Starting phenix.real_space_refine on Thu Feb 15 10:32:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly4_23587/02_2024/7ly4_23587_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly4_23587/02_2024/7ly4_23587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly4_23587/02_2024/7ly4_23587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly4_23587/02_2024/7ly4_23587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly4_23587/02_2024/7ly4_23587_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ly4_23587/02_2024/7ly4_23587_updated.pdb" } resolution = 3.8 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 51 5.16 5 C 7647 2.51 5 N 1989 2.21 5 O 2245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1174": "OE1" <-> "OE2" Residue "E TYR 1429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1607": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11934 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2599 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 12, 'TRANS': 310} Chain: "D" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2599 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 12, 'TRANS': 310} Chain: "E" Number of atoms: 6674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 828, 6674 Classifications: {'peptide': 828} Link IDs: {'PTRANS': 48, 'TRANS': 779} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.64, per 1000 atoms: 0.56 Number of scatterers: 11934 At special positions: 0 Unit cell: (90.06, 103.74, 182.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 P 2 15.00 O 2245 8.00 N 1989 7.00 C 7647 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: 5.05 Conformation dependent library (CDL) restraints added in 2.5 seconds 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2778 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 15 sheets defined 38.5% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 Proline residue: A 37 - end of helix removed outlier: 3.910A pdb=" N ALA A 43 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 56 Processing helix chain 'A' and resid 61 through 73 Processing helix chain 'A' and resid 84 through 87 No H-bonds generated for 'chain 'A' and resid 84 through 87' Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 101 through 104 Processing helix chain 'A' and resid 107 through 119 removed outlier: 3.531A pdb=" N ASN A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 143 No H-bonds generated for 'chain 'A' and resid 140 through 143' Processing helix chain 'A' and resid 159 through 169 removed outlier: 3.691A pdb=" N SER A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LEU A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 234 through 242 removed outlier: 4.987A pdb=" N ASP A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 240 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 257 through 271 removed outlier: 8.627A pdb=" N ALA A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ALA A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY A 264 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 285 removed outlier: 5.586A pdb=" N THR A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'D' and resid 31 through 34 No H-bonds generated for 'chain 'D' and resid 31 through 34' Processing helix chain 'D' and resid 36 through 45 removed outlier: 3.754A pdb=" N TYR D 40 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR D 45 " --> pdb=" O PHE D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 56 Processing helix chain 'D' and resid 61 through 73 Processing helix chain 'D' and resid 84 through 87 No H-bonds generated for 'chain 'D' and resid 84 through 87' Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 101 through 104 Processing helix chain 'D' and resid 107 through 119 removed outlier: 3.744A pdb=" N ASN D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 143 No H-bonds generated for 'chain 'D' and resid 140 through 143' Processing helix chain 'D' and resid 159 through 169 removed outlier: 3.729A pdb=" N SER D 168 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU D 