Starting phenix.real_space_refine on Tue Mar 19 11:41:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgm_23829/03_2024/7mgm_23829_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgm_23829/03_2024/7mgm_23829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgm_23829/03_2024/7mgm_23829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgm_23829/03_2024/7mgm_23829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgm_23829/03_2024/7mgm_23829_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mgm_23829/03_2024/7mgm_23829_updated.pdb" } resolution = 3.1 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 2 5.21 5 S 116 5.16 5 C 15418 2.51 5 N 4045 2.21 5 O 4487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1577": "OD1" <-> "OD2" Residue "A ASP 1632": "OD1" <-> "OD2" Residue "A PHE 1669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2014": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2023": "OD1" <-> "OD2" Residue "A PHE 2047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2810": "OE1" <-> "OE2" Residue "A PHE 2844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2874": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2889": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2893": "OD1" <-> "OD2" Residue "A PHE 2954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3510": "NH1" <-> "NH2" Residue "A PHE 3518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3537": "OE1" <-> "OE2" Residue "A PHE 3607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3955": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3961": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4019": "OD1" <-> "OD2" Residue "C PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 363": "OD1" <-> "OD2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 363": "OD1" <-> "OD2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24079 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 18363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2274, 18363 Classifications: {'peptide': 2274} Link IDs: {'PTRANS': 63, 'TRANS': 2210} Chain breaks: 11 Chain: "C" Number of atoms: 2821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2821 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain breaks: 3 Chain: "B" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2773 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain breaks: 4 Chain: "A" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 122 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 12.73, per 1000 atoms: 0.53 Number of scatterers: 24079 At special positions: 0 Unit cell: (100.87, 141.48, 192.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 11 15.00 Mg 2 11.99 O 4487 8.00 N 4045 7.00 C 15418 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.88 Conformation dependent library (CDL) restraints added in 4.3 seconds 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5642 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 103 helices and 29 sheets defined 45.0% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.49 Creating SS restraints... Processing helix chain 'A' and resid 1511 through 1531 removed outlier: 3.642A pdb=" N ILE A1519 " --> pdb=" O SER A1515 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER A1522 " --> pdb=" O MET A1518 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER A1524 " --> pdb=" O LYS A1520 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR A1525 " --> pdb=" O SER A1521 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE A1526 " --> pdb=" O SER A1522 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A1529 " --> pdb=" O THR A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1539 Processing helix chain 'A' and resid 1542 through 1550 removed outlier: 3.692A pdb=" N LYS A1547 " --> pdb=" O ASP A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1558 through 1560 No H-bonds generated for 'chain 'A' and resid 1558 through 1560' Processing helix chain 'A' and resid 1562 through 1565 No H-bonds generated for 'chain 'A' and resid 1562 through 1565' Processing helix chain 'A' and resid 1604 through 1632 removed outlier: 3.701A pdb=" N ILE A1610 " --> pdb=" O GLU A1606 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A1613 " --> pdb=" O ASN A1609 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A1616 " --> pdb=" O ASP A1612 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP A1632 " --> pdb=" O GLY A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1636 through 1641 removed outlier: 3.755A pdb=" N VAL A1640 " --> pdb=" O ILE A1636 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SER A1641 " --> pdb=" O GLU A1637 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1636 through 1641' Processing helix chain 'A' and resid 1645 through 1665 Processing helix chain 'A' and resid 1670 through 1688 removed outlier: 4.172A pdb=" N ASN A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1692 through 1716 removed outlier: 3.793A pdb=" N VAL A1703 " --> pdb=" O GLU A1699 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU A1704 " --> pdb=" O ALA A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1721 through 1730 removed outlier: 3.627A pdb=" N LYS A1730 " --> pdb=" O LEU A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1743 through 1745 No H-bonds generated for 'chain 'A' and resid 1743 through 1745' Processing helix chain 'A' and resid 1773 through 1788 removed outlier: 4.150A pdb=" N GLN A1788 " --> pdb=" O ASP A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1813 Processing helix chain 'A' and resid 1828 through 1841 Processing helix chain 'A' and resid 1850 through 1852 No H-bonds generated for 'chain 'A' and resid 1850 through 1852' Processing helix chain 'A' and resid 1855 through 1874 removed outlier: 3.786A pdb=" N SER A1862 " --> pdb=" O LEU A1858 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ALA A1863 " --> pdb=" O SER A1859 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASN A1864 " --> pdb=" O ALA A1860 " (cutoff:3.500A) Processing helix chain 'A' and resid 1910 through 1915 removed outlier: 4.454A pdb=" N SER A1915 " --> pdb=" O ASN A1911 " (cutoff:3.500A) Processing helix chain 'A' and resid 1926 through 1937 Processing helix chain 'A' and resid 1942 through 1959 Processing helix chain 'A' and resid 1970 through 1987 removed outlier: 3.831A pdb=" N SER A1981 " --> pdb=" O LEU A1977 " (cutoff:3.500A) Proline residue: A1982 - end of helix removed outlier: 5.290A pdb=" N SER A1985 " --> pdb=" O SER A1981 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLU