc_final: 0.9271 (m110) REVERT: B 2254 MET cc_start: 0.8973 (ppp) cc_final: 0.8617 (ppp) REVERT: B 2258 LYS cc_start: 0.9549 (mmtt) cc_final: 0.9318 (mmmt) REVERT: B 2276 TRP cc_start: 0.6789 (m100) cc_final: 0.6537 (m100) REVERT: B 2281 PHE cc_start: 0.8935 (t80) cc_final: 0.8709 (t80) REVERT: B 2451 LEU cc_start: 0.8188 (mt) cc_final: 0.7970 (mt) REVERT: B 2589 ILE cc_start: 0.8784 (mm) cc_final: 0.8440 (mt) REVERT: B 2599 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8388 (tm-30) REVERT: B 2603 LYS cc_start: 0.9529 (ptmm) cc_final: 0.9228 (pttp) REVERT: B 2609 THR cc_start: 0.8834 (m) cc_final: 0.8579 (m) REVERT: B 2630 GLU cc_start: 0.9134 (mp0) cc_final: 0.8881 (pm20) REVERT: B 2638 MET cc_start: 0.9212 (mmt) cc_final: 0.8930 (mmt) REVERT: B 2670 ARG cc_start: 0.9235 (ptt-90) cc_final: 0.8822 (mtm-85) REVERT: B 2674 TRP cc_start: 0.7679 (m-90) cc_final: 0.7458 (m-90) REVERT: D 63 MET cc_start: 0.9191 (tpt) cc_final: 0.8927 (tpp) REVERT: D 73 TRP cc_start: 0.8443 (m-10) cc_final: 0.8010 (m-10) REVERT: D 97 ASP cc_start: 0.9170 (m-30) cc_final: 0.8900 (m-30) REVERT: D 120 VAL cc_start: 0.7939 (t) cc_final: 0.7157 (t) REVERT: D 121 ILE cc_start: 0.7405 (tp) cc_final: 0.7193 (tp) REVERT: D 137 ARG cc_start: 0.8719 (ptp-170) cc_final: 0.7788 (tmt-80) REVERT: D 157 GLU cc_start: 0.9206 (mp0) cc_final: 0.8512 (mp0) REVERT: D 162 TYR cc_start: 0.8832 (m-80) cc_final: 0.8274 (m-80) REVERT: D 242 LEU cc_start: 0.8645 (mt) cc_final: 0.8423 (mt) REVERT: D 247 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8080 (tm-30) REVERT: D 313 TYR cc_start: 0.8570 (m-80) cc_final: 0.8357 (m-80) REVERT: D 387 TYR cc_start: 0.8429 (m-10) cc_final: 0.8105 (t80) REVERT: D 388 VAL cc_start: 0.8351 (m) cc_final: 0.8106 (p) REVERT: D 581 MET cc_start: 0.9400 (tmm) cc_final: 0.9128 (ppp) REVERT: D 2205 MET cc_start: 0.8499 (mmp) cc_final: 0.8050 (tpt) REVERT: D 2218 PHE cc_start: 0.9125 (m-80) cc_final: 0.8773 (m-10) REVERT: D 2242 ASP cc_start: 0.8357 (t70) cc_final: 0.8119 (t0) REVERT: D 2252 ASN cc_start: 0.9471 (m110) cc_final: 0.9087 (m110) REVERT: D 2258 LYS cc_start: 0.9475 (mmtt) cc_final: 0.9242 (mmmt) REVERT: D 2281 PHE cc_start: 0.8878 (t80) cc_final: 0.8500 (t80) REVERT: D 2294 PHE cc_start: 0.8921 (m-80) cc_final: 0.8342 (m-80) REVERT: D 2541 HIS cc_start: 0.7594 (t70) cc_final: 0.7247 (t-90) REVERT: D 2589 ILE cc_start: 0.8895 (mm) cc_final: 0.8581 (mt) REVERT: D 2600 LYS cc_start: 0.9109 (tppt) cc_final: 0.8852 (tppt) REVERT: D 2630 GLU cc_start: 0.9120 (mp0) cc_final: 0.8865 (pm20) REVERT: D 2670 ARG cc_start: 0.9304 (ptt-90) cc_final: 0.8887 (mtm-85) outliers start: 5 outliers final: 0 residues processed: 1096 average time/residue: 0.5612 time to fit residues: 1031.3127 Evaluate side-chains 880 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 880 time to evaluate : 6.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 689 optimal weight: 20.0000 chunk 469 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 616 optimal weight: 3.9990 chunk 341 optimal weight: 4.9990 chunk 706 optimal weight: 0.0370 chunk 571 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 422 optimal weight: 8.9990 chunk 742 optimal weight: 50.0000 chunk 208 optimal weight: 3.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 GLN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 GLN ** A2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2541 HIS A2715 GLN ** A2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2364 ASN ** B2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 ASN ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 ASN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 GLN ** D2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2541 HIS ** D2711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 50772 Z= 0.214 Angle : 0.742 12.064 66840 Z= 0.391 Chirality : 0.046 0.205 5064 Planarity : 0.005 0.085 10144 Dihedral : 7.359 96.405 8876 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.76 % Allowed : 12.03 % Favored : 87.21 % Rotamer: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 3.39 % Twisted General : 0.12 % 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: -1.12 (0.09), residues: 8436 helix: 1.01 (0.08), residues: 4940 sheet: -1.87 (0.37), residues: 220 loop : -3.62 (0.09), residues: 3276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 299 HIS 0.012 0.002 HIS C2640 PHE 0.049 0.002 PHE B 72 TYR 0.033 0.002 TYR A 313 ARG 0.015 0.001 ARG C2233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1076 time to evaluate : 6.049 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASP cc_start: 0.9231 (m-30) cc_final: 0.8885 (t70) REVERT: A 61 CYS cc_start: 0.8534 (t) cc_final: 0.8190 (m) REVERT: A 63 MET cc_start: 0.8855 (mmp) cc_final: 0.8463 (tpp) REVERT: A 73 TRP cc_start: 0.8751 (m-10) cc_final: 0.8464 (m-10) REVERT: A 97 ASP cc_start: 0.9143 (m-30) cc_final: 0.8637 (m-30) REVERT: A 102 GLN cc_start: 0.8968 (tm-30) cc_final: 0.8661 (tm-30) REVERT: A 125 HIS cc_start: 0.7569 (t-170) cc_final: 0.7079 (t70) REVERT: A 131 TYR cc_start: 0.7254 (m-80) cc_final: 0.6906 (m-80) REVERT: A 137 ARG cc_start: 0.8387 (ptp-170) cc_final: 0.8047 (ptm160) REVERT: A 157 GLU cc_start: 0.9052 (mp0) cc_final: 0.8583 (mp0) REVERT: A 162 TYR cc_start: 0.8715 (m-80) cc_final: 0.8175 (m-80) REVERT: A 224 MET cc_start: 0.8157 (mpp) cc_final: 0.7784 (mpp) REVERT: A 247 GLN cc_start: 0.9177 (mm-40) cc_final: 0.8098 (tm-30) REVERT: A 430 PHE cc_start: 0.8338 (m-80) cc_final: 0.8005 (m-80) REVERT: A 505 GLU cc_start: 0.9401 (pt0) cc_final: 0.9025 (pm20) REVERT: A 581 MET cc_start: 0.9451 (tmm) cc_final: 0.9166 (ppp) REVERT: A 2188 PHE cc_start: 0.7887 (m-10) cc_final: 0.7373 (m-10) REVERT: A 2205 MET cc_start: 0.8256 (mmt) cc_final: 0.7997 (mmt) REVERT: A 2242 ASP cc_start: 0.8362 (t0) cc_final: 0.8129 (t0) REVERT: A 2252 ASN cc_start: 0.9559 (m-40) cc_final: 0.9251 (m-40) REVERT: A 2258 LYS cc_start: 0.9486 (mmtm) cc_final: 0.9224 (mmmt) REVERT: A 2294 PHE cc_start: 0.8976 (m-80) cc_final: 0.8398 (m-80) REVERT: A 2392 PHE cc_start: 0.8907 (p90) cc_final: 0.8689 (p90) REVERT: A 2395 HIS cc_start: 0.8682 (m90) cc_final: 0.8320 (m90) REVERT: A 2524 LYS cc_start: 0.8697 (mmpt) cc_final: 0.8311 (mmtt) REVERT: A 2541 HIS cc_start: 0.7267 (t-90) cc_final: 0.6981 (t-90) REVERT: A 2605 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8279 (tm-30) REVERT: A 2624 LYS cc_start: 0.9435 (ttpp) cc_final: 0.9173 (mptt) REVERT: A 2641 TYR cc_start: 0.8963 (m-80) cc_final: 0.8605 (m-80) REVERT: A 2668 ARG cc_start: 0.9513 (mmt90) cc_final: 0.9277 (mtp85) REVERT: A 2670 ARG cc_start: 0.9141 (ptt-90) cc_final: 0.8746 (mtm-85) REVERT: C 45 ASP cc_start: 0.9001 (m-30) cc_final: 0.8703 (t70) REVERT: C 66 TYR cc_start: 0.7423 (m-80) cc_final: 0.7118 (m-80) REVERT: C 131 TYR cc_start: 0.7662 (m-80) cc_final: 0.7284 (m-80) REVERT: C 137 ARG cc_start: 0.8667 (ptp-170) cc_final: 0.7977 (ttt90) REVERT: C 162 TYR cc_start: 0.8659 (m-80) cc_final: 0.8083 (m-80) REVERT: C 242 LEU cc_start: 0.8738 (mt) cc_final: 0.8513 (mt) REVERT: C 247 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8180 (tm-30) REVERT: C 251 LEU cc_start: 0.8021 (tp) cc_final: 0.7552 (tp) REVERT: C 430 PHE cc_start: 0.8407 (m-80) cc_final: 0.8123 (m-80) REVERT: C 505 GLU cc_start: 0.9395 (pt0) cc_final: 0.9093 (pm20) REVERT: C 519 ILE cc_start: 