169 " --> pdb=" O LEU D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 231 No H-bonds generated for 'chain 'D' and resid 229 through 231' Processing helix chain 'D' and resid 234 through 242 removed outlier: 4.987A pdb=" N ASP D 238 " --> pdb=" O ILE D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 285 Proline residue: D 258 - end of helix removed outlier: 8.790A pdb=" N ALA D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ALA D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY D 264 " --> pdb=" O TYR D 260 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYR D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY D 273 " --> pdb=" O CYS D 269 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 304 Processing helix chain 'E' and resid 854 through 863 Processing helix chain 'E' and resid 886 through 899 Processing helix chain 'E' and resid 901 through 904 Processing helix chain 'E' and resid 934 through 950 Processing helix chain 'E' and resid 981 through 983 No H-bonds generated for 'chain 'E' and resid 981 through 983' Processing helix chain 'E' and resid 986 through 1001 Processing helix chain 'E' and resid 1014 through 1024 Processing helix chain 'E' and resid 1028 through 1043 Proline residue: E1042 - end of helix Processing helix chain 'E' and resid 1056 through 1058 No H-bonds generated for 'chain 'E' and resid 1056 through 1058' Processing helix chain 'E' and resid 1073 through 1085 Processing helix chain 'E' and resid 1090 through 1106 Processing helix chain 'E' and resid 1127 through 1129 No H-bonds generated for 'chain 'E' and resid 1127 through 1129' Processing helix chain 'E' and resid 1150 through 1166 removed outlier: 3.626A pdb=" N GLU E1166 " --> pdb=" O LEU E1162 " (cutoff:3.500A) Processing helix chain 'E' and resid 1172 through 1182 Processing helix chain 'E' and resid 1206 through 1210 Processing helix chain 'E' and resid 1244 through 1246 No H-bonds generated for 'chain 'E' and resid 1244 through 1246' Processing helix chain 'E' and resid 1249 through 1268 Processing helix chain 'E' and resid 1279 through 1288 removed outlier: 4.081A pdb=" N ALA E1283 " --> pdb=" O GLN E1279 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU E1284 " --> pdb=" O LYS E1280 " (cutoff:3.500A) Processing helix chain 'E' and resid 1300 through 1310 removed outlier: 3.526A pdb=" N PHE E1304 " --> pdb=" O LEU E1300 " (cutoff:3.500A) Processing helix chain 'E' and resid 1326 through 1343 Processing helix chain 'E' and resid 1359 through 1370 removed outlier: 3.529A pdb=" N ILE E1363 " --> pdb=" O VAL E1359 " (cutoff:3.500A) Processing helix chain 'E' and resid 1384 through 1393 Processing helix chain 'E' and resid 1410 through 1412 No H-bonds generated for 'chain 'E' and resid 1410 through 1412' Processing helix chain 'E' and resid 1447 through 1460 Processing helix chain 'E' and resid 1478 through 1488 removed outlier: 3.530A pdb=" N PHE E1485 " --> pdb=" O TYR E1482 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY E1486 " --> pdb=" O ASP E1483 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR E1487 " --> pdb=" O ILE E1484 " (cutoff:3.500A) Processing helix chain 'E' and resid 1503 through 1513 Processing helix chain 'E' and resid 1522 through 1531 removed outlier: 3.658A pdb=" N ASP E1530 " --> pdb=" O ASP E1526 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N HIS E1531 " --> pdb=" O LEU E1527 " (cutoff:3.500A) Processing helix chain 'E' and resid 1555 through 1562 Processing helix chain 'E' and resid 1640 through 1646 Processing sheet with id= A, first strand: chain 'A' and resid 14 through 16 Processing sheet with id= B, first strand: chain 'A' and resid 217 through 222 removed outlier: 6.732A pdb=" N PHE A 208 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL A 192 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYR A 251 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE A 313 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA A 316 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 14 through 16 Processing sheet with id= D, first