A1986 " --> pdb=" O PRO A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1991 through 2001 Processing helix chain 'A' and resid 2003 through 2005 No H-bonds generated for 'chain 'A' and resid 2003 through 2005' Processing helix chain 'A' and resid 2009 through 2021 Processing helix chain 'A' and resid 2032 through 2045 removed outlier: 3.728A pdb=" N CYS A2037 " --> pdb=" O ALA A2033 " (cutoff:3.500A) Processing helix chain 'A' and resid 2051 through 2063 Processing helix chain 'A' and resid 2080 through 2095 Processing helix chain 'A' and resid 2106 through 2108 No H-bonds generated for 'chain 'A' and resid 2106 through 2108' Processing helix chain 'A' and resid 2111 through 2114 No H-bonds generated for 'chain 'A' and resid 2111 through 2114' Processing helix chain 'A' and resid 2129 through 2139 Processing helix chain 'A' and resid 2144 through 2147 removed outlier: 4.072A pdb=" N ASN A2147 " --> pdb=" O THR A2144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2144 through 2147' Processing helix chain 'A' and resid 2160 through 2170 removed outlier: 4.445A pdb=" N ALA A2165 " --> pdb=" O GLU A2161 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N MET A2166 " --> pdb=" O TYR A2162 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN A2167 " --> pdb=" O VAL A2163 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER A2168 " --> pdb=" O GLU A2164 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL A2169 " --> pdb=" O ALA A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2204 through 2207 No H-bonds generated for 'chain 'A' and resid 2204 through 2207' Processing helix chain 'A' and resid 2222 through 2236 removed outlier: 3.738A pdb=" N GLU A2235 " --> pdb=" O ASN A2231 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A2236 " --> pdb=" O LYS A2232 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2256 removed outlier: 3.547A pdb=" N ASP A2251 " --> pdb=" O ASP A2247 " (cutoff:3.500A) Processing helix chain 'A' and resid 2259 through 2271 removed outlier: 4.397A pdb=" N ASN A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A2265 " --> pdb=" O SER A2261 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN A2270 " --> pdb=" O PHE A2266 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP A2271 " --> pdb=" O THR A2267 " (cutoff:3.500A) Processing helix chain 'A' and resid 2280 through 2282 No H-bonds generated for 'chain 'A' and resid 2280 through 2282' Processing helix chain 'A' and resid 2284 through 2302 removed outlier: 3.744A pdb=" N TYR A2298 " --> pdb=" O LEU A2294 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG A2299 " --> pdb=" O ILE A2295 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLN A2300 " --> pdb=" O SER A2296 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TRP A2301 " --> pdb=" O SER A2297 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE A2302 " --> pdb=" O TYR A2298 " (cutoff:3.500A) Processing helix chain 'A' and resid 2307 through 2326 Processing helix chain 'A' and resid 2332 through 2345 removed outlier: 3.655A pdb=" N GLN A2340 " --> pdb=" O ARG A2336 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A2341 " --> pdb=" O ALA A2337 " (cutoff:3.500A) Processing helix chain 'A' and resid 2371 through 2374 Processing helix chain 'A' and resid 2382 through 2386 removed outlier: 3.773A pdb=" N VAL A2385 " --> pdb=" O ALA A2382 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET A2386 " --> pdb=" O HIS A2383 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2382 through 2386' Processing helix chain 'A' and resid 2395 through 2410 Processing helix chain 'A' and resid 2424 through 2433 Processing helix chain 'A' and resid 2451 through 2457 Processing helix chain 'A' and resid 2501 through 2512 Processing helix chain 'A' and resid 2548 through 2553 removed outlier: 4.942A pdb=" N HIS A2553 " --> pdb=" O ARG A2549 " (cutoff:3.500A) Processing helix chain 'A' and resid 2564 through 2581 removed outlier: 3.991A pdb=" N ILE A2573 " --> pdb=" O GLN A2569 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR A2574 " --> pdb=" O ILE A2570 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU A2581 " --> pdb=" O ALA A2577 " (cutoff:3.500A) Processing helix chain 'A' and resid 2583 through 2606 removed outlier: 5.362A pdb=" N SER A2587 " --> pdb=" O GLU A2584 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A2589 " --> pdb=" O ARG A2586 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLU A2590 " --> pdb=" O SER A2587 " (cutoff:3.500A) Proline residue: A2591 - end of helix removed outlier: 3.534A pdb=" N ARG A2606 " --> pdb=" O CYS A2603 " (cutoff:3.500A) Processing helix chain 'A' and resid 2619 through 2634 Processing helix chain 'A' and resid 2641 through 2659 removed outlier: 4.438A pdb=" N ASP A2658 " --> pdb=" O ARG A2654 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ARG A2659 " --> pdb=" O ILE A2655 " (cutoff:3.500A) Processing helix chain 'A' and resid 2663 through 2680 Processing helix chain 'A' and resid 2709 through 2726 Processing helix chain 'A' and resid 2736 through 2749 Processing helix chain 'A' and resid 2766 through 2776 Processing helix chain 'A' and resid 2792 through 2808 Processing helix chain 'A' and resid 2819 through 2821 No H-bonds generated for 'chain 'A' and resid 2819 through 2821' Processing helix chain 'A' and resid 2825 through 2836 Processing helix chain 'A' and resid 2848 through 2862 Processing helix chain 'A' and resid 2870 through 2883 Processing helix chain 'A' and resid 2897 through 2904 removed outlier: 3.713A pdb=" N ALA A2901 " --> pdb=" O ASN A2897 " (cutoff:3.500A) Processing helix chain 'A' and resid 2906 through 2911 removed outlier: 3.847A pdb=" N ARG A2911 " --> pdb=" O ALA A2907 " (cutoff:3.500A) Processing helix chain 'A' and resid 2922 through 2934 Processing helix chain 'A' and resid 2961 through 2979 Processing helix chain 'A' and resid 2990 through 3033 removed outlier: 3.925A pdb=" N ALA A3005 " --> pdb=" O LYS A3001 " (cutoff:3.500A) Processing helix chain 'A' and resid 3290 through 3336 removed outlier: 4.702A pdb=" N PHE A3301 " --> pdb=" O LYS A3297 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLU A3302 " --> pdb=" O SER A3298 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N SER A3314 " --> pdb=" O THR A3310 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS A3315 " --> pdb=" O LYS A3311 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE A3321 " --> pdb=" O SER A3317 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLY A3322 " --> pdb=" O GLN A3318 