0.9406 (mp) cc_final: 0.9113 (mp) REVERT: C 2197 GLU cc_start: 0.8777 (tp30) cc_final: 0.8120 (tp30) REVERT: C 2242 ASP cc_start: 0.8515 (t70) cc_final: 0.8307 (t0) REVERT: C 2244 PHE cc_start: 0.9386 (t80) cc_final: 0.9173 (t80) REVERT: C 2248 GLU cc_start: 0.9359 (pm20) cc_final: 0.8907 (pm20) REVERT: C 2267 TYR cc_start: 0.9384 (p90) cc_final: 0.9169 (p90) REVERT: C 2281 PHE cc_start: 0.8921 (t80) cc_final: 0.8561 (t80) REVERT: C 2404 MET cc_start: 0.6807 (tpp) cc_final: 0.6345 (tmm) REVERT: C 2413 TYR cc_start: 0.7821 (m-80) cc_final: 0.7568 (m-80) REVERT: C 2589 ILE cc_start: 0.8844 (mm) cc_final: 0.8532 (mt) REVERT: C 2599 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8399 (tm-30) REVERT: C 2601 GLN cc_start: 0.8720 (pm20) cc_final: 0.8311 (pm20) REVERT: C 2624 LYS cc_start: 0.9321 (mmpt) cc_final: 0.8858 (mmmt) REVERT: C 2630 GLU cc_start: 0.9109 (mp0) cc_final: 0.8800 (pm20) REVERT: C 2647 LEU cc_start: 0.7408 (tp) cc_final: 0.7204 (tp) REVERT: C 2670 ARG cc_start: 0.9194 (ptt-90) cc_final: 0.8749 (mtm-85) REVERT: C 2674 TRP cc_start: 0.7597 (m-90) cc_final: 0.7158 (m-90) REVERT: B 5 MET cc_start: 0.7236 (pmm) cc_final: 0.6980 (pmm) REVERT: B 52 LYS cc_start: 0.8722 (tmtt) cc_final: 0.8507 (tptp) REVERT: B 125 HIS cc_start: 0.7730 (t-170) cc_final: 0.7374 (t-90) REVERT: B 137 ARG cc_start: 0.8910 (ptp-170) cc_final: 0.8522 (ttt90) REVERT: B 157 GLU cc_start: 0.9216 (mp0) cc_final: 0.8673 (mp0) REVERT: B 162 TYR cc_start: 0.9077 (m-10) cc_final: 0.8572 (m-80) REVERT: B 242 LEU cc_start: 0.8652 (mt) cc_final: 0.8274 (mt) REVERT: B 247 GLN cc_start: 0.9294 (mm-40) cc_final: 0.8340 (tm-30) REVERT: B 251 LEU cc_start: 0.8459 (tp) cc_final: 0.8243 (tp) REVERT: B 302 LEU cc_start: 0.9404 (tp) cc_final: 0.9165 (tp) REVERT: B 415 MET cc_start: 0.6654 (mpp) cc_final: 0.6401 (mpp) REVERT: B 430 PHE cc_start: 0.7983 (m-80) cc_final: 0.7681 (m-80) REVERT: B 505 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8785 (mp0) REVERT: B 573 TYR cc_start: 0.8990 (t80) cc_final: 0.8728 (t80) REVERT: B 2197 GLU cc_start: 0.9008 (tp30) cc_final: 0.8517 (tp30) REVERT: B 2205 MET cc_start: 0.7843 (tpt) cc_final: 0.7178 (mmm) REVERT: B 2248 GLU cc_start: 0.9544 (pm20) cc_final: 0.9254 (mp0) REVERT: B 2252 ASN cc_start: 0.9552 (m110) cc_final: 0.9263 (m110) REVERT: B 2254 MET cc_start: 0.8949 (ppp) cc_final: 0.8614 (ppp) REVERT: B 2258 LYS cc_start: 0.9514 (mmtt) cc_final: 0.9284 (mmmt) REVERT: B 2281 PHE cc_start: 0.8876 (t80) cc_final: 0.8574 (t80) REVERT: B 2294 PHE cc_start: 0.8887 (m-80) cc_final: 0.8226 (m-80) REVERT: B 2589 ILE cc_start: 0.8756 (mm) cc_final: 0.8393 (mt) REVERT: B 2599 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8293 (tm-30) REVERT: B 2600 LYS cc_start: 0.9053 (mmpt) cc_final: 0.8394 (mmmt) REVERT: B 2630 GLU cc_start: 0.9149 (mp0) cc_final: 0.8844 (pm20) REVERT: B 2638 MET cc_start: 0.8992 (mmt) cc_final: 0.8615 (mmm) REVERT: B 2666 MET cc_start: 0.8983 (mtp) cc_final: 0.8562 (ttm) REVERT: B 2670 ARG cc_start: 0.9191 (ptt-90) cc_final: 0.8753 (mtm-85) REVERT: B 2723 MET cc_start: 0.9796 (tpt) cc_final: 0.9590 (tpt) REVERT: D 5 MET cc_start: 0.7354 (pmm) cc_final: 0.7095 (pmm) REVERT: D 73 TRP cc_start: 0.8358 (m-10) cc_final: 0.7926 (m-10) REVERT: D 97 ASP cc_start: 0.9222 (m-30) cc_final: 0.8963 (m-30) REVERT: D 102 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8798 (tm-30) REVERT: D 120 VAL cc_start: 0.7941 (t) cc_final: 0.7104 (t) REVERT: D 131 TYR cc_start: 0.7566 (m-10) cc_final: 0.7148 (m-80) REVERT: D 137 ARG cc_start: 0.8738 (ptp-170) cc_final: 0.8420 (ptm160) REVERT: D 162 TYR cc_start: 0.8810 (m-80) cc_final: 0.8238 (m-80) REVERT: D 242 LEU cc_start: 0.8620 (mt) cc_final: 0.8394 (mt) REVERT: D 247 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8032 (tm-30) REVERT: D 387 TYR cc_start: 0.8485 (m-10) cc_final: 0.8109 (t80) REVERT: D 388 VAL cc_start: 0.8293 (m) cc_final: 0.8046 (p) REVERT: D 581 MET cc_start: 0.9379 (tmm) cc_final: 0.9091 (ppp) REVERT: D 2188 PHE cc_start: 0.8254 (m-10) cc_final: 0.7746 (m-80) REVERT: D 2205 MET cc_start: 0.8558 (mmp) cc_final: 0.8197 (tpt) REVERT: D 2218 PHE cc_start: 0.9153 (m-80) cc_final: 0.8841 (m-10) REVERT: D 2244 PHE cc_start: 0.9405 (t80) cc_final: 0.9124 (t80) REVERT: D 2252 ASN cc_start: 0.9465 (m110) cc_final: 0.9211 (m110) REVERT: D 2281 PHE cc_start: 0.8834 (t80) cc_final: 0.8470 (t80) REVERT: D 2294 PHE cc_start: 0.8843 (m-80) cc_final: 0.8399 (m-80) REVERT: D 2395 HIS cc_start: 0.8458 (m90) cc_final: 0.8115 (m90) REVERT: D 2541 HIS cc_start: 0.7541 (t-90) cc_final: 0.7233 (t-90) REVERT: D 2589 ILE cc_start: 0.8874 (mm) cc_final: 0.8529 (mt) REVERT: D 2600 LYS cc_start: 0.9079 (tppt) cc_final: 0.8789 (mmmm) REVERT: D 2603 LYS cc_start: 0.9655 (pttt) cc_final: 0.9422 (pttm) REVERT: D 2624 LYS cc_start: 0.9508 (ttpp) cc_final: 0.9123 (mptt) REVERT: D 2630 GLU cc_start: 0.9115 (mp0) cc_final: 0.8788 (pm20) REVERT: D 2670 ARG cc_start: 0.9233 (ptt-90) cc_final: 0.8856 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 1076 average time/residue: 0.5601 time to fit residues: 1010.9391 Evaluate side-chains 866 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 866 time to evaluate : 5.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 278 optimal weight: 1.9990 chunk 745 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 485 optimal weight: 0.1980 chunk 204 optimal weight: 0.8980 chunk 828 optimal weight: 6.9990 chunk 687 optimal weight: 30.0000 chunk 383 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 273 optimal weight: 5.9990 chunk 434 optimal weight: 8.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 HIS A 584 GLN ** A2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 HIS C2272 ASN ** C2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 HIS ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2364 ASN ** B2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 HIS ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 GLN ** D2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2364 ASN ** D2637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 50772 Z= 0.199 Angle : 0.727 13.030 66840 Z= 0.379 Chirality : 0.046 0.208 5064 Planarity : 0.005 0.081 10144 Dihedral : 7.215 95.623 8876 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.73 % Allowed : 11.97 % Favored : 87.29 % Rotamer: Outliers : 0.09 % Allowed : 3.27 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 3.39 % Twisted General : 0.11 % 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 (0.10), residues: 8436 helix: 1.14 (0.08), residues: 4936 sheet: -2.03 (0.32), residues: 276 loop : -3.56 (0.10), residues: 3224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 73 HIS 0.012 0.002 HIS C2395 PHE 0.038 0.002 PHE D 223 TYR 0.045 0.002 TYR D 313 ARG 0.013 0.001 ARG B2668 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1053 time to evaluate : 5.766 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: 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: 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: 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: 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 45 ASP cc_start: 0.9234 (m-30) cc_final: 0.8890 (t70) REVERT: A 61 CYS cc_start: 0.8477 (t) cc_final: 0.8160 (m) REVERT: A 73 TRP cc_start: 0.8759 (m-10) cc_final: 0.8439 (m-10) REVERT: A 102 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8673 (tm-30) REVERT: A 125 HIS cc_start: 0.7424 (t-170) cc_final: 0.7011 (t70) REVERT: A 131 TYR cc_start: 0.7333 (m-80) cc_final: 0.6892 (m-80) REVERT: A 157 GLU cc_start: 0.9047 (mp0) cc_final: 0.8558 (mp0) REVERT: A 162 TYR cc_start: 0.8689 (m-80) cc_final: 0.8140 (m-80) REVERT: A 224 MET cc_start: 0.8245 (mpp) cc_final: 0.7774 (mpp) REVERT: A 242 LEU cc_start: 0.8759 (mt) cc_final: 0.8490 (mt) REVERT: A 247 GLN cc_start: 0.9156 (mm-40) cc_final: 0.8079 (tm-30) REVERT: A 251 LEU cc_start: 0.7947 (tp) cc_final: 0.7579 (tp) REVERT: A 430 PHE cc_start: 0.8300 (m-80) cc_final: 0.7950 (m-80) REVERT: A 505 GLU cc_start: 0.9372 (pt0) cc_final: 0.8998 (pm20) REVERT: A 581 MET cc_start: 0.9454 (tmm) cc_final: 0.9158 (ppp) REVERT: A 2197 GLU cc_start: 0.8786 (mm-30) cc_final: 0.7700 (mm-30) REVERT: A 2205 MET cc_start: 0.8147 (mmt) cc_final: 0.7877 (mmt) REVERT: A 2208 ILE cc_start: 0.8734 (tp) cc_final: 0.8366 (tt) REVERT: A 2242 ASP cc_start: 0.8322 (t0) cc_final: 0.8047 (t0) REVERT: A 2244 PHE cc_start: 0.9483 (t80) cc_final: 0.9264 (t80) REVERT: A 2252 ASN cc_start: 0.9563 (m-40) cc_final: 0.9296 (m-40) REVERT: A 2258 LYS cc_start: 0.9470 (mmtm) cc_final: 0.9202 (mmmt) REVERT: A 2281 PHE cc_start: 0.8681 (t80) cc_final: 0.8271 (t80) REVERT: A 2294 PHE cc_start: 0.9002 (m-80) cc_final: 0.8428 (m-80) REVERT: A 2418 PHE cc_start: 0.6298 (t80) cc_final: 0.5926 (t80) REVERT: A 2541 HIS cc_start: 0.7391 (t-90) cc_final: 0.7103 (t-90) REVERT: A 2609 THR cc_start: 0.9042 (m) cc_final: 0.8784 (m) REVERT: A 2624 LYS cc_start: 0.9416 (ttpp) cc_final: 0.9152 (mptt) REVERT: A 2641 TYR cc_start: 0.8916 (m-80) cc_final: 0.8641 (m-80) REVERT: A 2670 ARG cc_start: 0.9127 (ptt-90) cc_final: 0.8716 (mtm-85) REVERT: C 45 ASP cc_start: 0.9035 (m-30) cc_final: 0.8735 (t70) REVERT: C 66 TYR cc_start: 0.7454 (m-80) cc_final: 0.6682 (m-10) REVERT: C 131 TYR cc_start: 0.7580 (m-80) cc_final: 0.7201 (m-80) REVERT: C 137 ARG cc_start: 0.8573 (ptp-170) cc_final: 0.7899 (ttt90) REVERT: C 157 GLU cc_start: 0.9232 (mp0) cc_final: 0.8887 (mp0) REVERT: C 162 TYR cc_start: 0.8662 (m-80) cc_final: 0.8073 (m-80) REVERT: C 170 ARG cc_start: 0.7891 (mpt-90) cc_final: 0.7623 (mpp-170) REVERT: C 218 TRP cc_start: 0.8070 (m-90) cc_final: 0.7775 (m-90) REVERT: C 242 LEU cc_start: 0.8721 (mt) cc_final: 0.8502 (mt) REVERT: C 247 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8187 (tm-30) REVERT: C 251 LEU cc_start: 0.8008 (tp) cc_final: 0.7559 (tp) REVERT: C 430 PHE cc_start: 0.8374 (m-80) cc_final: 0.8090 (m-80) REVERT: C 505 GLU cc_start: 0.9362 (pt0) cc_final: 0.9067 (pm20) REVERT: C 2205 MET cc_start: 0.7619 (tpt) cc_final: 0.6974 (mmm) REVERT: C 2244 PHE cc_start: 0.9384 (t80) cc_final: 0.9121 (t80) REVERT: C 2248 GLU cc_start: 0.9290 (pm20) cc_final: 0.8830 (pm20) REVERT: C 2254 MET cc_start: 0.8866 (ppp) cc_final: 0.8616 (ppp) REVERT: C 2259 LYS cc_start: 0.9585 (tmtt) cc_final: 0.9347 (mmtp) REVERT: C 2281 PHE cc_start: 0.8771 (t80) cc_final: 0.8213 (t80) REVERT: C 2294 PHE cc_start: 0.8841 (m-80) cc_final: 0.8081 (m-80) REVERT: C 2404 MET cc_start: 0.7298 (tpp) cc_final: 0.6962 (tmm) REVERT: C 2589 ILE cc_start: 0.8710 (mm) cc_final: 0.8364 (mt) REVERT: C 2624 LYS cc_start: 0.9270 (mmpt) cc_final: 0.8822 (mmmt) REVERT: C 2630 GLU cc_start: 0.9133 (mp0) cc_final: 0.8829 (pm20) REVERT: C 2647 LEU cc_start: 0.7153 (tp) cc_final: 0.6937 (tp) REVERT: C 2670 ARG cc_start: 0.9151 (ptt-90) cc_final: 0.8650 (mtm-85) REVERT: B 5 MET cc_start: 0.7273 (pmm) cc_final: 0.7037 (pmm) REVERT: B 66 TYR cc_start: 0.7247 (m-80) cc_final: 0.6397 (m-10) REVERT: B 125 HIS cc_start: 0.7741 (t-170) cc_final: 0.7369 (t-170) REVERT: B 137 ARG cc_start: 0.9053 (ptp-170) cc_final: 0.8655 (ptm160) REVERT: B 157 GLU cc_start: 0.9160 (mp0) cc_final: 0.8907 (mp0) REVERT: B 162 TYR cc_start: 0.9038 (m-10) cc_final: 0.8544 (m-80) REVERT: B 242 LEU cc_start: 0.8656 (mt) cc_final: 0.8287 (mt) REVERT: B 247 GLN cc_start: 0.9295 (mm-40) cc_final: 0.8352 (tm-30) REVERT: B 302 LEU cc_start: 0.9428 (tp) cc_final: 0.9174 (tp) REVERT: B 430 PHE cc_start: 0.8081 (m-80) cc_final: 0.7786 (m-80) REVERT: B 505 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8748 (mp0) REVERT: B 573 TYR cc_start: 0.8935 (t80) cc_final: 0.8611 (t80) REVERT: B 2197 GLU cc_start: 0.8935 (tp30) cc_final: 0.8535 (tp30) REVERT: B 2205 MET cc_start: 0.7752 (tpt) cc_final: 0.6990 (mmm) REVERT: B 2248 GLU cc_start: 0.9519 (pm20) cc_final: 0.9257 (mp0) REVERT: B 2252 ASN cc_start: 0.9540 (m110) cc_final: 0.9261 (m110) REVERT: B 2254 MET cc_start: 0.8931 (ppp) cc_final: 0.8713 (ppp) REVERT: B 2276 TRP cc_start: 0.7390 (m100) cc_final: 0.7017 (m100) REVERT: B 2281 PHE cc_start: 0.8741 (t80) cc_final: 0.8395 (t80) REVERT: B 2294 PHE cc_start: 0.8901 (m-80) cc_final: 0.8272 (m-80) REVERT: B 2589 ILE cc_start: 0.8926 (mm) cc_final: 0.8528 (mt) REVERT: B 2599 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8220 (tm-30) REVERT: B 2600 LYS cc_start: 0.9036 (mmpt) cc_final: 0.8308 (mmmt) REVERT: B 2630 GLU cc_start: 0.9157 (mp0) cc_final: 0.8844 (pm20) REVERT: B 2665 GLU cc_start: 0.9583 (tp30) cc_final: 0.9372 (tp30) REVERT: B 2666 MET cc_start: 0.9043 (mtp) cc_final: 0.8625 (ttm) REVERT: B 2670 ARG cc_start: 0.9216 (ptt-90) cc_final: 0.8813 (mtm-85) REVERT: D 5 MET cc_start: 0.7572 (pmm) cc_final: 0.7355 (pmm) REVERT: D 63 MET cc_start: 0.8523 (mmp) cc_final: 0.8259 (tpp) REVERT: D 73 TRP cc_start: 0.8322 (m-10) cc_final: 0.7943 (m-10) REVERT: D 97 ASP cc_start: 0.9230 (m-30) cc_final: 0.8958 (m-30) REVERT: D 102 GLN cc_start: 0.9025 (tm-30) cc_final: 0.8766 (tm-30) REVERT: D 126 LEU cc_start: 0.9203 (mt) cc_final: 0.8994 (mt) REVERT: D 131 TYR cc_start: 0.7575 (m-80) cc_final: 0.7095 (m-80) REVERT: D 137 ARG cc_start: 0.8778 (ptp-170) cc_final: 0.8562 (ptm160) REVERT: D 161 PHE cc_start: 0.7254 (m-80) cc_final: 0.7032 (m-80) REVERT: D 162 TYR cc_start: 0.8845 (m-80) cc_final: 0.8229 (m-80) REVERT: D 242 LEU cc_start: 0.8481 (mt) cc_final: 0.8036 (mt) REVERT: D 247 GLN cc_start: 0.9155 (mm-40) cc_final: 0.8152 (tm-30) REVERT: D 387 TYR cc_start: 0.8524 (m-10) cc_final: 0.8118 (t80) REVERT: D 388 VAL cc_start: 0.8305 (m) cc_final: 0.8037 (p) REVERT: D 581 MET cc_start: 0.9373 (tmm) cc_final: 0.9070 (ppp) REVERT: D 2188 PHE cc_start: 0.8191 (m-10) cc_final: 0.7762 (m-80) REVERT: D 2205 MET cc_start: 0.8664 (mmp) cc_final: 0.8084 (tpt) REVERT: D 2218 PHE cc_start: 0.9058 (m-80) cc_final: 0.8608 (m-10) REVERT: D 2252 ASN cc_start: 0.9442 (m110) cc_final: 0.9160 (m110) REVERT: D 2254 MET cc_start: 0.9027 (ppp) cc_final: 0.8728 (ppp) REVERT: D 2258 LYS cc_start: 0.9412 (mmtt) cc_final: 0.9193 (mmmt) REVERT: D 2281 PHE cc_start: 0.8814 (t80) cc_final: 0.8497 (t80) REVERT: D 2294 PHE cc_start: 0.8786 (m-80) cc_final: 0.8304 (m-80) REVERT: D 2451 LEU cc_start: 0.7958 (mt) cc_final: 0.7710 (mt) REVERT: D 2541 HIS cc_start: 0.7551 (t-90) cc_final: 0.7269 (t-90) REVERT: D 2589 ILE cc_start: 0.8832 (mm) cc_final: 0.8510 (mt) REVERT: D 2603 LYS cc_start: 0.9692 (pttt) cc_final: 0.9430 (pttp) REVERT: D 2609 THR cc_start: 0.9041 (m) cc_final: 0.8510 (m) REVERT: D 2630 GLU cc_start: 0.9150 (mp0) cc_final: 0.8775 (pm20) REVERT: D 2666 MET cc_start: 0.8384 (ptm) cc_final: 0.7947 (ptm) REVERT: D 2670 ARG cc_start: 0.9212 (ptt-90) cc_final: 0.8714 (mtm-85) outliers start: 3 outliers final: 2 residues processed: 1056 average time/residue: 0.5573 time to fit residues: 992.3661 Evaluate side-chains 862 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 860 time to evaluate : 6.