Starting phenix.real_space_refine on Wed Feb 14 22:18:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw6_13676/02_2024/7pw6_13676_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw6_13676/02_2024/7pw6_13676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw6_13676/02_2024/7pw6_13676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw6_13676/02_2024/7pw6_13676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw6_13676/02_2024/7pw6_13676_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pw6_13676/02_2024/7pw6_13676_updated.pdb" } resolution = 3.05 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= 0.003 sd= 0.073 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 6 5.49 5 S 53 5.16 5 Cl 1 4.86 5 C 6645 2.51 5 N 1851 2.21 5 O 1837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 1389": "OD1" <-> "OD2" Residue "A ASP 2335": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10393 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1418, 10393 Unusual residues: {'88C': 1, 'IHP': 1} Inner-chain residues flagged as termini: ['pdbres="VAL A3661 "'] Classifications: {'peptide': 1416, 'undetermined': 2} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 300} Link IDs: {'PTRANS': 51, 'TRANS': 1364, None: 2} Not linked: pdbres="VAL A3661 " pdbres="IHP A3701 " Not linked: pdbres="IHP A3701 " pdbres="88C A3702 " Chain breaks: 26 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 904 Unresolved non-hydrogen angles: 1166 Unresolved non-hydrogen dihedrals: 669 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 14, 'UNK:plan-1': 74, 'ASP:plan': 33, 'TYR:plan': 2, 'ASN:plan1': 13, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 55, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 566 Time building chain proxies: 5.99, per 1000 atoms: 0.58 Number of scatterers: 10393 At special positions: 0 Unit cell: (120.87, 105.549, 107.251, 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) Cl 1 17.00 S 53 16.00 P 6 15.00 O 1837 8.00 N 1851 7.00 C 6645 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: 4.20 Conformation dependent library (CDL) restraints added in 1.8 seconds 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2718 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 3 sheets defined 68.3% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'A' and resid 792 through 806 removed outlier: 3.652A pdb=" N ARG A 797 " --> pdb=" O ASP A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 823 removed outlier: 3.560A pdb=" N LYS A 819 " --> pdb=" O GLN A 815 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 829 No H-bonds generated for 'chain 'A' and resid 826 through 829' Processing helix chain 'A' and resid 836 through 850 removed outlier: 3.530A pdb=" N ILE A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 871 Processing helix chain 'A' and resid 882 through 890 Processing helix chain 'A' and resid 903 through 907 removed outlier: 4.041A pdb=" N LYS A 907 " --> pdb=" O ASN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 926 Processing helix chain 'A' and resid 936 through 955 removed outlier: 4.047A pdb=" N PHE A 940 " --> pdb=" O ALA A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 998 removed outlier: 3.767A pdb=" N GLY A 974 " --> pdb=" O ASP A 970 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN A 977 " --> pdb=" O HIS A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1018 removed outlier: 3.567A pdb=" N THR A1018 " --> pdb=" O THR A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1040 removed outlier: 4.446A pdb=" N LEU A1032 " --> pdb=" O THR A1028 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N SER A1033 " --> pdb=" O ARG A1029 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A1036 " --> pdb=" O LEU A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1057 Processing helix chain 'A' and resid 1069 through 1083 Processing helix chain 'A' and resid 1086 through 1098 removed outlier: 3.995A pdb=" N SER A1098 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1115 removed outlier: 3.550A pdb=" N GLN A1113 " --> pdb=" O SER A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1133 Processing helix chain 'A' and resid 1144 through 1150 removed outlier: 3.677A pdb=" N LEU A1149 " --> pdb=" O SER A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1196 removed outlier: 3.833A pdb=" N ASN A1184 " --> pdb=" O PRO