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLY A3335 " --> pdb=" O GLU A3331 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N HIS A3336 " --> pdb=" O THR A3332 " (cutoff:3.500A) Processing helix chain 'A' and resid 3339 through 3355 Processing helix chain 'A' and resid 3366 through 3370 Processing helix chain 'A' and resid 3373 through 3382 Processing helix chain 'A' and resid 3388 through 3399 Processing helix chain 'A' and resid 3413 through 3425 removed outlier: 6.643A pdb=" N ASN A3424 " --> pdb=" O ASN A3420 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LYS A3425 " --> pdb=" O TYR A3421 " (cutoff:3.500A) Processing helix chain 'A' and resid 3436 through 3446 Processing helix chain 'A' and resid 3455 through 3457 No H-bonds generated for 'chain 'A' and resid 3455 through 3457' Processing helix chain 'A' and resid 3460 through 3467 removed outlier: 5.151A pdb=" N ARG A3464 " --> pdb=" O ILE A3461 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A3467 " --> pdb=" O ARG A3464 " (cutoff:3.500A) Processing helix chain 'A' and resid 3507 through 3510 No H-bonds generated for 'chain 'A' and resid 3507 through 3510' Processing helix chain 'A' and resid 3522 through 3537 Processing helix chain 'A' and resid 3539 through 3571 removed outlier: 3.616A pdb=" N LEU A3567 " --> pdb=" O GLU A3563 " (cutoff:3.500A) Processing helix chain 'A' and resid 3583 through 3606 removed outlier: 4.062A pdb=" N ASN A3588 " --> pdb=" O MET A3584 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A3605 " --> pdb=" O LEU A3601 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU A3606 " --> pdb=" O SER A3602 " (cutoff:3.500A) Processing helix chain 'A' and resid 3608 through 3638 removed outlier: 5.713A pdb=" N ILE A3620 " --> pdb=" O GLU A3616 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE A3621 " --> pdb=" O GLU A3617 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY A3622 " --> pdb=" O TYR A3618 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A3638 " --> pdb=" O LYS A3634 " (cutoff:3.500A) Processing helix chain 'A' and resid 3640 through 3642 No H-bonds generated for 'chain 'A' and resid 3640 through 3642' Processing helix chain 'A' and resid 3646 through 3658 removed outlier: 3.826A pdb=" N VAL A3656 " --> pdb=" O CYS A3652 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE A3658 " --> pdb=" O LYS A3654 " (cutoff:3.500A) Processing helix chain 'A' and resid 3670 through 3686 Processing helix chain 'A' and resid 3692 through 3710 removed outlier: 4.076A pdb=" N ASP A3709 " --> pdb=" O LEU A3705 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3727 Processing helix chain 'A' and resid 3742 through 3752 removed outlier: 4.080A pdb=" N TYR A3746 " --> pdb=" O ASP A3742 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A3747 " --> pdb=" O ASP A3743 " (cutoff:3.500A) Processing helix chain 'A' and resid 3756 through 3767 removed outlier: 4.224A pdb=" N PHE A3763 " --> pdb=" O ALA A3759 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS A3764 " --> pdb=" O LEU A3760 " (cutoff:3.500A) Processing helix chain 'A' and resid 3774 through 3779 Processing helix chain 'A' and resid 3797 through 3806 Processing helix chain 'A' and resid 3819 through 3835 removed outlier: 3.894A pdb=" N ILE A3834 " --> pdb=" O SER A3830 " (cutoff:3.500A) Processing helix chain 'A' and resid 3844 through 3846 No H-bonds generated for 'chain 'A' and resid 3844 through 3846' Processing helix chain 'A' and resid 3848 through 3860 removed outlier: 3.615A pdb=" N LEU A3855 " --> pdb=" O VAL A3851 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N HIS A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) Processing helix chain 'A' and resid 3886 through 3891 removed outlier: 3.567A pdb=" N ARG A3891 " --> pdb=" O PRO A3887 " (cutoff:3.500A) Processing helix chain 'A' and resid 3904 through 3913 removed outlier: 3.676A pdb=" N SER A3913 " --> pdb=" O ASP A3909 " (cutoff:3.500A) Processing helix chain 'A' and resid 3923 through 3944 removed outlier: 4.057A pdb=" N ARG A3944 " --> pdb=" O THR A3940 " (cutoff:3.500A) Processing helix chain 'A' and resid 3958 through 3974 Processing helix chain 'A' and resid 3982 through 3991 Processing helix chain 'A' and resid 4001 through 4014 Processing helix chain 'A' and resid 4038 through 4051 Processing helix chain 'A' and resid 4058 through 4061 No H-bonds generated for 'chain 'A' and resid 4058 through 4061' Processing helix chain 'A' and resid 4067 through 4090 removed outlier: 3.620A pdb=" N ASP A4072 " --> pdb=" O GLU A4068 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR A4073 " --> pdb=" O SER A4069 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A4081 " --> pdb=" O GLN A4077 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 368 Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'B' and resid 363 through 368 Processing sheet with id= A, first strand: chain 'A' and resid 1589 through 1591 removed outlier: 3.607A pdb=" N GLY A1581 " --> pdb=" O ILE A1573 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1748 through 1751 Processing sheet with id= C, first strand: chain 'A' and resid 1916 through 1920 removed outlier: 6.927A pdb=" N GLY A1791 " --> pdb=" O ARG A1917 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N PHE A1919 " --> pdb=" O GLY A1791 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N CYS A1793 " --> pdb=" O PHE A1919 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A1897 " --> pdb=" O PHE A1847 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1878 through 1881 removed outlier: 3.812A pdb=" N LEU A1881 " --> pdb=" O GLU A1884 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A1884 " --> pdb=" O LEU A1881 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 2211 through 2215 removed outlier: 8.808A pdb=" N LEU A2070 " --> pdb=" O PHE A2190 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE A2192 " --> pdb=" O LEU A2070 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LEU A2072 " --> pdb=" O ILE A2192 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE A2194 " --> pdb=" O LEU A2072 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N GLY A2074 " --> pdb=" O PHE A2194 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N THR A2196 " --> pdb=" O GLY A2074 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ARG A2191 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ILE A2150 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU A2193 " --> pdb=" O ILE A2150 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL A2152 " --> pdb=" O LEU A2193 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLU A2195 " --> pdb=" O VAL A2152 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE A2154 " --> pdb=" O GLU A2195 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA A2098 " --> pdb=" O ARG A2149 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N TRP A2151 " --> pdb=" O ALA A2098 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL A2100 " --> pdb=" O TRP A2151 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL A2153 " --> pdb=" O VAL A2100 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR A2102 " --> pdb=" O VAL A2153 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ASP A2155 " --> pdb=" O TYR A2102 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE A2104 " --> pdb=" O ASP A2155 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 2116 through 2119 Processing sheet with id= G, first strand: chain 'A' and resid 2175 through 2177 Processing sheet with id= H, first strand: chain 'A' and resid 2357 through 2360 Processing sheet with id= I, first strand: chain 'A' and resid 2554 through 2558 removed outlier: 6.611A pdb=" N GLY A2413 " --> pdb=" O ALA A2555 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU A2557 " --> pdb=" O GLY A2413 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A2415 " --> pdb=" O LEU A2557 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A2414 " --> pdb=" O ILE A2531 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU A2482 " --> pdb=" O HIS A2530 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL A2532 " --> pdb=" O LEU A2482 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU A2484 " --> pdb=" O VAL A2532 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ALA A2534 " --> pdb=" O LEU A2484 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N CYS A2486 " --> pdb=" O ALA A2534 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 2462 through 2465 Processing sheet with id= K, first strand: chain 'A' and resid 2514 through 2517 removed outlier: 3.732A pdb=" N LYS A2522 " --> pdb=" O LYS A2517 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 2780 through 2783 removed outlier: 6.602A pdb=" N MET A2756 " --> pdb=" O PHE A2889 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE A2891 " --> pdb=" O MET A2756 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU A2758 " --> pdb=" O ILE A2891 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 3513 through 3517 removed outlier: 6.431A pdb=" N VAL A3404 " --> pdb=" O ARG A3514 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL A3516 " --> pdb=" O VAL A3404 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE A3406 " --> pdb=" O VAL A3516 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 3471 through 3473 removed outlier: 3.621A pdb=" N ILE A3481 " --> pdb=" O HIS A3484 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS A3484 " --> pdb=" O ILE A3481 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 3893 through 3896 removed outlier: 8.690A pdb=" N PHE A3786 " --> pdb=" O PHE A3871 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N MET A3873 " --> pdb=" O PHE A3786 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N MET A3788 " --> pdb=" O MET A3873 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N MET A3875 " --> pdb=" O MET A3788 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N SER A3790 " --> pdb=" O MET A3875 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N CYS A3877 " --> pdb=" O SER A3790 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY A3837 " --> pdb=" O LYS A3872 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N PHE A3874 " --> pdb=" O GLY A3837 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE A3839 " --> pdb=" O PHE A3874 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR A3876 " --> pdb=" O ILE A3839 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A3841 " --> pdb=" O THR A3876 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N HIS A3878 " --> pdb=" O LEU A3841 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 150 through 153 removed outlier: 4.351A pdb=" N LYS C 488 " --> pdb=" O GLY C 484 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 192 through 195 removed outlier: 3.684A pdb=" N ALA C 192 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR C 174 " --> pdb=" O LYS C 178 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER C 160 " --> pdb=" O ALA C 173 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 201 through 208 removed outlier: 6.913A pdb=" N ALA C 225 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N MET C 204 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL C 223 " --> pdb=" O MET C 204 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL C 206 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL C 221 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU C 220 " --> pdb=" O TRP C 236 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG C 247 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LYS C 235 " --> pdb=" O GLN C 245 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLN C 245 " --> pdb=" O LYS C 235 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL C 237 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N PHE C 243 " --> pdb=" O VAL C 237 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 256 through 263 removed outlier: 6.622A pdb=" N CYS C 273 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL C 259 " --> pdb=" O ALA C 271 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA C 271 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE C 261 " --> pdb=" O HIS C 269 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N HIS C 269 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS C 291 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ASP C 283 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER C 289 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 300 through 306 removed outlier: 6.758A pdb=" N GLY C 313 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE C 303 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE C 311 " --> pdb=" O ILE C 303 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL C 305 " --> pdb=" O TYR C 309 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N HIS C 323 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLY C 329 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 340 through 345 removed outlier: 6.615A pdb=" N ALA C 376 " --> pdb=" O GLU C 341 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL C 343 