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 798 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 chunk 471 optimal weight: 8.9990 chunk 604 optimal weight: 6.9990 chunk 468 optimal weight: 4.9990 chunk 697 optimal weight: 40.0000 chunk 462 optimal weight: 30.0000 chunk 825 optimal weight: 5.9990 chunk 516 optimal weight: 50.0000 chunk 503 optimal weight: 40.0000 chunk 380 optimal weight: 50.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 GLN ** A2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2272 ASN ** A2395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2257 GLN ** C2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2715 GLN ** C2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2272 ASN ** B2711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 GLN ** D2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2272 ASN D2364 ASN ** D2637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.5963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 50772 Z= 0.292 Angle : 0.783 9.920 66840 Z= 0.416 Chirality : 0.049 0.272 5064 Planarity : 0.005 0.082 10144 Dihedral : 7.442 104.543 8876 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 26.28 Ramachandran Plot: Outliers : 0.72 % Allowed : 13.15 % Favored : 86.13 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 3.39 % Twisted General : 0.13 % 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: -0.95 (0.10), residues: 8436 helix: 1.15 (0.08), residues: 4928 sheet: -1.74 (0.33), residues: 272 loop : -3.56 (0.10), residues: 3236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 282 HIS 0.019 0.002 HIS C2640 PHE 0.040 0.003 PHE B2575 TYR 0.027 0.002 TYR B 567 ARG 0.016 0.001 ARG A2233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1013 time to evaluate : 5.934 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8964 (mmp) cc_final: 0.8425 (tpp) REVERT: A 73 TRP cc_start: 0.8882 (m-10) cc_final: 0.8612 (m-10) REVERT: A 102 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8658 (tm-30) REVERT: A 131 TYR cc_start: 0.7298 (m-80) cc_final: 0.6849 (m-80) REVERT: A 157 GLU cc_start: 0.9172 (mp0) cc_final: 0.8964 (mp0) REVERT: A 162 TYR cc_start: 0.8596 (m-80) cc_final: 0.7948 (m-80) REVERT: A 224 MET cc_start: 0.8101 (mpp) cc_final: 0.7641 (mpp) REVERT: A 247 GLN cc_start: 0.9184 (mm-40) cc_final: 0.8114 (tm-30) REVERT: A 505 GLU cc_start: 0.9404 (pt0) cc_final: 0.9043 (pm20) REVERT: A 2197 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8539 (tp30) REVERT: A 2242 ASP cc_start: 0.8496 (t0) cc_final: 0.8205 (t0) REVERT: A 2244 PHE cc_start: 0.9463 (t80) cc_final: 0.9244 (t80) REVERT: A 2252 ASN cc_start: 0.9650 (m-40) cc_final: 0.9370 (m-40) REVERT: A 2281 PHE cc_start: 0.8717 (t80) cc_final: 0.8148 (t80) REVERT: A 2294 PHE cc_start: 0.9022 (m-80) cc_final: 0.8523 (m-80) REVERT: A 2418 PHE cc_start: 0.6570 (t80) cc_final: 0.6256 (t80) REVERT: A 2541 HIS cc_start: 0.7636 (t-90) cc_final: 0.7380 (t-90) REVERT: A 2624 LYS cc_start: 0.9450 (ttpp) cc_final: 0.9240 (mptt) REVERT: A 2670 ARG cc_start: 0.9215 (ptt-90) cc_final: 0.8806 (mtm-85) REVERT: C 66 TYR cc_start: 0.7742 (m-80) cc_final: 0.7359 (m-80) REVERT: C 97 ASP cc_start: 0.9360 (t0) cc_final: 0.8850 (t0) REVERT: C 131 TYR cc_start: 0.7602 (m-80) cc_final: 0.7195 (m-80) REVERT: C 137 ARG cc_start: 0.8731 (ptp-170) cc_final: 0.7595 (tmt170) REVERT: C 162 TYR cc_start: 0.8730 (m-80) cc_final: 0.8126 (m-80) REVERT: C 170 ARG cc_start: 0.8100 (mpt-90) cc_final: 0.7660 (mpp-170) REVERT: C 174 ASP cc_start: 0.9136 (m-30) cc_final: 0.8931 (m-30) REVERT: C 218 TRP cc_start: 0.8364 (m-90) cc_final: 0.7955 (m-90) REVERT: C 247 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8211 (tm-30) REVERT: C 505 GLU cc_start: 0.9408 (pt0) cc_final: 0.9036 (pm20) REVERT: C 573 TYR cc_start: 0.8592 (t80) cc_final: 0.8237 (t80) REVERT: C 2206 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8531 (tm-30) REVERT: C 2244 PHE cc_start: 0.9344 (t80) cc_final: 0.9074 (t80) REVERT: C 2248 GLU cc_start: 0.9277 (pm20) cc_final: 0.8894 (pm20) REVERT: C 2254 MET cc_start: 0.8965 (ppp) cc_final: 0.8531 (ppp) REVERT: C 2258 LYS cc_start: 0.9581 (mmtt) cc_final: 0.9136 (mmtt) REVERT: C 2281 PHE cc_start: 0.8742 (t80) cc_final: 0.8170 (t80) REVERT: C 2624 LYS cc_start: 0.9334 (mmpt) cc_final: 0.8897 (mmmt) REVERT: C 2630 GLU cc_start: 0.9188 (mp0) cc_final: 0.8809 (pm20) REVERT: C 2641 TYR cc_start: 0.9039 (m-80) cc_final: 0.8741 (m-80) REVERT: C 2666 MET cc_start: 0.8940 (ttm) cc_final: 0.8702 (ptm) REVERT: C 2669 GLU cc_start: 0.8854 (mp0) cc_final: 0.8477 (mp0) REVERT: C 2670 ARG cc_start: 0.9148 (ptt-90) cc_final: 0.8652 (mtm-85) REVERT: B 5 MET cc_start: 0.7298 (pmm) cc_final: 0.7077 (pmm) REVERT: B 63 MET cc_start: 0.9058 (tpp) cc_final: 0.8806 (tpp) REVERT: B 66 TYR cc_start: 0.6930 (m-80) cc_final: 0.5194 (m-10) REVERT: B 69 GLN cc_start: 0.9187 (pt0) cc_final: 0.8865 (pp30) REVERT: B 125 HIS cc_start: 0.7861 (t-170) cc_final: 0.7594 (t-170) REVERT: B 137 ARG cc_start: 0.9112 (ptp-170) cc_final: 0.8686 (ptm160) REVERT: B 157 GLU cc_start: 0.9281 (mp0) cc_final: 0.8908 (mp0) REVERT: B 162 TYR cc_start: 0.9147 (m-10) cc_final: 0.8708 (m-80) REVERT: B 247 GLN cc_start: 0.9309 (mm-40) cc_final: 0.8386 (tm-30) REVERT: B 251 LEU cc_start: 0.8517 (tp) cc_final: 0.8301 (tp) REVERT: B 302 LEU cc_start: 0.9377 (tp) cc_final: 0.9104 (tp) REVERT: B 505 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8872 (mp0) REVERT: B 573 TYR cc_start: 0.8999 (t80) cc_final: 0.8772 (t80) REVERT: B 2197 GLU cc_start: 0.8985 (tp30) cc_final: 0.8427 (tp30) REVERT: B 2205 MET cc_start: 0.7879 (tpt) cc_final: 0.7253 (mmm) REVERT: B 2242 ASP cc_start: 0.8485 (t70) cc_final: 0.8227 (t0) REVERT: B 2248 GLU cc_start: 0.9488 (pm20) cc_final: 0.9129 (pm20) REVERT: B 2252 ASN cc_start: 0.9596 (m110) cc_final: 0.9375 (m110) REVERT: B 2254 MET cc_start: 0.9051 (ppp) cc_final: 0.8641 (ppp) REVERT: B 2258 LYS cc_start: 0.9494 (mmpt) cc_final: 0.9131 (mmmt) REVERT: B 2281 PHE cc_start: 0.8833 (t80) cc_final: 0.8471 (t80) REVERT: B 2294 PHE cc_start: 0.8944 (m-80) cc_final: 0.8396 (m-80) REVERT: B 2404 MET cc_start: 0.7925 (tpp) cc_final: 0.7159 (tmm) REVERT: B 2522 GLN cc_start: 0.9075 (pm20) cc_final: 0.8731 (pm20) REVERT: B 2524 LYS cc_start: 0.8603 (mmpt) cc_final: 0.8261 (mmtt) REVERT: B 2599 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8402 (tm-30) REVERT: B 2600 LYS cc_start: 0.9105 (mmpt) cc_final: 0.8426 (mmmt) REVERT: B 2630 GLU cc_start: 0.9182 (mp0) cc_final: 0.8832 (pm20) REVERT: B 2665 GLU cc_start: 0.9659 (tp30) cc_final: 0.9319 (tp30) REVERT: B 2666 MET cc_start: 0.9088 (mtp) cc_final: 0.8834 (mtp) REVERT: B 2669 GLU cc_start: 0.9154 (mp0) cc_final: 0.8930 (pm20) REVERT: B 2670 ARG cc_start: 0.9221 (ptt-90) cc_final: 0.8794 (mtm-85) REVERT: D 5 MET cc_start: 0.7431 (pmm) cc_final: 0.7218 (pmm) REVERT: D 61 CYS cc_start: 0.8315 (t) cc_final: 0.8104 (m) REVERT: D 63 MET cc_start: 0.8688 (mmp) cc_final: 0.8477 (tpp) REVERT: D 73 TRP cc_start: 0.8336 (m-10) cc_final: 0.7981 (m-10) REVERT: D 102 GLN cc_start: 0.9086 (tm-30) cc_final: 0.8857 (tm-30) REVERT: D 131 