A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1217 Processing helix chain 'A' and resid 1228 through 1238 Processing helix chain 'A' and resid 1243 through 1251 removed outlier: 4.091A pdb=" N LEU A1251 " --> pdb=" O GLU A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1304 Processing helix chain 'A' and resid 1318 through 1331 Processing helix chain 'A' and resid 1333 through 1340 Processing helix chain 'A' and resid 1348 through 1366 Processing helix chain 'A' and resid 1371 through 1373 No H-bonds generated for 'chain 'A' and resid 1371 through 1373' Processing helix chain 'A' and resid 1379 through 1383 removed outlier: 3.619A pdb=" N ARG A1383 " --> pdb=" O GLU A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1409 removed outlier: 3.738A pdb=" N TYR A1399 " --> pdb=" O GLN A1395 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A1402 " --> pdb=" O ARG A1398 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU A1408 " --> pdb=" O ASN A1404 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS A1409 " --> pdb=" O GLN A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1435 removed outlier: 3.805A pdb=" N ARG A1435 " --> pdb=" O PHE A1431 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1449 Processing helix chain 'A' and resid 1459 through 1465 removed outlier: 3.699A pdb=" N VAL A1463 " --> pdb=" O ALA A1459 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A1464 " --> pdb=" O GLN A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1493 Processing helix chain 'A' and resid 1497 through 1513 removed outlier: 4.048A pdb=" N LYS A1513 " --> pdb=" O ILE A1509 " (cutoff:3.500A) Processing helix chain 'A' and resid 1519 through 1534 removed outlier: 3.527A pdb=" N LYS A1523 " --> pdb=" O TYR A1519 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A1528 " --> pdb=" O SER A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1536 through 1550 removed outlier: 5.052A pdb=" N GLY A1541 " --> pdb=" O LYS A1537 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLN A1542 " --> pdb=" O GLU A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1560 through 1569 removed outlier: 3.504A pdb=" N THR A1567 " --> pdb=" O LYS A1563 " (cutoff:3.500A) Processing helix chain 'A' and resid 1596 through 1611 removed outlier: 3.917A pdb=" N ILE A1600 " --> pdb=" O GLU A1596 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A1601 " --> pdb=" O PRO A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1636 removed outlier: 3.812A pdb=" N LEU A1622 " --> pdb=" O SER A1618 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS A1632 " --> pdb=" O ARG A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1647 through 1655 Processing helix chain 'A' and resid 1664 through 1673 Processing helix chain 'A' and resid 1704 through 1716 Processing helix chain 'A' and resid 1729 through 1740 Processing helix chain 'A' and resid 1742 through 1758 Processing helix chain 'A' and resid 1782 through 1798 removed outlier: 3.813A pdb=" N ALA A1788 " --> pdb=" O MET A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1811 removed outlier: 3.909A pdb=" N HIS A1809 " --> pdb=" O GLN A1805 " (cutoff:3.500A) Processing helix chain 'A' and resid 1817 through 1819 No H-bonds generated for 'chain 'A' and resid 1817 through 1819' Processing helix chain 'A' and resid 1823 through 1828 Processing helix chain 'A' and resid 1835 through 1849 Processing helix chain 'A' and resid 1857 through 1864 Processing helix chain 'A' and resid 1925 through 1938 removed outlier: 4.382A pdb=" N CYS A1929 " --> pdb=" O MET A1925 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TYR A1930 " --> pdb=" O MET A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1942 through 1957 Processing helix chain 'A' and resid 1963 through 1975 Processing helix chain 'A' and resid 2007 through 2019 Processing helix chain 'A' and resid 2036 through 2055 removed outlier: 7.074A pdb=" N ASP A2046 " --> pdb=" O ASP A2042 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ALA A2047 " --> pdb=" O ASN A2043 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE A2048 " --> pdb=" O TYR A2044 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLU A2049 " --> pdb=" O GLY A2045 " (cutoff:3.500A) Processing helix chain 'A' and resid 2069 through 2082 Processing helix chain 'A' and resid 2161 through 2177 removed outlier: 3.534A pdb=" N ARG A2165 " --> pdb=" O HIS A2161 