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL C 374 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N PHE C 345 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N TYR C 372 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER C 377 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 411 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU C 386 " --> pdb=" O CYS C 409 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N CYS C 409 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 420 through 426 removed outlier: 6.725A pdb=" N CYS C 433 " --> pdb=" O ARG C 421 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE C 423 " --> pdb=" O PHE C 431 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE C 431 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE C 425 " --> pdb=" O TYR C 429 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS C 451 " --> pdb=" O CYS C 441 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP C 443 " --> pdb=" O CYS C 449 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N CYS C 449 " --> pdb=" O ASP C 443 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 150 through 153 removed outlier: 4.333A pdb=" N LYS B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 192 through 195 removed outlier: 4.738A pdb=" N LYS B 178 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 160 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 201 through 208 removed outlier: 6.848A pdb=" N ALA B 225 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N MET B 204 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B 223 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL B 206 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL B 221 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU B 220 " --> pdb=" O TRP B 236 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LYS B 235 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLN B 245 " --> pdb=" O LYS B 235 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL B 237 " --> pdb=" O PHE B 243 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N PHE B 243 " --> pdb=" O VAL B 237 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 256 through 263 removed outlier: 6.710A pdb=" N CYS B 273 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL B 259 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA B 271 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE B 261 " --> pdb=" O HIS B 269 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N HIS B 269 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 291 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ASP B 283 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N SER B 289 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 300 through 306 removed outlier: 6.563A pdb=" N GLY B 313 " --> pdb=" O ARG B 301 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE B 303 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 311 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL B 305 " --> pdb=" O TYR B 309 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N TYR B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N HIS B 323 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLY B 329 " --> pdb=" O HIS B 323 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 411 through 414 removed outlier: 4.484A pdb=" N THR B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 377 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS B 373 " --> pdb=" O TRP B 385 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 420 through 426 removed outlier: 6.707A pdb=" N CYS B 433 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE B 423 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE B 431 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE B 425 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TYR B 429 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 434 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS B 451 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASP B 443 " --> pdb=" O CYS B 449 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N CYS B 449 " --> pdb=" O ASP B 443 " (cutoff:3.500A) 1064 hydrogen bonds defined for protein. 3078 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: 14.63 Time building geometry restraints manager: 10.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3936 1.31 - 1.44: 6611 1.44 - 1.56: 13857 1.56 - 1.69: 18 1.69 - 1.81: 177 Bond restraints: 24599 Sorted by residual: bond pdb=" C4 ADP A4104 " pdb=" C5 ADP A4104 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C5 ADP A4104 " pdb=" C6 ADP A4104 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C PRO A2937 " pdb=" O PRO A2937 " ideal model delta sigma weight residual 1.235 1.183 0.053 1.30e-02 5.92e+03 1.63e+01 bond pdb=" N VAL A2935 " pdb=" CA VAL A2935 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.07e-02 8.73e+03 7.76e+00 bond pdb=" N PRO A2937 " pdb=" CA PRO A2937 " ideal model delta sigma weight residual 1.469 1.439 0.030 1.28e-02 6.10e+03 5.57e+00 ... (remaining 24594 not shown) Histogram of bond angle deviations from ideal: 98.89 - 105.93: 407 105.93 - 112.97: 13674 112.97 - 120.01: 8316 120.01 - 127.05: 10606 127.05 - 134.09: 300 Bond angle restraints: 33303 Sorted by residual: angle pdb=" PB ATP A4103 " pdb=" O3B ATP A4103 " pdb=" PG ATP A4103 " ideal model delta sigma weight residual 139.87 127.95 11.92 1.00e+00 1.00e+00 1.42e+02 angle pdb=" PB ATP A4102 " pdb=" O3B ATP A4102 " pdb=" PG ATP A4102 " ideal model delta sigma weight residual 139.87 128.25 11.62 1.00e+00 1.00e+00 1.35e+02 angle pdb=" PB ATP A4101 " pdb=" O3B ATP A4101 " pdb=" PG ATP A4101 " ideal model delta sigma weight residual 139.87 128.32 11.55 1.00e+00 1.00e+00 1.33e+02 angle pdb=" PA ATP A4103 " pdb=" O3A ATP A4103 " pdb=" PB ATP A4103 " ideal model delta sigma weight residual 136.83 129.63 7.20 1.00e+00 1.00e+00 5.19e+01 angle pdb=" PA ATP A4102 " pdb=" O3A ATP A4102 " pdb=" PB ATP A4102 " ideal model delta sigma weight residual 136.83 129.83 7.00 1.00e+00 1.00e+00 4.90e+01 ... (remaining 33298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.80: 14460 34.80 - 69.60: 281 69.60 - 104.40: 18 104.40 - 139.20: 0 139.20 - 174.00: 2 Dihedral angle restraints: 14761 sinusoidal: 6087 harmonic: 8674 Sorted by residual: dihedral pdb=" O1B ADP A4104 " pdb=" O3A ADP A4104 " pdb=" PB ADP A4104 " pdb=" PA ADP A4104 " ideal model delta sinusoidal sigma weight residual -60.00 114.00 -174.00 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP A4104 " pdb=" O5' ADP