strand: chain 'D' and resid 217 through 222 removed outlier: 6.794A pdb=" N PHE D 208 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL D 192 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR D 251 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ILE D 313 " --> pdb=" O TYR D 251 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 1212 through 1219 removed outlier: 6.796A pdb=" N GLU E 879 " --> pdb=" O ARG E1214 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE E1216 " --> pdb=" O TYR E 877 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR E 877 " --> pdb=" O ILE E1216 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ALA E1218 " --> pdb=" O GLN E 875 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLN E 875 " --> pdb=" O ALA E1218 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU E 974 " --> pdb=" O GLN E 967 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLN E 967 " --> pdb=" O LEU E 974 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N CYS E 976 " --> pdb=" O ALA E 965 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ALA E 965 " --> pdb=" O CYS E 976 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG E 978 " --> pdb=" O LEU E 963 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU E 963 " --> pdb=" O ARG E 978 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ASP E 980 " --> pdb=" O PHE E 961 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE E 961 " --> pdb=" O ASP E 980 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLU E 925 " --> pdb=" O ALA E 965 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLN E 967 " --> pdb=" O GLU E 925 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLU E 927 " --> pdb=" O GLN E 967 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N GLN E 969 " --> pdb=" O GLU E 927 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 905 through 907 Processing sheet with id= G, first strand: chain 'E' and resid 1064 through 1071 Processing sheet with id= H, first strand: chain 'E' and resid 1110 through 1117 Processing sheet with id= I, first strand: chain 'E' and resid 1374 through 1378 removed outlier: 6.336A pdb=" N ILE E1398 " --> pdb=" O GLY E1352 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LEU E1354 " --> pdb=" O ILE E1398 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU E1400 " --> pdb=" O LEU E1354 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 1468 through 1471 removed outlier: 6.832A pdb=" N THR E1493 " --> pdb=" O ILE E1469 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLY E1471 " --> pdb=" O THR E1493 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL E1495 " --> pdb=" O GLY E1471 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'E' and resid 1517 through 1520 removed outlier: 6.691A pdb=" N LEU E1543 " --> pdb=" O TRP E1518 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N THR E1520 " --> pdb=" O LEU E1543 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU E1545 " --> pdb=" O THR E1520 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP E1567 " --> pdb=" O VAL E1544 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU E1546 " --> pdb=" O ASP E1567 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE E1569 " --> pdb=" O LEU E1546 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 1605 through 1610 removed outlier: 4.419A pdb=" N GLY E1629 " --> pdb=" O PRO E1655 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 1663 through 1666 Processing sheet with id= N, first strand: chain 'E' and resid 1315 through 1318 removed outlier: 6.625A pdb=" N LEU E1324 " --> pdb=" O ALA E1316 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 1427 through 1433 removed outlier: 7.215A pdb=" N ILE E1445 " --> pdb=" O ALA E1428 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL E1430 " --> pdb=" O VAL E1443 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL E1443 " --> pdb=" O VAL E1430 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR E1432 " --> pdb=" O LYS E1441 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LYS E1441 " --> pdb=" O TYR E1432 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1188 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: 4.81 Time building geometry restraints manager: 5.