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A2176 " --> pdb=" O ILE A2172 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE A2177 " --> pdb=" O VAL A2173 " (cutoff:3.500A) Processing helix chain 'A' and resid 2180 through 2182 No H-bonds generated for 'chain 'A' and resid 2180 through 2182' Processing helix chain 'A' and resid 2214 through 2231 removed outlier: 3.760A pdb=" N TYR A2218 " --> pdb=" O LEU A2214 " (cutoff:3.500A) Processing helix chain 'A' and resid 2251 through 2264 removed outlier: 3.584A pdb=" N LYS A2256 " --> pdb=" O LEU A2252 " (cutoff:3.500A) Proline residue: A2259 - end of helix removed outlier: 3.661A pdb=" N VAL A2264 " --> pdb=" O ALA A2260 " (cutoff:3.500A) Processing helix chain 'A' and resid 2277 through 2288 Processing helix chain 'A' and resid 2295 through 2303 Processing helix chain 'A' and resid 2307 through 2331 Processing helix chain 'A' and resid 2338 through 2340 No H-bonds generated for 'chain 'A' and resid 2338 through 2340' Processing helix chain 'A' and resid 2362 through 2364 No H-bonds generated for 'chain 'A' and resid 2362 through 2364' Processing helix chain 'A' and resid 2377 through 2383 removed outlier: 3.928A pdb=" N LEU A2383 " --> pdb=" O ILE A2379 " (cutoff:3.500A) Processing helix chain 'A' and resid 2391 through 2405 Processing helix chain 'A' and resid 2407 through 2418 Processing helix chain 'A' and resid 3608 through 3621 Processing helix chain 'A' and resid 3633 through 3645 Processing helix chain 'A' and resid 3647 through 3651 Processing helix chain 'A' and resid 3655 through 3657 No H-bonds generated for 'chain 'A' and resid 3655 through 3657' Processing sheet with id= A, first strand: chain 'A' and resid 2089 through 2091 removed outlier: 3.576A pdb=" N ILE A2128 " --> pdb=" O LEU A2090 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N THR A2127 " --> pdb=" O LEU A2141 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU A2141 " --> pdb=" O THR A2127 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 2211 through 2213 Processing sheet with id= C, first strand: chain 'A' and resid 2121 through 2124 removed outlier: 6.677A pdb=" N LEU A2143 " --> pdb=" O HIS A2122 " (cutoff:3.500A) 604 hydrogen bonds defined for protein. 1800 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: 3.45 Time building geometry restraints manager: 4.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3009 1.34 - 1.45: 1536 1.45 - 1.57: 5952 1.57 - 1.69: 7 1.69 - 1.81: 80 Bond restraints: 10584 Sorted by residual: bond pdb=" C13 88C A3702 " pdb=" N35 88C A3702 " ideal model delta sigma weight residual 1.325 1.398 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C28 88C A3702 " pdb=" N30 88C A3702 " ideal model delta sigma weight residual 1.352 1.424 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C26 88C A3702 " pdb=" N27 88C A3702 " ideal model delta sigma weight residual 1.391 1.462 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C28 88C A3702 " pdb=" N27 88C A3702 " ideal model delta sigma weight residual 1.376 1.443 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C13 88C A3702 " pdb=" N12 88C A3702 " ideal model delta sigma weight residual 1.364 1.417 -0.053 2.00e-02 2.50e+03 7.14e+00 ... (remaining 10579 not shown) Histogram of bond angle deviations from ideal: 99.93 - 106.75: 285 106.75 - 113.57: 6090 113.57 - 120.40: 3749 120.40 - 127.22: 4192 127.22 - 134.04: 131 Bond angle restraints: 14447 Sorted by residual: angle pdb=" C ALA A1002 " pdb=" N ASN A1003 " pdb=" CA ASN A1003 " ideal model delta sigma weight residual 121.54 128.41 -6.87 1.91e+00 2.74e-01 1.29e+01 angle pdb=" N VAL A1390 " pdb=" CA VAL A1390 " pdb=" C VAL A1390 " ideal model delta sigma weight residual 112.83 109.30 3.53 9.90e-01 1.02e+00 1.27e+01 angle pdb=" O12 IHP A3701 " pdb=" P2 IHP A3701 " pdb=" O32 IHP A3701 " ideal model delta sigma weight residual 100.47 109.56 -9.09 3.00e+00 1.11e-01 9.19e+00 angle pdb=" C09 88C A3702 " pdb=" S06 88C A3702 " pdb=" N03 88C A3702 " ideal model delta sigma weight residual 102.09 110.79 -8.70 3.00e+00 1.11e-01 8.42e+00 angle pdb=" O16 IHP A3701 " pdb=" P6 IHP A3701 " pdb=" O36 IHP A3701 " ideal model delta sigma weight residual 101.25 109.51 -8.26 3.00e+00 1.11e-01 7.58e+00 ... (remaining 14442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.03: 6175 33.03 - 66.06: 116 66.06 - 99.09: 23 99.09 - 132.12: 4 132.12 - 165.16: 