TYR cc_start: 0.7449 (m-80) cc_final: 0.7050 (m-80) REVERT: D 137 ARG cc_start: 0.8868 (ptp-170) cc_final: 0.8609 (ptm160) REVERT: D 156 ASN cc_start: 0.8431 (m-40) cc_final: 0.8146 (m-40) REVERT: D 161 PHE cc_start: 0.7292 (m-80) cc_final: 0.6988 (m-80) REVERT: D 162 TYR cc_start: 0.9051 (m-80) cc_final: 0.8452 (m-80) REVERT: D 242 LEU cc_start: 0.8852 (mt) cc_final: 0.8483 (mt) REVERT: D 247 GLN cc_start: 0.9155 (mm-40) cc_final: 0.8200 (tm-30) REVERT: D 387 TYR cc_start: 0.8634 (m-10) cc_final: 0.8335 (t80) REVERT: D 581 MET cc_start: 0.9398 (tmm) cc_final: 0.9096 (ppp) REVERT: D 2218 PHE cc_start: 0.9094 (m-80) cc_final: 0.8692 (m-10) REVERT: D 2243 PHE cc_start: 0.9295 (t80) cc_final: 0.8778 (t80) REVERT: D 2244 PHE cc_start: 0.9335 (t80) cc_final: 0.9109 (t80) REVERT: D 2252 ASN cc_start: 0.9552 (m110) cc_final: 0.9270 (m110) REVERT: D 2254 MET cc_start: 0.9178 (ppp) cc_final: 0.8742 (ppp) REVERT: D 2258 LYS cc_start: 0.9449 (mmtt) cc_final: 0.9169 (mmmt) REVERT: D 2281 PHE cc_start: 0.8779 (t80) cc_final: 0.8355 (t80) REVERT: D 2294 PHE cc_start: 0.8878 (m-80) cc_final: 0.8420 (m-80) REVERT: D 2599 GLU cc_start: 0.8700 (pp20) cc_final: 0.8410 (tm-30) REVERT: D 2600 LYS cc_start: 0.9331 (mmpt) cc_final: 0.8706 (mmmt) REVERT: D 2630 GLU cc_start: 0.9168 (mp0) cc_final: 0.8799 (pm20) REVERT: D 2638 MET cc_start: 0.9177 (mmt) cc_final: 0.8831 (mmt) REVERT: D 2670 ARG cc_start: 0.9258 (ptt-90) cc_final: 0.8813 (mtm-85) REVERT: D 2681 MET cc_start: 0.8323 (tmm) cc_final: 0.7993 (tmm) REVERT: D 2706 MET cc_start: 0.8763 (ptp) cc_final: 0.8478 (ptp) outliers start: 0 outliers final: 0 residues processed: 1013 average time/residue: 0.5596 time to fit residues: 957.3246 Evaluate side-chains 803 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 803 time to evaluate : 6.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 510 optimal weight: 10.0000 chunk 329 optimal weight: 6.9990 chunk 492 optimal weight: 50.0000 chunk 248 optimal weight: 50.0000 chunk 162 optimal weight: 50.0000 chunk 159 optimal weight: 30.0000 chunk 524 optimal weight: 30.0000 chunk 562 optimal weight: 40.0000 chunk 407 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 648 optimal weight: 8.9990 overall best weight: 10.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 GLN ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 GLN ** A2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2541 HIS ** A2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 ASN ** C2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2375 ASN ** C2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 GLN ** D2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.148 50772 Z= 0.398 Angle : 0.885 13.556 66840 Z= 0.474 Chirality : 0.053 0.340 5064 Planarity : 0.006 0.081 10144 Dihedral : 7.903 105.910 8876 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 34.37 Ramachandran Plot: Outliers : 0.73 % Allowed : 14.43 % Favored : 84.84 % Rotamer: Outliers : 0.03 % Allowed : 2.07 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 3.39 % Twisted General : 0.23 % 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: -1.24 (0.09), residues: 8436 helix: 0.85 (0.08), residues: 4920 sheet: -1.83 (0.31), residues: 324 loop : -3.59 (0.10), residues: 3192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP C2276 HIS 0.026 0.003 HIS A2640 PHE 0.054 0.004 PHE B2575 TYR 0.027 0.003 TYR B2295 ARG 0.016 0.001 ARG D2233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 986 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 985 time to evaluate : 6.798 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9175 (mmp) cc_final: 0.8610 (tpp) REVERT: A 73 TRP cc_start: 0.8984 (m-10) cc_final: 0.8733 (m-10) REVERT: A 102 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8513 (tm-30) REVERT: A 131 TYR cc_start: 0.7296 (m-80) cc_final: 0.7008 (m-80) REVERT: A 162 TYR cc_start: 0.8620 (m-80) cc_final: 0.8179 (m-80) REVERT: A 170 ARG cc_start: 0.8203 (mpt-90) cc_final: 0.7937 (mpp-170) REVERT: A 247 GLN cc_start: 0.9239 (mm-40) cc_final: 0.8237 (tm-30) REVERT: A 430 PHE cc_start: 0.8296 (m-80) cc_final: 0.8076 (m-80) REVERT: A 573 TYR cc_start: 0.8765 (t80) cc_final: 0.8448 (t80) REVERT: A 581 MET cc_start: 0.9509 (tmm) cc_final: 0.9276 (ppp) REVERT: A 2197 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8617 (tp30) REVERT: A 2205 MET cc_start: 0.8000 (mmt) cc_final: 0.7709 (mmt) REVERT: A 2242 ASP cc_start: 0.8686 (t0) cc_final: 0.8437 (t0) REVERT: A 2281 PHE cc_start: 0.8789 (t80) cc_final: 0.8165 (t80) REVERT: A 2541 HIS cc_start: 0.8320 (t70) cc_final: 0.8111 (t-90) REVERT: A 2668 ARG cc_start: 0.9599 (mtt-85) cc_final: 0.9333 (mtp85) REVERT: A 2670 ARG cc_start: 0.9236 (ptt-90) cc_final: 0.8785 (mtm-85) REVERT: C 63 MET cc_start: 0.9005 (mmp) cc_final: 0.8714 (tpp) REVERT: C 131 TYR cc_start: 0.7597 (m-80) cc_final: 0.7170 (m-80) REVERT: C 137 ARG cc_start: 0.8782 (ptp-170) cc_final: 0.7797 (tmt170) REVERT: C 157 GLU cc_start: 0.9379 (mp0) cc_final: 0.9097 (mp0) REVERT: C 162 TYR cc_start: 0.8782 (m-80) cc_final: 0.8389 (m-80) REVERT: C 170 ARG cc_start: 0.8330 (mpt-90) cc_final: 0.7837 (mtm-85) REVERT: C 174 ASP cc_start: 0.9173 (m-30) cc_final: 0.8961 (m-30) REVERT: C 218 TRP cc_start: 0.8516 (m-90) cc_final: 0.7989 (m-90) REVERT: C 247 GLN cc_start: 0.9248 (mm-40) cc_final: 0.8249 (tm-30) REVERT: C 573 TYR cc_start: 0.8793 (t80) cc_final: 0.8286 (t80) REVERT: C 2206 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8707 (tm-30) REVERT: C 2244 PHE cc_start: 0.9365 (t80) cc_final: 0.9039 (t80) REVERT: C 2248 GLU cc_start: 0.9383 (pm20) cc_final: 0.9065 (pm20) REVERT: C 2254 MET cc_start: 0.9101 (ppp) cc_final: 0.8895 (ppp) REVERT: C 2258 LYS cc_start: 0.9570 (mmtt) cc_final: 0.9259 (mmtt) REVERT: C 2281 PHE cc_start: 0.8773 (t80) cc_final: 0.8140 (t80) REVERT: C 2599 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8797 (tm-30) REVERT: C 2624 LYS cc_start: 0.9242 (mmpt) cc_final: 0.8745 (mmmt) REVERT: C 2630 GLU cc_start: 0.9243 (mp0) cc_final: 0.8835 (pm20) REVERT: C 2641 TYR cc_start: 0.9139 (m-80) cc_final: 0.8797 (m-80) REVERT: C 2666 MET cc_start: 0.8874 (ttm) cc_final: 0.8538 (tpt) REVERT: C 2670 ARG cc_start: 0.9196 (ptt-90) cc_final: 0.8866 (mtm-85) REVERT: B 67 SER cc_start: 0.9434 (m) cc_final: 0.9182 (m) REVERT: B 69 GLN cc_start: 0.9209 (pt0) cc_final: 0.8824 (pp30) REVERT: B 125 HIS cc_start: 0.7746 (t-170) cc_final: 0.7498 (t-170) REVERT: B 137 ARG cc_start: 0.9077 (ptp-170) cc_final: 0.8316 (ttt90) REVERT: B 157 GLU cc_start: 0.9257 (mp0) cc_final: 0.8847 (mp0) REVERT: B 247 GLN cc_start: 0.9318 (mm-40) cc_final: 0.8432 (tm-30) REVERT: B 251 LEU cc_start: 0.8180 (tp) cc_final: 0.7883 (tp) REVERT: B 302 LEU cc_start: 0.9388 (tp) cc_final: 0.9117 (tp) REVERT: B 305 PHE cc_start: 0.7715 (m-80) cc_final: 0.7503 (m-80) REVERT: B 505 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8661 (mp0) REVERT: B 573 TYR cc_start: 0.9055 (t80) cc_final: 0.8837 (t80) REVERT: B 2197 GLU cc_start: 0.8893 (tp30) cc_final: 0.8582 (tp30) REVERT: B 2205 MET cc_start: 0.7969 (tpt) cc_final: 0.7446 (mmm) REVERT: B 2206 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8329 (tm-30) REVERT: B 2242 ASP cc_start: 0.8551 (t70) cc_final: 0.8274 (t0) REVERT: B 2248 GLU cc_start: 0.9472 (pm20) cc_final: 0.9121 (pm20) REVERT: B 2254 MET cc_start: 