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2775 1.32 - 1.46: 3728 1.46 - 1.59: 5616 1.59 - 1.72: 16 1.72 - 1.85: 87 Bond restraints: 12222 Sorted by residual: bond pdb=" C10 FMN D 401 " pdb=" C4A FMN D 401 " ideal model delta sigma weight residual 1.390 1.549 -0.159 2.00e-02 2.50e+03 6.29e+01 bond pdb=" C10 FMN A 401 " pdb=" C4A FMN A 401 " ideal model delta sigma weight residual 1.390 1.542 -0.152 2.00e-02 2.50e+03 5.80e+01 bond pdb=" C4 FMN D 401 " pdb=" C4A FMN D 401 " ideal model delta sigma weight residual 1.390 1.534 -0.144 2.00e-02 2.50e+03 5.21e+01 bond pdb=" CB HIS E1301 " pdb=" CG HIS E1301 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.20e+01 bond pdb=" CG ARG E1120 " pdb=" CD ARG E1120 " ideal model delta sigma weight residual 1.520 1.327 0.193 3.00e-02 1.11e+03 4.13e+01 ... (remaining 12217 not shown) Histogram of bond angle deviations from ideal: 92.96 - 101.18: 14 101.18 - 109.41: 2186 109.41 - 117.63: 6808 117.63 - 125.86: 7414 125.86 - 134.08: 176 Bond angle restraints: 16598 Sorted by residual: angle pdb=" N LEU E1602 " pdb=" CA LEU E1602 " pdb=" C LEU E1602 " ideal model delta sigma weight residual 111.03 125.16 -14.13 1.11e+00 8.12e-01 1.62e+02 angle pdb=" N ILE A 274 " pdb=" CA ILE A 274 " pdb=" C ILE A 274 " ideal model delta sigma weight residual 110.21 97.64 12.57 1.13e+00 7.83e-01 1.24e+02 angle pdb=" N SER E 873 " pdb=" CA SER E 873 " pdb=" C SER E 873 " ideal model delta sigma weight residual 109.83 97.67 12.16 1.27e+00 6.20e-01 9.16e+01 angle pdb=" C ARG E1666 " pdb=" N PRO E1667 " pdb=" CA PRO E1667 " ideal model delta sigma weight residual 119.82 128.29 -8.47 9.80e-01 1.04e+00 7.46e+01 angle pdb=" C ASP E1499 " pdb=" N PRO E1500 " pdb=" CA PRO E1500 " ideal model delta sigma weight residual 119.56 128.13 -8.57 1.02e+00 9.61e-01 7.06e+01 ... (remaining 16593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.91: 7192 32.91 - 65.82: 85 65.82 - 98.73: 9 98.73 - 131.63: 1 131.63 - 164.54: 3 Dihedral angle restraints: 7290 sinusoidal: 2967 harmonic: 4323 Sorted by residual: dihedral pdb=" C10 FMN A 401 " pdb=" C1' FMN A 401 " pdb=" N10 FMN A 401 " pdb=" C2' FMN A 401 " ideal model delta sinusoidal sigma weight residual 257.59 93.05 164.54 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C5' FMN A 401 " pdb=" O5' FMN A 401 " pdb=" P FMN A 401 " pdb=" O1P FMN A 401 " ideal model delta sinusoidal sigma weight residual 75.26 -120.91 -163.83 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C10 FMN D 401 " pdb=" C1' FMN D 401 " pdb=" N10 FMN D 401 " pdb=" C2' FMN D 401 " ideal model delta sinusoidal sigma weight residual 257.59 102.93 154.66 1 2.00e+01 2.50e-03 4.57e+01 ... (remaining 7287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1306 0.103 - 0.206: 429 0.206 - 0.309: 73 0.309 - 0.412: 0 0.412 - 0.515: 2 Chirality restraints: 1810 Sorted by residual: chirality pdb=" CA PHE A 36 " pdb=" N PHE A 36 " pdb=" C PHE A 36 " pdb=" CB PHE A 36 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.62e+00 chirality pdb=" CA ARG E1120 " pdb=" N ARG E1120 " pdb=" C ARG E1120 " pdb=" CB ARG E1120 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.23e+00 chirality pdb=" CA LEU E1041 " pdb=" N LEU E1041 " pdb=" C LEU E1041 " pdb=" CB LEU E1041 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 1807 not shown) Planarity restraints: 2145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN A 401 " 0.683 2.00e-02 2.50e+03 2.38e-01 2.69e+03 pdb=" C10 FMN A 401 " 0.026 2.00e-02 2.50e+03 pdb=" C2 FMN A 401 " -0.240 2.00e-02 2.50e+03 pdb=" C4 FMN A 401 " 0.128 2.00e-02 2.50e+03 pdb=" C4A FMN A 401 " 0.105 2.00e-02 2.50e+03 pdb=" C5A FMN A 401 " 0.073 2.00e-02 2.50e+03 pdb=" C6 FMN A 401 " 0.004 2.00e-02 2.50e+03 pdb=" C7 FMN A 401 " -0.085 2.00e-02 2.50e+03 pdb=" C7M FMN A 401 " -0.148 2.00e-02 2.50e+03 pdb=" C8 FMN A 401 " -0.123 2.00e-02 2.50e+03 pdb=" C8M FMN A 401 " -0.235 2.00e-02 