3 Dihedral angle restraints: 6321 sinusoidal: 2175 harmonic: 4146 Sorted by residual: dihedral pdb=" C6 IHP A3701 " pdb=" C1 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" O12 IHP A3701 " ideal model delta sinusoidal sigma weight residual 61.05 -104.11 165.16 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C4 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O12 IHP A3701 " ideal model delta sinusoidal sigma weight residual 60.90 -159.10 -140.00 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" O12 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O13 IHP A3701 " ideal model delta sinusoidal sigma weight residual 64.08 -72.56 136.64 1 3.00e+01 1.11e-03 1.84e+01 ... (remaining 6318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.005: 1751 1.005 - 2.010: 0 2.010 - 3.015: 0 3.015 - 4.020: 0 4.020 - 5.026: 3 Chirality restraints: 1754 Sorted by residual: chirality pdb=" C2 IHP A3701 " pdb=" C1 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O12 IHP A3701 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.31e+02 chirality pdb=" C4 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" C5 IHP A3701 " pdb=" O14 IHP A3701 " both_signs ideal model delta sigma weight residual False 2.48 -2.52 5.00 2.00e-01 2.50e+01 6.26e+02 chirality pdb=" C1 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C6 IHP A3701 " pdb=" O11 IHP A3701 " both_signs ideal model delta sigma weight residual False 2.32 -2.48 4.80 2.00e-01 2.50e+01 5.75e+02 ... (remaining 1751 not shown) Planarity restraints: 1790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A2246 " 0.049 5.00e-02 4.00e+02 7.48e-02 8.95e+00 pdb=" N PRO A2247 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A2247 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A2247 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A1333 " -0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO A1334 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A1334 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1334 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1281 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO A1282 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A1282 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1282 " -0.023 5.00e-02 4.00e+02 ... (remaining 1787 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 135 2.70 - 3.25: 10237 3.25 - 3.80: 16181 3.80 - 4.35: 19869 4.35 - 4.90: 34278 Nonbonded interactions: 80700 Sorted by model distance: nonbonded pdb=" OH TYR A2193 " pdb=" O ILE A2353 " model vdw 2.146 2.440 nonbonded pdb=" O TRP A1106 " pdb=" OG SER A1109 " model vdw 2.172 2.440 nonbonded pdb=" O GLU A1068 " pdb=" OG1 THR A1072 " model vdw 2.285 2.440 nonbonded pdb=" O GLN A 963 " pdb=" NH2 ARG A 979 " model vdw 2.285 2.520 nonbonded pdb=" OE1 GLU A 991 " pdb=" NH2 ARG A1049 " model vdw 2.298 2.520 ... (remaining 80695 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.440 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 30.170 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10584 Z= 0.217 Angle : 0.647 9.093 14447 Z= 0.346 Chirality : 0.208 5.026 1754 Planarity : 0.004 0.075 1790 Dihedral : 15.204 165.156 3603 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.10 % Allowed : 0.10 % Favored : 99.79 % 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: 1.97 (0.24), residues: 1298 helix: 2.42 (0.18), residues: 878 sheet: -0.27 (0.80), residues: 36 loop : -1.28 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1393 HIS 0.007 0.001 HIS A2352 PHE 0.012 0.001 PHE A1827 TYR 0.020 0.001 TYR A 998 ARG 0.003 0.000 ARG A 930 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 1.174 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.2593 time to fit residues: 40.7098 Evaluate side-chains 81 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.0470 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 72 optimal weight: 0.0870 chunk 57 optimal weight: 0.0050 chunk 110 optimal weight: 0.9980 chunk 42 optimal weight: 0.0270 chunk 67 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 128 optimal weight: 0.5980 overall best weight: 0.1528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1344 GLN A2377 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10584 Z= 0.116 Angle : 0.454 9.972 14447 Z= 0.208 Chirality : 0.037 0.419 1754 Planarity : 0.004 0.059 1790 Dihedral : 9.161 121.906 