0.9213 (ppp) cc_final: 0.8852 (ppp) REVERT: B 2281 PHE cc_start: 0.8927 (t80) cc_final: 0.8528 (t80) REVERT: B 2394 TYR cc_start: 0.7449 (m-10) cc_final: 0.7141 (m-10) REVERT: B 2522 GLN cc_start: 0.9025 (pm20) cc_final: 0.8653 (pm20) REVERT: B 2524 LYS cc_start: 0.8642 (mmpt) cc_final: 0.8309 (mmtt) REVERT: B 2544 ARG cc_start: 0.8582 (tmt170) cc_final: 0.8377 (ptm160) REVERT: B 2599 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8470 (tm-30) REVERT: B 2600 LYS cc_start: 0.9229 (mmpt) cc_final: 0.8619 (mmmt) REVERT: B 2630 GLU cc_start: 0.9227 (mp0) cc_final: 0.8838 (pm20) REVERT: B 2638 MET cc_start: 0.9271 (mmt) cc_final: 0.9035 (mmp) REVERT: B 2665 GLU cc_start: 0.9608 (tp30) cc_final: 0.9368 (tp30) REVERT: B 2666 MET cc_start: 0.9235 (mtp) cc_final: 0.9004 (mtp) REVERT: B 2697 ASN cc_start: 0.8357 (m-40) cc_final: 0.7895 (p0) REVERT: D 61 CYS cc_start: 0.8448 (t) cc_final: 0.8209 (m) REVERT: D 63 MET cc_start: 0.9203 (mmp) cc_final: 0.8892 (tpp) REVERT: D 73 TRP cc_start: 0.8482 (m-10) cc_final: 0.8024 (m-10) REVERT: D 102 GLN cc_start: 0.9055 (tm-30) cc_final: 0.8701 (tm-30) REVERT: D 131 TYR cc_start: 0.7553 (m-80) cc_final: 0.7165 (m-80) REVERT: D 137 ARG cc_start: 0.9022 (ptp-170) cc_final: 0.8778 (ptm160) REVERT: D 156 ASN cc_start: 0.8583 (m-40) cc_final: 0.8122 (m-40) REVERT: D 161 PHE cc_start: 0.6913 (m-80) cc_final: 0.6546 (m-80) REVERT: D 162 TYR cc_start: 0.9099 (m-80) cc_final: 0.8580 (m-80) REVERT: D 247 GLN cc_start: 0.9192 (mm-40) cc_final: 0.8376 (tm-30) REVERT: D 387 TYR cc_start: 0.8835 (m-10) cc_final: 0.8409 (t80) REVERT: D 581 MET cc_start: 0.9436 (tmm) cc_final: 0.9148 (ppp) REVERT: D 2197 GLU cc_start: 0.8850 (tp30) cc_final: 0.8462 (tp30) REVERT: D 2218 PHE cc_start: 0.9070 (m-80) cc_final: 0.8770 (m-10) REVERT: D 2244 PHE cc_start: 0.9385 (t80) cc_final: 0.9074 (t80) REVERT: D 2254 MET cc_start: 0.9324 (ppp) cc_final: 0.9003 (ppp) REVERT: D 2281 PHE cc_start: 0.8686 (t80) cc_final: 0.8210 (t80) REVERT: D 2294 PHE cc_start: 0.8952 (m-80) cc_final: 0.8498 (m-80) REVERT: D 2524 LYS cc_start: 0.8697 (mptt) cc_final: 0.8417 (mmtt) REVERT: D 2602 LYS cc_start: 0.9268 (mmtt) cc_final: 0.8885 (mmmt) REVERT: D 2630 GLU cc_start: 0.9241 (mp0) cc_final: 0.8848 (pm20) REVERT: D 2670 ARG cc_start: 0.9268 (ptt-90) cc_final: 0.8754 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 986 average time/residue: 0.5728 time to fit residues: 953.9034 Evaluate side-chains 788 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 788 time to evaluate : 6.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 750 optimal weight: 40.0000 chunk 790 optimal weight: 2.9990 chunk 721 optimal weight: 40.0000 chunk 768 optimal weight: 8.9990 chunk 462 optimal weight: 50.0000 chunk 334 optimal weight: 8.9990 chunk 603 optimal weight: 6.9990 chunk 235 optimal weight: 10.0000 chunk 694 optimal weight: 20.0000 chunk 727 optimal weight: 50.0000 chunk 766 optimal weight: 50.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 ASN A 584 GLN ** A2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2375 ASN ** A2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2729 GLN ** A2738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 ASN ** C2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 GLN ** D2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2729 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.6454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 50772 Z= 0.303 Angle : 0.801 11.311 66840 Z= 0.427 Chirality : 0.050 0.325 5064 Planarity : 0.005 0.081 10144 Dihedral : 7.720 105.689 8876 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 28.62 Ramachandran Plot: Outliers : 0.62 % Allowed : 13.48 % Favored : 85.91 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 3.39 % Twisted General : 0.22 % 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: -1.12 (0.10), residues: 8436 helix: 0.98 (0.08), residues: 4884 sheet: -1.65 (0.34), residues: 276 loop : -3.54 (0.10), residues: 3276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP A2276 HIS 0.018 0.003 HIS B2640 PHE 0.046 0.003 PHE A2392 TYR 0.036 0.003 TYR A2413 ARG 0.013 0.001 ARG D2233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 981 time to evaluate : 6.073 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: 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: 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: 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: 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 63 MET cc_start: 0.9164 (mmp) cc_final: 0.8749 (tpp) REVERT: A 66 TYR cc_start: 0.7548 (m-80) cc_final: 0.7209 (m-80) REVERT: A 73 TRP cc_start: 0.8958 (m-10) cc_final: 0.8689 (m-10) REVERT: A 102 GLN cc_start: 0.9057 (tm-30) cc_final: 0.8718 (tm-30) REVERT: A 162 TYR cc_start: 0.8644 (m-80) cc_final: 0.8047 (m-80) REVERT: A 185 ASN cc_start: 0.9548 (t0) cc_final: 0.8985 (t0) REVERT: A 247 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8227 (tm-30) REVERT: A 430 PHE cc_start: 0.8270 (m-80) cc_final: 0.8060 (m-80) REVERT: A 444 ASP cc_start: 0.8659 (m-30) cc_final: 0.8449 (m-30) REVERT: A 573 TYR cc_start: 0.8778 (t80) cc_final: 0.8433 (t80) REVERT: A 581 MET cc_start: 0.9507 (tmm) cc_final: 0.9269 (ppp) REVERT: A 2197 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8553 (tp30) REVERT: A 2242 ASP cc_start: 0.8586 (t0) cc_final: 0.8296 (t0) REVERT: A 2254 MET cc_start: 0.9260 (ppp) cc_final: 0.8869 (ppp) REVERT: A 2273 MET cc_start: 0.7206 (tpp) cc_final: 0.6957 (mmt) REVERT: A 2281 PHE cc_start: 0.8611 (t80) cc_final: 0.7946 (t80) REVERT: A 2609 THR cc_start: 0.8877 (m) cc_final: 0.8395 (m) REVERT: A 2624 LYS cc_start: 0.8893 (mptt) cc_final: 0.8580 (mmtp) REVERT: A 2665 GLU cc_start: 0.9671 (tp30) cc_final: 0.9389 (tp30) REVERT: A 2666 MET cc_start: 0.9159 (ptp) cc_final: 0.8946 (ptm) REVERT: A 2669 GLU cc_start: 0.8994 (mp0) cc_final: 0.8702 (mp0) REVERT: A 2670 ARG cc_start: 0.9191 (ptt-90) cc_final: 0.8682 (mtm-85) REVERT: C 45 ASP cc_start: 0.9411 (m-30) cc_final: 0.9155 (t70) REVERT: C 63 MET cc_start: 0.9021 (mmp) cc_final: 0.8749 (tpp) REVERT: C 66 TYR cc_start: 0.8060 (m-80) cc_final: 0.7742 (m-80) REVERT: C 131 TYR cc_start: 0.7520 (m-80) cc_final: 0.7247 (m-80) REVERT: C 137 ARG cc_start: 0.8811 (ptp-170) cc_final: 0.7745 (tmt170) REVERT: C 162 TYR cc_start: 0.8712 (m-80) cc_final: 0.8168 (m-80) REVERT: C 174 ASP cc_start: 0.9156 (m-30) cc_final: 0.8952 (m-30) REVERT: C 185 ASN cc_start: 0.9528 (t0) cc_final: 0.8955 (t0) REVERT: C 218 TRP cc_start: 0.8493 (m-90) cc_final: 0.7975 (m-90) REVERT: C 247 GLN cc_start: 0.9242 (mm-40) cc_final: 0.8210 (tm-30) REVERT: C 573 TYR cc_start: 0.8751 (t80) cc_final: 0.8306 (t80) REVERT: C 2205 MET cc_start: 0.7639 (tpt) cc_final: 0.7396 (tpp) REVERT: C 2206 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8701 (tm-30) REVERT: C 2244 PHE cc_start: 0.9345 (t80) cc_final: 0.8976 (t80) REVERT: C 2248 GLU cc_start: 0.9228 (pm20) cc_final: 0.8953 (pm20) REVERT: C 2254 MET cc_start: 0.9002 (ppp) cc_final: 0.8738 (ppp) REVERT: C 2258 LYS cc_start: 0.9587 (mmtt) cc_final: 0.9226 (mmmt) REVERT: C 2281 PHE cc_start: 0.8662 (t80) cc_final: 0.8146 (t80) REVERT: C 2599 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8759 (tm-30) REVERT: C 2624 LYS cc_start: 0.9224 (mmpt) cc_final: 0.8746 (mmmt) REVERT: C 2630 GLU cc_start: 