A4104 " pdb=" PA ADP A4104 " pdb=" O2A ADP A4104 " ideal model delta sinusoidal sigma weight residual 300.00 126.71 173.29 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP A4104 " pdb=" O3A ADP A4104 " pdb=" PA ADP A4104 " pdb=" PB ADP A4104 " ideal model delta sinusoidal sigma weight residual -60.00 28.57 -88.57 1 2.00e+01 2.50e-03 2.34e+01 ... (remaining 14758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2826 0.044 - 0.089: 692 0.089 - 0.133: 238 0.133 - 0.177: 7 0.177 - 0.222: 4 Chirality restraints: 3767 Sorted by residual: chirality pdb=" CA LEU A2873 " pdb=" N LEU A2873 " pdb=" C LEU A2873 " pdb=" CB LEU A2873 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA VAL A2935 " pdb=" N VAL A2935 " pdb=" C VAL A2935 " pdb=" CB VAL A2935 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C3' ADP A4104 " pdb=" C2' ADP A4104 " pdb=" C4' ADP A4104 " pdb=" O3' ADP A4104 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.20 2.00e-01 2.50e+01 9.92e-01 ... (remaining 3764 not shown) Planarity restraints: 4169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A2618 " 0.037 5.00e-02 4.00e+02 5.63e-02 5.08e+00 pdb=" N PRO A2619 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A2619 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A2619 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A2875 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C ASP A2875 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP A2875 " 0.013 2.00e-02 2.50e+03 pdb=" N TRP A2876 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP A4102 " -0.026 2.00e-02 2.50e+03 1.14e-02 3.59e+00 pdb=" C2 ATP A4102 " 0.002 2.00e-02 2.50e+03 pdb=" C4 ATP A4102 " 0.009 2.00e-02 2.50e+03 pdb=" C5 ATP A4102 " 0.007 2.00e-02 2.50e+03 pdb=" C6 ATP A4102 " 0.004 2.00e-02 2.50e+03 pdb=" C8 ATP A4102 " -0.001 2.00e-02 2.50e+03 pdb=" N1 ATP A4102 " -0.006 2.00e-02 2.50e+03 pdb=" N3 ATP A4102 " 0.007 2.00e-02 2.50e+03 pdb=" N6 ATP A4102 " -0.017 2.00e-02 2.50e+03 pdb=" N7 ATP A4102 " 0.007 2.00e-02 2.50e+03 pdb=" N9 ATP A4102 " 0.013 2.00e-02 2.50e+03 ... (remaining 4166 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 110 2.48 - 3.08: 16648 3.08 - 3.69: 34997 3.69 - 4.29: 54096 4.29 - 4.90: 90538 Nonbonded interactions: 196389 Sorted by model distance: nonbonded pdb=" O2B ATP A4103 " pdb="MG MG A4106 " model vdw 1.874 2.170 nonbonded pdb=" O2G ATP A4103 " pdb="MG MG A4106 " model vdw 1.917 2.170 nonbonded pdb=" O2B ATP A4101 " pdb="MG MG A4105 " model vdw 2.014 2.170 nonbonded pdb=" OG1 THR A1803 " pdb="MG MG A4105 " model vdw 2.016 2.170 nonbonded pdb=" OG1 THR A2081 " pdb="MG MG A4106 " model vdw 2.018 2.170 ... (remaining 196384 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 'B' selection = (chain 'C' and (resid 139 through 350 or resid 355 through 400 or resid 405 thro \ ugh 493 or (resid 494 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD or name NE or name CZ or name NH1 or name NH2)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 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: 0.020 Extract box with map and model: 7.230 Check model and map are aligned: 0.420 Set scattering table: 0.240 Process input model: 72.130 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 24599 Z= 0.283 Angle : 0.553 11.917 33303 Z= 0.328 Chirality : 0.043 0.222 3767 Planarity : 0.003 0.056 4169 Dihedral : 14.451 174.003 9119 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.04 % Allowed : 0.26 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.16), residues: 2922 helix: 2.19 (0.15), residues: 1315 sheet: -0.07 (0.24), residues: 482 loop : -1.29 (0.17), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 288 HIS 0.007 0.001 HIS C 254 PHE 0.019 0.001 PHE A1850 TYR 0.019 0.001 TYR A2874 ARG 0.005 0.000 ARG A2620 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 2.886 Fit side-chains REVERT: A 1741 LEU cc_start: 0.8135 (mm) cc_final: 0.7740 (tp) REVERT: A 2386 MET cc_start: 0.9024 (mmm) cc_final: 0.8742 (mmt) REVERT: A 2873 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8671 (mt) REVERT: A 3398 MET cc_start: 0.9127 (mmm) cc_final: 0.8353 (mmm) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.3303 time to fit residues: 41.2784 Evaluate side-chains 67 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2873 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 1.9990 chunk 223 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 172 optimal weight: 0.9990 chunk 267 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2348 HIS A2931 ASN B 232 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.0409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24599 Z= 0.230 Angle : 0.472 6.734 33303 Z= 0.253 Chirality : 0.041 0.148 3767 Planarity : 0.003 0.051 4169 Dihedral : 8.665 168.304 3277 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.22 % Allowed : 3.10 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.16), residues: 2922 helix: 2.32 (0.15), residues: 1317 sheet: 0.15 (0.24), residues: 492 loop : -1.17 (0.17), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2084 HIS 0.005 0.001 HIS C 254 PHE 0.015 0.001 PHE A1850 TYR 0.014 0.001 TYR A2571 ARG 0.003 0.000 ARG A2620 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 2.906 Fit side-chains REVERT: A 1741 LEU cc_start: 0.8124 (mm) cc_final: 0.7921 (mm) REVERT: A 1963 MET cc_start: 0.8209 (mtp) cc_final: 0.7758 (mtt) REVERT: A 2386 MET cc_start: 0.9031 (mmm) cc_final: 0.8730 (mmt) REVERT: A 2738 MET cc_start: 0.9026 (ttm) cc_final: 0.8805 (ttt) REVERT: A 3398 MET cc_start: 0.9097 (mmm) cc_final: 0.8352 (mmm) REVERT: A 3875 MET cc_start: 0.8640 (mtp) cc_final: 0.8366 (mtm) outliers start: 6 outliers final: 4 residues processed: 69 average time/residue: 0.3460 time to fit residues: 42.1185 Evaluate side-chains 69 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 3290 ASP Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain B residue 479 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 148 optimal weight: 7.9990 chunk 83 optimal weight: 0.0770 chunk 222 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 268 optimal weight: 0.3980 chunk 289 optimal weight: 20.0000 chunk 239 optimal weight: 8.9990 chunk 266 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 overall best weight: 2.8944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2348 HIS A3542 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.0580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24599 Z= 0.287 Angle : 0.480 6.728 33303 Z= 0.256 Chirality : 0.042 0.141 3767 