1564 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.41 % Allowed : 6.22 % Favored : 93.36 % 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: 2.47 (0.24), residues: 1298 helix: 2.79 (0.18), residues: 870 sheet: 0.51 (0.90), residues: 36 loop : -1.03 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A2221 HIS 0.004 0.001 HIS A2352 PHE 0.011 0.001 PHE A1754 TYR 0.017 0.001 TYR A 998 ARG 0.003 0.000 ARG A1329 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 1.179 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 87 average time/residue: 0.2423 time to fit residues: 30.5104 Evaluate side-chains 81 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 866 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 114 optimal weight: 0.0970 chunk 127 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1831 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10584 Z= 0.261 Angle : 0.508 8.873 14447 Z= 0.247 Chirality : 0.039 0.325 1754 Planarity : 0.004 0.054 1790 Dihedral : 9.784 122.145 1564 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.14 % Allowed : 7.47 % Favored : 91.39 % 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: 1.95 (0.24), residues: 1298 helix: 2.39 (0.18), residues: 863 sheet: 0.33 (0.86), residues: 38 loop : -1.17 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2207 HIS 0.005 0.001 HIS A2337 PHE 0.017 0.002 PHE A 940 TYR 0.019 0.001 TYR A 998 ARG 0.003 0.000 ARG A2374 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 1.227 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 91 average time/residue: 0.2435 time to fit residues: 31.6297 Evaluate side-chains 85 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1744 TYR Chi-restraints excluded: chain A residue 1831 ASN Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 3661 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1831 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10584 Z= 0.215 Angle : 0.483 8.009 14447 Z= 0.235 Chirality : 0.038 0.324 1754 Planarity : 0.004 0.050 1790 Dihedral : 9.742 122.376 1564 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 8.82 % Favored : 89.94 % 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: 1.88 (0.24), residues: 1298 helix: 2.29 (0.18), residues: 867 sheet: 0.04 (0.88), residues: 40 loop : -1.09 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2207 HIS 0.005 0.001 HIS A2337 PHE 0.014 0.002 PHE A1754 TYR 0.018 0.001 TYR A 998 ARG 0.002 0.000 ARG A1329 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 1.159 Fit side-chains REVERT: A 2136 LYS cc_start: 0.8444 (mmpt) cc_final: 0.8174 (mmtp) outliers start: 12 outliers final: 12 residues processed: 86 average time/residue: 0.2459 time to fit residues: 30.3297 Evaluate side-chains 86 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1463 VAL Chi-restraints excluded: chain A residue 1744 TYR Chi-restraints excluded: chain A residue 1831 ASN Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3661 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 122 optimal weight: 0.0050 chunk 34 optimal weight: 5.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1019 ASN A1460 GLN A1831 ASN A2189 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10584 Z= 0.328 Angle : 0.559 8.065 14447 Z= 0.273 Chirality : 0.041 0.350 1754 Planarity : 0.005 0.050 1790 Dihedral : 9.916 123.270 1564 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.87 % Allowed : 9.54 % Favored : 88.59 % 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: 1.43 (0.24), residues: 1298 helix: 1.90 (0.18), residues: 870 sheet: 0.10 (0.86), residues: 40 loop : -1.20 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A2207 HIS 0.007 0.001 HIS A2337 PHE 0.016 0.002 PHE A1754 TYR 0.019 0.002 TYR A 998 ARG 0.004 0.000 ARG A 892 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 1.044 Fit side-chains REVERT: A 2136 LYS cc_start: 0.8504 (mmpt) cc_final: 0.8243 (mmtp) outliers start: 18 outliers final: 13 residues processed: 97 average time/residue: 0.2466 time to fit residues: 33.8993 Evaluate side-chains 91 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1463 VAL Chi-restraints excluded: chain A residue 1744 TYR Chi-restraints excluded: chain A residue 1831 ASN Chi-restraints excluded: chain A residue 2180 ILE Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3661 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 0.9980 