0.9310 (mp0) cc_final: 0.8909 (pm20) REVERT: C 2641 TYR cc_start: 0.9138 (m-80) cc_final: 0.8891 (m-80) REVERT: C 2666 MET cc_start: 0.8825 (ttm) cc_final: 0.8608 (tpt) REVERT: C 2670 ARG cc_start: 0.9162 (ptt-90) cc_final: 0.8882 (mtm-85) REVERT: C 2678 MET cc_start: 0.7325 (ppp) cc_final: 0.7103 (ppp) REVERT: B 67 SER cc_start: 0.9381 (m) cc_final: 0.9028 (p) REVERT: B 69 GLN cc_start: 0.9169 (pt0) cc_final: 0.8848 (pp30) REVERT: B 125 HIS cc_start: 0.8057 (t-170) cc_final: 0.7706 (t-170) REVERT: B 137 ARG cc_start: 0.9089 (ptp-170) cc_final: 0.8665 (ptm160) REVERT: B 162 TYR cc_start: 0.9128 (m-10) cc_final: 0.8625 (m-80) REVERT: B 247 GLN cc_start: 0.9267 (mm-40) cc_final: 0.8290 (tm-30) REVERT: B 251 LEU cc_start: 0.8289 (tp) cc_final: 0.8048 (tp) REVERT: B 302 LEU cc_start: 0.9425 (tp) cc_final: 0.9154 (tp) REVERT: B 305 PHE cc_start: 0.7631 (m-80) cc_final: 0.7419 (m-80) REVERT: B 573 TYR cc_start: 0.9102 (t80) cc_final: 0.8868 (t80) REVERT: B 2197 GLU cc_start: 0.8876 (tp30) cc_final: 0.8619 (tp30) REVERT: B 2205 MET cc_start: 0.7957 (tpt) cc_final: 0.7344 (mmm) REVERT: B 2206 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8400 (tm-30) REVERT: B 2248 GLU cc_start: 0.9424 (pm20) cc_final: 0.9185 (pm20) REVERT: B 2254 MET cc_start: 0.9200 (ppp) cc_final: 0.8812 (ppp) REVERT: B 2258 LYS cc_start: 0.9490 (mmpt) cc_final: 0.9227 (mmmt) REVERT: B 2522 GLN cc_start: 0.8995 (pm20) cc_final: 0.8655 (pm20) REVERT: B 2524 LYS cc_start: 0.8549 (mmpt) cc_final: 0.8188 (mmtt) REVERT: B 2589 ILE cc_start: 0.8933 (mm) cc_final: 0.8506 (mt) REVERT: B 2599 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8285 (tm-30) REVERT: B 2600 LYS cc_start: 0.9231 (mmpt) cc_final: 0.8562 (mmmt) REVERT: B 2624 LYS cc_start: 0.9603 (ttpp) cc_final: 0.9291 (mmtp) REVERT: B 2630 GLU cc_start: 0.9243 (mp0) cc_final: 0.8848 (pm20) REVERT: D 63 MET cc_start: 0.9184 (mmp) cc_final: 0.8854 (tpp) REVERT: D 66 TYR cc_start: 0.8228 (m-80) cc_final: 0.7959 (m-10) REVERT: D 69 GLN cc_start: 0.8032 (tm-30) cc_final: 0.6876 (tm-30) REVERT: D 102 GLN cc_start: 0.9180 (tm-30) cc_final: 0.8836 (tm-30) REVERT: D 131 TYR cc_start: 0.7679 (m-80) cc_final: 0.7309 (m-80) REVERT: D 137 ARG cc_start: 0.8969 (ptp-170) cc_final: 0.8759 (ptm160) REVERT: D 157 GLU cc_start: 0.9153 (mp0) cc_final: 0.8873 (mp0) REVERT: D 161 PHE cc_start: 0.7019 (m-80) cc_final: 0.6640 (m-80) REVERT: D 162 TYR cc_start: 0.8995 (m-80) cc_final: 0.8433 (m-80) REVERT: D 247 GLN cc_start: 0.9145 (mm-40) cc_final: 0.8284 (tm-30) REVERT: D 581 MET cc_start: 0.9440 (tmm) cc_final: 0.9129 (ppp) REVERT: D 2218 PHE cc_start: 0.9027 (m-80) cc_final: 0.8680 (m-10) REVERT: D 2254 MET cc_start: 0.9242 (ppp) cc_final: 0.8775 (ppp) REVERT: D 2258 LYS cc_start: 0.9523 (mmtt) cc_final: 0.9277 (mmmt) REVERT: D 2273 MET cc_start: 0.5553 (mmm) cc_final: 0.4565 (mmm) REVERT: D 2294 PHE cc_start: 0.8963 (m-80) cc_final: 0.8542 (m-80) REVERT: D 2404 MET cc_start: 0.8223 (tpp) cc_final: 0.7809 (tmm) REVERT: D 2524 LYS cc_start: 0.8677 (mptt) cc_final: 0.8398 (mmtt) REVERT: D 2602 LYS cc_start: 0.9257 (mmtt) cc_final: 0.8932 (mmmt) REVERT: D 2605 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8662 (tm-30) REVERT: D 2624 LYS cc_start: 0.9582 (ttpp) cc_final: 0.9152 (mmtm) REVERT: D 2630 GLU cc_start: 0.9272 (mp0) cc_final: 0.8906 (pm20) REVERT: D 2638 MET cc_start: 0.9145 (mmt) cc_final: 0.8856 (mmt) REVERT: D 2670 ARG cc_start: 0.9198 (ptt-90) cc_final: 0.8567 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 981 average time/residue: 0.6050 time to fit residues: 1011.1821 Evaluate side-chains 778 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 778 time to evaluate : 6.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 504 optimal weight: 10.0000 chunk 812 optimal weight: 8.9990 chunk 496 optimal weight: 7.9990 chunk 385 optimal weight: 0.0980 chunk 565 optimal weight: 0.9990 chunk 852 optimal weight: 10.0000 chunk 784 optimal weight: 20.0000 chunk 679 optimal weight: 6.9990 chunk 70 optimal weight: 0.2980 chunk 524 optimal weight: 20.0000 chunk 416 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 ASN ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 GLN ** A2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 ASN ** C2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 GLN ** D2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.6708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 50772 Z= 0.198 Angle : 0.744 11.515 66840 Z= 0.387 Chirality : 0.048 0.272 5064 Planarity : 0.005 0.082 10144 Dihedral : 7.341 103.184 8876 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.55 % Allowed : 12.02 % Favored : 87.43 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 3.39 % Twisted General : 0.14 % 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: -0.83 (0.10), residues: 8436 helix: 1.24 (0.08), residues: 4888 sheet: -1.82 (0.33), residues: 312 loop : -3.45 (0.10), residues: 3236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP D 73 HIS 0.010 0.002 HIS D2192 PHE 0.049 0.002 PHE D2392 TYR 0.030 0.002 TYR A 567 ARG 0.011 0.001 ARG C2677 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16872 Ramachandran restraints generated. 8436 Oldfield, 0 Emsley, 8436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1010 time to evaluate : 7.120 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9061 (mmp) cc_final: 0.8673 (tpp) REVERT: A 66 TYR cc_start: 0.7056 (m-80) cc_final: 0.6765 (m-80) REVERT: A 73 TRP cc_start: 0.8827 (m-10) cc_final: 0.8597 (m-10) REVERT: A 102 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8661 (tm-30) REVERT: A 131 TYR cc_start: 0.7342 (m-80) cc_final: 0.7041 (m-80) REVERT: A 156 ASN cc_start: 0.9070 (m-40) cc_final: 0.8586 (m-40) REVERT: A 162 TYR cc_start: 0.8617 (m-80) cc_final: 0.7871 (m-80) REVERT: A 185 ASN cc_start: 0.9561 (t0) cc_final: 0.8976 (t0) REVERT: A 224 MET cc_start: 0.8013 (mpp) cc_final: 0.7694 (mmt) REVERT: A 247 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8050 (tm-30) REVERT: A 251 LEU cc_start: 0.7997 (tp) cc_final: 0.7661 (tp) REVERT: A 302 LEU cc_start: 0.9455 (tp) cc_final: 0.9224 (tp) REVERT: A 444 ASP cc_start: 0.8558 (m-30) cc_final: 0.8349 (m-30) REVERT: A 505 GLU cc_start: 0.9269 (pt0) cc_final: 0.8902 (pm20) REVERT: A 573 TYR cc_start: 0.8861 (t80) cc_final: 0.8632 (t80) REVERT: A 581 MET cc_start: 0.9487 (tmm) cc_final: 0.9230 (ppp) REVERT: A 2195 GLN cc_start: 0.8422 (mp10) cc_final: 0.8090 (mp10) REVERT: A 2197 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8404 (tp30) REVERT: A 2205 MET cc_start: 0.8075 (mmt) cc_final: 0.7672 (mmt) REVERT: A 2242 ASP cc_start: 0.8350 (t0) cc_final: 0.8135 (t0) REVERT: A 2254 MET cc_start: 0.9123 (ppp) cc_final: 0.8606 (ppp) REVERT: A 2258 LYS cc_start: 0.9400 (mmpt) cc_final: 0.9122 (mmmt) REVERT: A 2281 PHE cc_start: 0.8545 (t80) cc_final: 0.7995 (t80) REVERT: A 2418 PHE cc_start: 0.7131 (t80) cc_final: 0.6865 (t80) REVERT: A 2624 LYS cc_start: 0.8944 (mmtm) cc_final: 0.8698 (mmmt) REVERT: A 2669 GLU cc_start: 0.9124 (mp0) cc_final: 0.8883 (mp0) REVERT: A 2670 ARG cc_start: 0.9097 (ptt-90) cc_final: 0.8595 (mtm-85) REVERT: C 63 MET cc_start: 0.8974 (mmp) cc_final: 0.8661 (tpp) REVERT: C 131 TYR cc_start: 0.7375 (m-80) cc_final: 0.7019 (m-80) REVERT: C 137 ARG cc_start: 0.8762 (ptp-170) cc_final: 0.7679 (tmt170) REVERT: C 157 