Planarity : 0.003 0.051 4169 Dihedral : 8.220 177.232 3275 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.33 % Allowed : 5.50 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.16), residues: 2922 helix: 2.33 (0.15), residues: 1317 sheet: 0.22 (0.24), residues: 493 loop : -1.13 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 288 HIS 0.003 0.001 HIS C 254 PHE 0.018 0.001 PHE A1850 TYR 0.016 0.001 TYR A2571 ARG 0.003 0.000 ARG A2620 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 2.907 Fit side-chains REVERT: A 1963 MET cc_start: 0.8303 (mtp) cc_final: 0.8027 (mtt) REVERT: A 2386 MET cc_start: 0.9093 (mmm) cc_final: 0.8827 (mmt) REVERT: A 3398 MET cc_start: 0.9047 (mmm) cc_final: 0.8452 (mmm) REVERT: A 3875 MET cc_start: 0.8638 (mtp) cc_final: 0.8319 (mtm) outliers start: 9 outliers final: 4 residues processed: 71 average time/residue: 0.3262 time to fit residues: 42.2593 Evaluate side-chains 70 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2503 VAL Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain B residue 479 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 265 optimal weight: 7.9990 chunk 201 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 chunk 269 optimal weight: 2.9990 chunk 285 optimal weight: 7.9990 chunk 140 optimal weight: 0.0970 chunk 255 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2598 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24599 Z= 0.142 Angle : 0.410 6.708 33303 Z= 0.221 Chirality : 0.040 0.138 3767 Planarity : 0.003 0.045 4169 Dihedral : 7.548 144.966 3275 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.26 % Allowed : 6.42 % Favored : 93.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.16), residues: 2922 helix: 2.52 (0.15), residues: 1318 sheet: 0.39 (0.24), residues: 488 loop : -1.00 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2084 HIS 0.003 0.000 HIS C 254 PHE 0.013 0.001 PHE A1620 TYR 0.012 0.001 TYR A2571 ARG 0.002 0.000 ARG A2620 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 3.019 Fit side-chains REVERT: A 1963 MET cc_start: 0.8304 (mtp) cc_final: 0.8003 (mtt) REVERT: A 2386 MET cc_start: 0.8986 (mmm) cc_final: 0.8684 (mmt) REVERT: A 3345 MET cc_start: 0.9029 (mmm) cc_final: 0.8805 (mmm) REVERT: A 3398 MET cc_start: 0.9022 (mmm) cc_final: 0.8486 (mmm) REVERT: A 3722 MET cc_start: 0.8545 (mmt) cc_final: 0.8233 (mmt) outliers start: 7 outliers final: 3 residues processed: 72 average time/residue: 0.3289 time to fit residues: 42.8256 Evaluate side-chains 70 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 3290 ASP Chi-restraints excluded: chain C residue 370 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 237 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 212 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 243 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 145 optimal weight: 0.9980 chunk 255 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3011 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.0763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24599 Z= 0.291 Angle : 0.469 6.711 33303 Z= 0.249 Chirality : 0.041 0.138 3767 Planarity : 0.003 0.048 4169 Dihedral : 7.583 130.725 3275 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.44 % Allowed : 7.12 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.16), residues: 2922 helix: 2.46 (0.15), residues: 1319 sheet: 0.34 (0.24), residues: 488 loop : -1.02 (0.17), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2084 HIS 0.003 0.001 HIS C 254 PHE 0.014 0.001 PHE A1850 TYR 0.016 0.001 TYR A2571 ARG 0.003 0.000 ARG A2620 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 3.041 Fit side-chains REVERT: A 1963 MET cc_start: 0.8371 (mtp) cc_final: 0.8143 (mtt) REVERT: A 2386 MET cc_start: 0.9097 (mmm) cc_final: 0.8781 (mmt) REVERT: A 3345 MET cc_start: 0.9100 (mmm) cc_final: 0.8882 (mmp) REVERT: A 3398 MET cc_start: 0.9033 (mmm) cc_final: 0.8514 (mmm) outliers start: 12 outliers final: 7 residues processed: 75 average time/residue: 0.3717 time to fit residues: 49.7544 Evaluate side-chains 73 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2348 HIS Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2503 VAL Chi-restraints excluded: chain A residue 3290 ASP Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 493 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 95 optimal weight: 4.9990 chunk 256 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 285 optimal weight: 6.9990 chunk 236 optimal weight: 0.0770 chunk 132 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24599 Z= 0.224 Angle : 0.442 6.651 33303 Z= 0.235 Chirality : 0.041 0.136 3767 Planarity : 0.003 0.046 4169 Dihedral : 7.413 114.038 3275 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.63 % Allowed : 7.49 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.16), residues: 2922 helix: 2.50 (0.15), residues: 1319 sheet: 0.38 (0.24), residues: 488 loop : -0.98 (0.17), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2084 HIS 0.003 0.001 HIS C 254 PHE 0.013 0.001 PHE A1620 TYR 0.013 0.001 TYR A2571 ARG 0.002 0.000 ARG A2620 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 2.920 Fit side-chains REVERT: A 1963 MET cc_start: 0.8373 (mtp) cc_final: 0.8168 (mtt) REVERT: A 2386 MET cc_start: 0.9108 (mmm) cc_final: 0.8779 (mmt) REVERT: A 3345 MET cc_start: 0.9074 (mmm) cc_final: 0.8858 (mmp) REVERT: A 3398 MET cc_start: 0.9030 (mmm) cc_final: 0.8616 (mmm) REVERT: A 3722 MET cc_start: 0.8595 (mmt) cc_final: 0.8379 (mmt) REVERT: A 3846 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.7919 (mmp) outliers start: 17 outliers final: 12 residues processed: 76 average time/residue: 0.3371 time to fit residues: 46.3431 Evaluate side-chains 79 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 3.