chunk 122 optimal weight: 0.2980 chunk 26 optimal weight: 0.0570 chunk 80 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 0.0770 chunk 71 optimal weight: 0.0000 chunk 131 optimal weight: 0.9980 overall best weight: 0.2660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1831 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10584 Z= 0.127 Angle : 0.425 7.657 14447 Z= 0.209 Chirality : 0.036 0.303 1754 Planarity : 0.004 0.046 1790 Dihedral : 9.577 120.274 1564 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.24 % Allowed : 10.89 % Favored : 87.86 % 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: 2.08 (0.24), residues: 1298 helix: 2.42 (0.18), residues: 874 sheet: 0.23 (0.89), residues: 40 loop : -1.03 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1393 HIS 0.004 0.001 HIS A2352 PHE 0.010 0.001 PHE A1754 TYR 0.015 0.001 TYR A 998 ARG 0.003 0.000 ARG A 930 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 1.224 Fit side-chains REVERT: A 2136 LYS cc_start: 0.8482 (mmpt) cc_final: 0.8241 (mmtp) REVERT: A 2196 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8962 (t) outliers start: 12 outliers final: 8 residues processed: 93 average time/residue: 0.2372 time to fit residues: 32.0502 Evaluate side-chains 87 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1463 VAL Chi-restraints excluded: chain A residue 1831 ASN Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 2228 LEU Chi-restraints excluded: chain A residue 3625 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 114 optimal weight: 0.2980 chunk 76 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1460 GLN A1831 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10584 Z= 0.252 Angle : 0.499 7.661 14447 Z= 0.244 Chirality : 0.039 0.330 1754 Planarity : 0.004 0.046 1790 Dihedral : 9.694 120.464 1564 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.87 % Allowed : 10.48 % Favored : 87.66 % 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: 1.83 (0.24), residues: 1298 helix: 2.21 (0.18), residues: 869 sheet: 0.33 (0.91), residues: 40 loop : -1.06 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2207 HIS 0.005 0.001 HIS A2337 PHE 0.015 0.002 PHE A1754 TYR 0.019 0.001 TYR A 998 ARG 0.005 0.000 ARG A 930 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 1.620 Fit side-chains REVERT: A 2136 LYS cc_start: 0.8490 (mmpt) cc_final: 0.8207 (mmtp) outliers start: 18 outliers final: 17 residues processed: 94 average time/residue: 0.2636 time to fit residues: 36.5886 Evaluate side-chains 95 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 959 GLN Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1463 VAL Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1744 TYR Chi-restraints excluded: chain A residue 1831 ASN Chi-restraints excluded: chain A residue 2180 ILE Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 2228 LEU Chi-restraints excluded: chain A residue 2288 MET Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3661 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 86 optimal weight: 0.0970 chunk 92 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1831 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10584 Z= 0.157 Angle : 0.444 7.441 14447 Z= 0.218 Chirality : 0.036 0.310 1754 Planarity : 0.004 0.046 1790 Dihedral : 9.588 118.955 1564 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.56 % Allowed : 11.00 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.24), residues: 1298 helix: 2.42 (0.18), residues: 867 sheet: 0.59 (0.94), residues: 40 loop : -1.02 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2207 HIS 0.004 0.001 HIS A2352 PHE 0.012 0.001 PHE A1754 TYR 0.016 0.001 TYR A 998 ARG 0.003 0.000 ARG A 930 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 1.164 Fit side-chains REVERT: A 1364 VAL cc_start: 0.8985 (t) cc_final: 0.8737 (t) REVERT: A 2136 LYS cc_start: 0.8476 (mmpt) cc_final: 0.8201 (mmtp) outliers start: 15 outliers final: 12 residues processed: 93 average time/residue: 0.2296 time to fit residues: 31.1715 Evaluate side-chains 90 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1463 VAL Chi-restraints excluded: chain A residue 1744 TYR Chi-restraints excluded: chain A residue 1831 ASN Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 2228 LEU Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3661 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.1980 