GLU cc_start: 0.9291 (mp0) cc_final: 0.8625 (mp0) REVERT: C 162 TYR cc_start: 0.8620 (m-80) cc_final: 0.7890 (m-80) REVERT: C 174 ASP cc_start: 0.9079 (m-30) cc_final: 0.8879 (m-30) REVERT: C 185 ASN cc_start: 0.9494 (t0) cc_final: 0.8783 (t0) REVERT: C 218 TRP cc_start: 0.8417 (m-90) cc_final: 0.7871 (m-90) REVERT: C 224 MET cc_start: 0.8132 (mpp) cc_final: 0.7864 (mpp) REVERT: C 242 LEU cc_start: 0.8828 (mt) cc_final: 0.8623 (mt) REVERT: C 247 GLN cc_start: 0.9195 (mm-40) cc_final: 0.8165 (tm-30) REVERT: C 251 LEU cc_start: 0.7921 (tp) cc_final: 0.7491 (tp) REVERT: C 440 VAL cc_start: 0.9658 (t) cc_final: 0.9247 (t) REVERT: C 573 TYR cc_start: 0.8853 (t80) cc_final: 0.8487 (t80) REVERT: C 2205 MET cc_start: 0.7569 (tpt) cc_final: 0.7142 (tpp) REVERT: C 2244 PHE cc_start: 0.9294 (t80) cc_final: 0.9091 (t80) REVERT: C 2258 LYS cc_start: 0.9578 (mmtt) cc_final: 0.9188 (mmtt) REVERT: C 2281 PHE cc_start: 0.8417 (t80) cc_final: 0.8079 (t80) REVERT: C 2589 ILE cc_start: 0.8960 (mm) cc_final: 0.8624 (mt) REVERT: C 2599 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8171 (tm-30) REVERT: C 2600 LYS cc_start: 0.9025 (mmmt) cc_final: 0.8390 (mmmt) REVERT: C 2624 LYS cc_start: 0.9264 (mmpt) cc_final: 0.8961 (mmmt) REVERT: C 2630 GLU cc_start: 0.9296 (mp0) cc_final: 0.8863 (pm20) REVERT: C 2641 TYR cc_start: 0.9036 (m-80) cc_final: 0.8771 (m-80) REVERT: C 2666 MET cc_start: 0.8766 (ttm) cc_final: 0.8564 (ttp) REVERT: C 2670 ARG cc_start: 0.9094 (ptt-90) cc_final: 0.8683 (mtm-85) REVERT: C 2678 MET cc_start: 0.7316 (ppp) cc_final: 0.6991 (ppp) REVERT: C 2679 ARG cc_start: 0.7807 (ttp80) cc_final: 0.7528 (tmm160) REVERT: B 63 MET cc_start: 0.8896 (mmp) cc_final: 0.8670 (tpp) REVERT: B 67 SER cc_start: 0.9331 (m) cc_final: 0.8965 (p) REVERT: B 69 GLN cc_start: 0.9184 (pt0) cc_final: 0.8827 (pp30) REVERT: B 125 HIS cc_start: 0.8000 (t-170) cc_final: 0.7604 (t-170) REVERT: B 137 ARG cc_start: 0.9070 (ptp-170) cc_final: 0.8673 (ptm160) REVERT: B 162 TYR cc_start: 0.9130 (m-10) cc_final: 0.8870 (m-80) REVERT: B 247 GLN cc_start: 0.9213 (mm-40) cc_final: 0.8228 (tm-30) REVERT: B 302 LEU cc_start: 0.9403 (tp) cc_final: 0.9144 (tp) REVERT: B 573 TYR cc_start: 0.9024 (t80) cc_final: 0.8756 (t80) REVERT: B 2197 GLU cc_start: 0.8721 (tp30) cc_final: 0.8330 (tp30) REVERT: B 2205 MET cc_start: 0.7842 (tpt) cc_final: 0.7076 (mmm) REVERT: B 2254 MET cc_start: 0.9085 (ppp) cc_final: 0.8745 (ppp) REVERT: B 2258 LYS cc_start: 0.9414 (mmpt) cc_final: 0.9195 (mmmt) REVERT: B 2273 MET cc_start: 0.5394 (mtt) cc_final: 0.5084 (mtt) REVERT: B 2599 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8375 (tm-30) REVERT: B 2600 LYS cc_start: 0.9143 (mmpt) cc_final: 0.8610 (mmmt) REVERT: B 2630 GLU cc_start: 0.9271 (mp0) cc_final: 0.8899 (pm20) REVERT: B 2665 GLU cc_start: 0.9555 (tp30) cc_final: 0.9281 (tp30) REVERT: D 63 MET cc_start: 0.9089 (mmp) cc_final: 0.8859 (tpp) REVERT: D 102 GLN cc_start: 0.9127 (tm-30) cc_final: 0.8769 (tm-30) REVERT: D 137 ARG cc_start: 0.8966 (ptp-170) cc_final: 0.8625 (ptm160) REVERT: D 156 ASN cc_start: 0.8377 (m-40) cc_final: 0.8003 (m-40) REVERT: D 161 PHE cc_start: 0.6843 (m-80) cc_final: 0.6478 (m-80) REVERT: D 162 TYR cc_start: 0.8895 (m-80) cc_final: 0.8211 (m-80) REVERT: D 185 ASN cc_start: 0.9445 (t0) cc_final: 0.8903 (t0) REVERT: D 224 MET cc_start: 0.8094 (mpp) cc_final: 0.7774 (mpp) REVERT: D 247 GLN cc_start: 0.9123 (mm-40) cc_final: 0.8154 (tm-30) REVERT: D 430 PHE cc_start: 0.7973 (m-80) cc_final: 0.7740 (m-80) REVERT: D 581 MET cc_start: 0.9419 (tmm) cc_final: 0.9097 (ppp) REVERT: D 2205 MET cc_start: 0.7355 (tpt) cc_final: 0.6780 (mmm) REVERT: D 2206 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8182 (tm-30) REVERT: D 2218 PHE cc_start: 0.8979 (m-80) cc_final: 0.8631 (m-10) REVERT: D 2254 MET cc_start: 0.9165 (ppp) cc_final: 0.8812 (ppp) REVERT: D 2258 LYS cc_start: 0.9469 (mmtt) cc_final: 0.9223 (mmmt) REVERT: D 2281 PHE cc_start: 0.8426 (t80) cc_final: 0.8169 (t80) REVERT: D 2294 PHE cc_start: 0.8908 (m-80) cc_final: 0.8480 (m-80) REVERT: D 2404 MET cc_start: 0.8198 (tpp) cc_final: 0.7954 (tmm) REVERT: D 2524 LYS cc_start: 0.8601 (mptt) cc_final: 0.8341 (mmtt) REVERT: D 2541 HIS cc_start: 0.7739 (t-90) cc_final: 0.7527 (t-90) REVERT: D 2589 ILE cc_start: 0.8936 (mm) cc_final: 0.8544 (mt) REVERT: D 2602 LYS cc_start: 0.9156 (mmtt) cc_final: 0.8770 (mmtt) REVERT: D 2624 LYS cc_start: 0.9532 (ttpp) cc_final: 0.9234 (tppt) REVERT: D 2630 GLU cc_start: 0.9229 (mp0) cc_final: 0.8854 (pm20) REVERT: D 2670 ARG cc_start: 0.9099 (ptt-90) cc_final: 0.8435 (mtm-85) REVERT: D 2678 MET cc_start: 0.8029 (pmm) cc_final: 0.7817 (pmm) outliers start: 0 outliers final: 0 residues processed: 1010 average time/residue: 0.5551 time to fit residues: 948.6340 Evaluate side-chains 810 residues out of total 7788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 810 time to evaluate : 6.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 856 random chunks: chunk 539 optimal weight: 0.0770 chunk 723 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 chunk 626 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 680 optimal weight: 40.0000 chunk 284 optimal weight: 0.4980 chunk 698 optimal weight: 40.0000 chunk 86 optimal weight: 30.0000 chunk 125 optimal weight: 0.6980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 ASN A 584 GLN ** A2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 ASN C 107 ASN C 122 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN C2361 ASN ** C2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2207 GLN ** B2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 HIS ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 GLN ** D2255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.150527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.113835 restraints weight = 171736.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.113963 restraints weight = 141769.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.114140 restraints weight = 119685.545| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3962 r_free = 0.3962 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 88 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3962 r_free = 0.3962 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 94 | |-----------------------------------------------------------------------------| r_final: 0.3962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.7000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 50772 Z= 0.182 Angle : 0.730 10.560 66840 Z= 0.377 Chirality : 0.047 0.244 5064 Planarity : 0.005 0.082 10144 Dihedral : 7.045 102.201 8876 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.52 % Allowed : 11.25 % Favored : 88.23 % Rotamer: Outliers : 0.03 % Allowed : 0.73 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 3.39 % Twisted General : 0.10 % 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: -0.70 (0.10), residues: 8436 helix: 1.30 (0.08), residues: 4956 sheet: -1.66 (0.33), residues: 312 loop : -3.42 (0.10), residues: 3168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D2674 HIS 0.011 0.001 HIS B2192 PHE 0.047 0.002 PHE D2392 TYR 0.029 0.002 TYR A 567 ARG 0.013 0.001 ARG A2668 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15757.76 seconds wall clock time: 280 minutes 45.73 seconds (16845.73 seconds total)