2.50e+03 pdb=" C9 FMN A 401 " -0.051 2.00e-02 2.50e+03 pdb=" C9A FMN A 401 " 0.056 2.00e-02 2.50e+03 pdb=" N1 FMN A 401 " -0.150 2.00e-02 2.50e+03 pdb=" N10 FMN A 401 " 0.151 2.00e-02 2.50e+03 pdb=" N3 FMN A 401 " 0.022 2.00e-02 2.50e+03 pdb=" N5 FMN A 401 " 0.132 2.00e-02 2.50e+03 pdb=" O2 FMN A 401 " -0.555 2.00e-02 2.50e+03 pdb=" O4 FMN A 401 " 0.209 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN D 401 " -0.777 2.00e-02 2.50e+03 2.29e-01 2.50e+03 pdb=" C10 FMN D 401 " 0.033 2.00e-02 2.50e+03 pdb=" C2 FMN D 401 " 0.220 2.00e-02 2.50e+03 pdb=" C4 FMN D 401 " -0.086 2.00e-02 2.50e+03 pdb=" C4A FMN D 401 " -0.079 2.00e-02 2.50e+03 pdb=" C5A FMN D 401 " -0.076 2.00e-02 2.50e+03 pdb=" C6 FMN D 401 " -0.049 2.00e-02 2.50e+03 pdb=" C7 FMN D 401 " 0.049 2.00e-02 2.50e+03 pdb=" C7M FMN D 401 " 0.050 2.00e-02 2.50e+03 pdb=" C8 FMN D 401 " 0.143 2.00e-02 2.50e+03 pdb=" C8M FMN D 401 " 0.245 2.00e-02 2.50e+03 pdb=" C9 FMN D 401 " 0.123 2.00e-02 2.50e+03 pdb=" C9A FMN D 401 " 0.001 2.00e-02 2.50e+03 pdb=" N1 FMN D 401 " 0.187 2.00e-02 2.50e+03 pdb=" N10 FMN D 401 " -0.055 2.00e-02 2.50e+03 pdb=" N3 FMN D 401 " 0.076 2.00e-02 2.50e+03 pdb=" N5 FMN D 401 " -0.148 2.00e-02 2.50e+03 pdb=" O2 FMN D 401 " 0.342 2.00e-02 2.50e+03 pdb=" O4 FMN D 401 " -0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 265 " -0.076 2.00e-02 2.50e+03 4.12e-02 3.40e+01 pdb=" CG TYR D 265 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR D 265 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR D 265 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR D 265 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR D 265 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR D 265 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR D 265 " -0.065 2.00e-02 2.50e+03 ... (remaining 2142 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3462 2.81 - 3.34: 11430 3.34 - 3.86: 20113 3.86 - 4.38: 24970 4.38 - 4.90: 38845 Nonbonded interactions: 98820 Sorted by model distance: nonbonded pdb=" N ILE A 274 " pdb=" O ILE A 274 " model vdw 2.293 2.496 nonbonded pdb=" N ASP E1478 " pdb=" OD1 ASP E1478 " model vdw 2.377 2.520 nonbonded pdb=" NZ LYS E1147 " pdb=" OD1 ASP E1613 " model vdw 2.382 2.520 nonbonded pdb=" OD2 ASP E1074 " pdb=" NZ LYS E1078 " model vdw 2.391 2.520 nonbonded pdb=" N LYS E1147 " pdb=" N GLN E1148 " model vdw 2.402 2.560 ... (remaining 98815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.620 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: 22.900 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 36.470 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 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 : 0.019 0.193 12222 Z= 1.251 Angle : 1.728 16.647 16598 Z= 1.183 Chirality : 0.097 0.515 1810 Planarity : 0.012 0.238 2145 Dihedral : 11.371 164.542 4512 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.34 % Allowed : 1.84 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.07 % 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: 0.65 (0.20), residues: 1466 helix: 0.01 (0.20), residues: 517 sheet: 0.91 (0.31), residues: 279 loop : 0.81 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.009 TRP E1323 HIS 0.010 0.002 HIS D 122 PHE 0.034 0.007 PHE D 162 TYR 0.076 0.010 TYR D 265 ARG 0.007 0.001 ARG D 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 MET cc_start: 0.8226 (mtt) cc_final: 0.7939 (mtt) REVERT: D 103 ILE cc_start: 0.8368 (pt) cc_final: 0.7982 (mt) REVERT: D 257 MET cc_start: 0.8811 (mmm) cc_final: 0.8443 (mmm) REVERT: E 984 MET cc_start: 0.5465 (ptm) cc_final: 0.4355 (ppp) REVERT: E 1018 MET cc_start: 0.7223 (mmm) cc_final: 0.6881 (tpp) REVERT: E 1079 LEU cc_start: 0.8598 (mt) cc_final: 0.8188 (pp) REVERT: E 1175 PHE cc_start: 0.9220 (t80) cc_final: 0.8938 (t80) REVERT: E 1207 TRP cc_start: 0.6880 (m100) cc_final: 0.6320 (m100) REVERT: E 1241 ASN cc_start: 0.8061 (m-40) cc_final: 0.7489 (m-40) REVERT: E 1366 MET cc_start: 0.8683 (mmm) cc_final: 0.8459 (mmm) REVERT: E 1525 MET cc_start: 0.8731 (tpp) cc_final: 0.8380 (tpp) REVERT: E 1665 MET cc_start: 0.8302 (ttt) cc_final: 