chunk 130 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 99 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 114 optimal weight: 0.3980 chunk 119 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 81 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1460 GLN A1831 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10584 Z= 0.152 Angle : 0.432 7.395 14447 Z= 0.212 Chirality : 0.036 0.307 1754 Planarity : 0.004 0.046 1790 Dihedral : 9.530 117.580 1564 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.45 % Allowed : 11.51 % Favored : 87.03 % 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: 2.19 (0.24), residues: 1298 helix: 2.49 (0.18), residues: 873 sheet: 0.69 (0.95), residues: 40 loop : -0.99 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A2221 HIS 0.004 0.001 HIS A2352 PHE 0.012 0.001 PHE A1754 TYR 0.016 0.001 TYR A 998 ARG 0.003 0.000 ARG A 930 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 1.166 Fit side-chains REVERT: A 1364 VAL cc_start: 0.8942 (t) cc_final: 0.8711 (t) REVERT: A 2136 LYS cc_start: 0.8474 (mmpt) cc_final: 0.8196 (mmtp) outliers start: 14 outliers final: 14 residues processed: 93 average time/residue: 0.2235 time to fit residues: 30.5330 Evaluate side-chains 94 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1463 VAL Chi-restraints excluded: chain A residue 1744 TYR Chi-restraints excluded: chain A residue 1831 ASN Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 2228 LEU Chi-restraints excluded: chain A residue 2288 MET Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3657 TRP Chi-restraints excluded: chain A residue 3661 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 0.0980 chunk 93 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 0.2980 chunk 119 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1831 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10584 Z= 0.177 Angle : 0.449 7.412 14447 Z= 0.221 Chirality : 0.037 0.306 1754 Planarity : 0.004 0.046 1790 Dihedral : 9.540 116.728 1564 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.56 % Allowed : 11.31 % Favored : 87.14 % 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: 2.16 (0.24), residues: 1298 helix: 2.46 (0.18), residues: 872 sheet: 0.71 (0.95), residues: 40 loop : -0.99 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A2221 HIS 0.004 0.001 HIS A2352 PHE 0.012 0.001 PHE A1754 TYR 0.017 0.001 TYR A 998 ARG 0.003 0.000 ARG A 930 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 1.173 Fit side-chains REVERT: A 1364 VAL cc_start: 0.8964 (t) cc_final: 0.8730 (t) REVERT: A 2136 LYS cc_start: 0.8482 (mmpt) cc_final: 0.8204 (mmtp) outliers start: 15 outliers final: 14 residues processed: 92 average time/residue: 0.2225 time to fit residues: 30.2081 Evaluate side-chains 93 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1463 VAL Chi-restraints excluded: chain A residue 1744 TYR Chi-restraints excluded: chain A residue 1831 ASN Chi-restraints excluded: chain A residue 2196 THR Chi-restraints excluded: chain A residue 2228 LEU Chi-restraints excluded: chain A residue 2288 MET Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3657 TRP Chi-restraints excluded: chain A residue 3661 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 chunk 98 optimal weight: 30.0000 chunk 6 optimal weight: 0.7980 chunk 80 optimal weight: 20.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1460 GLN A1831 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.136412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.118655 restraints weight = 14219.836| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.19 r_work: 0.3244 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10584 Z= 0.209 Angle : 0.466 7.476 14447 Z= 0.229 Chirality : 0.037 0.305 1754 Planarity : 0.004 0.045 1790 Dihedral : 9.599 116.313 1564 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.76 % Allowed : 11.31 % Favored : 86.93 % 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: 2.04 (0.24), residues: 1298 helix: 2.35 (0.18), residues: 875 sheet: 0.70 (0.95), residues: 40 loop : -1.01 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2207 HIS 0.005 0.001 HIS A2337 PHE 0.013 0.001 PHE A1754 TYR 0.018 0.001 TYR A 998 ARG 0.003 0.000 ARG A 930 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2203.34 seconds wall clock time: 40 minutes 46.12 seconds (2446.12 seconds total)