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 2348 HIS Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2432 LEU Chi-restraints excluded: chain A residue 2503 VAL Chi-restraints excluded: chain A residue 3290 ASP Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 493 MET Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 479 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 275 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 240 optimal weight: 0.0060 chunk 159 optimal weight: 0.7980 chunk 284 optimal weight: 0.2980 chunk 177 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1867 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24599 Z= 0.109 Angle : 0.390 6.684 33303 Z= 0.209 Chirality : 0.039 0.137 3767 Planarity : 0.003 0.043 4169 Dihedral : 6.745 89.582 3275 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.26 % Allowed : 8.04 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.16), residues: 2922 helix: 2.68 (0.15), residues: 1319 sheet: 0.51 (0.24), residues: 499 loop : -0.81 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2084 HIS 0.003 0.000 HIS A2735 PHE 0.014 0.001 PHE A2877 TYR 0.009 0.001 TYR A3555 ARG 0.002 0.000 ARG A2620 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 3.158 Fit side-chains REVERT: A 3398 MET cc_start: 0.9007 (mmm) cc_final: 0.8640 (mmm) REVERT: A 3722 MET cc_start: 0.8530 (mmt) cc_final: 0.8293 (mmt) outliers start: 7 outliers final: 4 residues processed: 72 average time/residue: 0.3387 time to fit residues: 44.7406 Evaluate side-chains 70 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 3.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2503 VAL Chi-restraints excluded: chain A residue 3290 ASP Chi-restraints excluded: chain C residue 468 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 175 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 180 optimal weight: 9.9990 chunk 193 optimal weight: 1.9990 chunk 140 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 258 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1867 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24599 Z= 0.317 Angle : 0.478 7.411 33303 Z= 0.252 Chirality : 0.042 0.141 3767 Planarity : 0.003 0.046 4169 Dihedral : 7.156 85.410 3275 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.48 % Allowed : 8.49 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.16), residues: 2922 helix: 2.57 (0.15), residues: 1319 sheet: 0.45 (0.24), residues: 490 loop : -0.90 (0.17), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A2084 HIS 0.003 0.001 HIS A2201 PHE 0.013 0.001 PHE A1850 TYR 0.018 0.001 TYR A2571 ARG 0.003 0.000 ARG A2747 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 2.896 Fit side-chains REVERT: A 3398 MET cc_start: 0.9056 (mmm) cc_final: 0.8638 (mmm) REVERT: A 3846 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8013 (mmp) REVERT: C 481 VAL cc_start: 0.9490 (OUTLIER) cc_final: 0.9269 (p) outliers start: 13 outliers final: 10 residues processed: 74 average time/residue: 0.3348 time to fit residues: 44.3133 Evaluate side-chains 78 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 2348 HIS Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2432 LEU Chi-restraints excluded: chain A residue 2503 VAL Chi-restraints excluded: chain A residue 3290 ASP Chi-restraints excluded: chain A residue 3846 MET Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 493 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 272 optimal weight: 0.6980 chunk 248 optimal weight: 0.9990 chunk 264 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 250 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24599 Z= 0.136 Angle : 0.408 7.995 33303 Z= 0.217 Chirality : 0.040 0.137 3767 Planarity : 0.003 0.044 4169 Dihedral : 6.839 89.760 3275 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.41 % Allowed : 8.63 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.16), residues: 2922 helix: 2.66 (0.15), residues: 1319 sheet: 0.57 (0.24), residues: 493 loop : -0.81 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2084 HIS 0.003 0.000 HIS C 254 PHE 0.012 0.001 PHE A2877 TYR 0.012 0.001 TYR A2571 ARG 0.001 0.000 ARG A2830 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 2.900 Fit side-chains REVERT: A 3398 MET cc_start: 0.9049 (mmm) cc_final: 0.8665 (mmm) outliers start: 11 outliers final: 10 residues processed: 75 average time/residue: 0.3275 time to fit residues: 44.3774 Evaluate side-chains 77 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1655 MET Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2432 LEU Chi-restraints excluded: chain A residue 2503 VAL Chi-restraints excluded: chain A residue 3290 ASP Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 480 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 171 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 293 optimal weight: 9.9990 chunk 270 optimal weight: 0.6980 chunk 234 optimal weight: 0.0570 chunk 24 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 185 optimal weight: 0.0050 chunk 249 optimal weight: 3.9990 overall best weight: 0.5512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24599 Z= 0.102 Angle : 0.385 8.931 33303 Z= 0.204 Chirality : 0.039 0.133 3767 Planarity : 0.003 0.042 4169 Dihedral : 6.378 80.825 3275 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.30 % Allowed : 8.82 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.16), residues: 2922 helix: 2.82 (0.15), residues: 1311 sheet: 0.70 (0.24), residues: 505 loop : -0.70 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2084 HIS 0.002 0.000 HIS A2741 PHE 0.013 0.001 PHE A2877 TYR 0.008 0.001 TYR A2571 ARG 0.002 0.000 ARG C 301 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 3.207 Fit side-chains REVERT: A 3398 MET cc_start: 0.9021 (mmm) cc_final: 0.8692 (mmm) REVERT: B 240 GLU cc_start: 0.8493 (mp0) cc_final: 0.8143 (mp0) outliers start: 8 outliers final: 5 residues processed: 74 average time/residue: 0.3149 time to fit residues: 41.9470 Evaluate side-chains 72 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain C residue 176 HIS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 480 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 71 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 234 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 240 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 205 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.045753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.036744 restraints weight = 118095.075| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.75 r_work: 0.2727 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24599 Z= 0.119 Angle : 0.392 10.372 33303 Z= 0.208 Chirality : 0.039 0.138 3767 Planarity : 0.003 0.041 4169 Dihedral : 6.347 80.763 3275 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.22 % Allowed : 9.08 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.16), residues: 2922 helix: 2.86 (0.15), residues: 1310 sheet: 0.74 (0.24), residues: 506 loop : -0.66 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2084 HIS 0.002 0.000 HIS A2735 PHE 0.012 0.001 PHE A2877 TYR 0.011 0.001 TYR A2571 ARG 0.001 0.000 ARG A2763 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3629.92 seconds wall clock time: 68 minutes 1.50 seconds (4081.50 seconds total)