0.7846 (tpp) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2961 time to fit residues: 84.6028 Evaluate side-chains 94 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 85 optimal weight: 0.0870 chunk 132 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1169 HIS E1560 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12222 Z= 0.212 Angle : 0.648 8.949 16598 Z= 0.347 Chirality : 0.045 0.157 1810 Planarity : 0.004 0.066 2145 Dihedral : 8.794 171.764 1637 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.18 % Favored : 97.61 % Rotamer: Outliers : 1.86 % Allowed : 5.21 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.99 (0.21), residues: 1466 helix: 0.82 (0.22), residues: 518 sheet: 0.73 (0.32), residues: 269 loop : 0.70 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E1076 HIS 0.009 0.001 HIS E1382 PHE 0.025 0.002 PHE E1150 TYR 0.015 0.001 TYR E1098 ARG 0.005 0.000 ARG E 904 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6984 (tpp) REVERT: E 932 MET cc_start: 0.4576 (mtm) cc_final: 0.4078 (mmt) REVERT: E 984 MET cc_start: 0.4972 (ptm) cc_final: 0.4255 (ppp) REVERT: E 1018 MET cc_start: 0.6944 (mmm) cc_final: 0.6594 (tpp) REVERT: E 1175 PHE cc_start: 0.9325 (t80) cc_final: 0.8853 (t80) REVERT: E 1185 MET cc_start: 0.7381 (tpp) cc_final: 0.6825 (ttm) REVERT: E 1525 MET cc_start: 0.8751 (tpp) cc_final: 0.8516 (tpp) REVERT: E 1624 ASP cc_start: 0.8268 (m-30) cc_final: 0.8001 (t0) REVERT: E 1665 MET cc_start: 0.8115 (ttt) cc_final: 0.7877 (tpp) outliers start: 24 outliers final: 13 residues processed: 144 average time/residue: 0.2339 time to fit residues: 51.3187 Evaluate side-chains 97 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain E residue 977 PHE Chi-restraints excluded: chain E residue 1011 SER Chi-restraints excluded: chain E residue 1101 VAL Chi-restraints excluded: chain E residue 1117 VAL Chi-restraints excluded: chain E residue 1165 LEU Chi-restraints excluded: chain E residue 1194 VAL Chi-restraints excluded: chain E residue 1226 ASP Chi-restraints excluded: chain E residue 1281 ASP Chi-restraints excluded: chain E residue 1313 ASP Chi-restraints excluded: chain E residue 1403 ASP Chi-restraints excluded: chain E residue 1418 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1087 GLN ** E1382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12222 Z= 0.291 Angle : 0.676 9.081 16598 Z= 0.355 Chirality : 0.046 0.146 1810 Planarity : 0.005 0.070 2145 Dihedral : 8.500 164.195 1637 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.14 % Favored : 96.73 % Rotamer: Outliers : 2.25 % Allowed : 7.30 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.58 (0.21), residues: 1466 helix: 0.83 (0.23), residues: 517 sheet: 0.33 (0.31), residues: 277 loop : 0.23 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E1518 HIS 0.008 0.002 HIS E1382 PHE 0.025 0.002 PHE E 850 TYR 0.025 0.002 TYR E 999 ARG 0.010 0.001 ARG E 891 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 88 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LYS cc_start: 0.7426 (pttt) cc_final: 0.7048 (mmmm) REVERT: D 257 MET cc_start: 0.9005 (mmm) cc_final: 0.8800 (mmm) REVERT: E 1024 MET cc_start: 0.6639 (ptp) cc_final: 0.6425 (ptm) REVERT: E 1185 MET cc_start: 0.7770 (tpp) cc_final: 0.7204 (ttm) REVERT: E 1207 TRP cc_start: 0.6864 (m100) cc_final: 0.6177 (m100) REVERT: E 1281 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7630 (p0) REVERT: E 1418 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8268 (tt) REVERT: E 1525 MET cc_start: 0.8852 (tpp) cc_final: 0.8629 (tpp) REVERT: E 1607 TYR cc_start: 0.9071 (OUTLIER) cc_final: 0.8697 (m-80) outliers start: 29 outliers final: 18 residues processed: 108 average time/residue: 0.2311 time to fit residues: 38.4651 Evaluate side-chains 93 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 72 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 977 PHE Chi-restraints excluded: chain E residue 1011 SER Chi-restraints excluded: chain E residue 1117 VAL Chi-restraints excluded: chain E residue 1194 VAL Chi-restraints excluded: chain E residue 1264 ASP Chi-restraints excluded: chain E residue 1281 ASP Chi-restraints excluded: chain E residue 1313 ASP Chi-restraints excluded: chain E residue 1401 ASP Chi-restraints excluded: chain E residue 1403 ASP Chi-restraints excluded: chain E residue 1418 LEU Chi-restraints excluded: chain E residue 1473 SER Chi-restraints excluded: chain E residue 1476 CYS Chi-restraints excluded: chain E residue 1520 THR Chi-restraints excluded: chain E residue 1583 TYR Chi-restraints excluded: chain E residue 1607 TYR Chi-restraints excluded: chain E residue 1659 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 HIS ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1382 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12222 Z= 0.191 Angle : 0.576 8.838 16598 Z= 0.296 Chirality : 0.043 0.153 1810 Planarity : 0.004 0.065 2145 Dihedral : 8.214 166.961 1637 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.21 % Favored : 96.59 % Rotamer: Outliers : 1.71 % Allowed : 8.08 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.22), residues: 1466 helix: 1.05 (0.23), residues: 514 sheet: 0.32 (0.31), residues: 279 loop : 0.35 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E1076 HIS 0.006 0.001 HIS E 998 PHE 0.013 0.001 PHE E1304 TYR 0.015 0.001 TYR E1036 ARG 0.003 0.000 ARG E1168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 LYS cc_start: 0.7436 (pttt) cc_final: 0.7136 (mmmm) REVERT: A 285 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7783 (m-30) REVERT: D 16 MET cc_start: 0.8236 (mtt) cc_final: 0.7884 (mtt) REVERT: D 257 MET cc_start: 0.9027 (mmm) cc_final: 0.8693 (mmm) REVERT: E 948 MET cc_start: 0.3454 (ttt) cc_final: 0.2687 (tpt) REVERT: E 984 MET cc_start: 0.4325 (ptm) cc_final: 0.4102 (ppp) REVERT: E 1018 MET cc_start: 0.6696 (tpp) cc_final: 0.6422 (tpp) REVERT: E 1024 MET cc_start: 0.7164 (ptp) cc_final: 0.6843 (ptt) REVERT: E 1168 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.7012 (ptm160) REVERT: E 1185 MET cc_start: 0.7828 (tpp) cc_final: 0.7319 (ttm) REVERT: E 1191 MET cc_start: 0.9033 (mmm) cc_final: 0.8775 (mmm) REVERT: E 1207 TRP cc_start: 0.6918 (m100) cc_final: 0.6169 (m100) REVERT: E 1593 TRP cc_start: 0.7255 (OUTLIER) cc_final: 0.6210 (p90) REVERT: E 1607 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.8274 (m-80) outliers start: 22 outliers final: 13 residues processed: 93 average time/residue: 0.2127 time to fit residues: 31.1298 Evaluate side-chains 83 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 977 PHE Chi-restraints excluded: chain E residue 1011 SER Chi-restraints excluded: chain E residue 1117 VAL Chi-restraints excluded: chain E residue 1168 ARG Chi-restraints excluded: chain E residue 1194 VAL Chi-restraints excluded: chain E residue 1313 ASP Chi-restraints excluded: chain E residue 1401 ASP Chi-restraints excluded: chain E residue 1583 TYR Chi-restraints excluded: chain E residue 1593 TRP Chi-restraints excluded: chain E residue 1607 TYR Chi-restraints excluded: chain E residue 1659 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 0.2980 chunk 80 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1001 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12222 Z= 0.199 Angle : 0.567 8.265 16598 Z= 0.292 Chirality : 0.043 0.150 1810 Planarity : 0.004 0.065 2145 Dihedral : 8.051 167.288 1637 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.89 % Favored : 95.91 % Rotamer: Outliers : 1.94 % Allowed : 9.01 % Favored : 89.04 % 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: 0.73 (0.22), residues: 1466 helix: 1.08 (0.23), residues: 516 sheet: 0.23 (0.31), residues: 283 loop : 0.29 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E1076 HIS 0.005 0.001 HIS E1001 PHE 0.012 0.001 PHE E 977 TYR 0.016 0.001 TYR E1036 ARG 0.004 0.000 ARG E1168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 71 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 VAL cc_start: 0.7055 (t) cc_final: 0.6850 (m) REVERT: D 16 MET cc_start: 0.8285 (mtt) cc_final: 0.7955 (mtt) REVERT: D 42 PHE cc_start: 0.6230 (OUTLIER) cc_final: 0.5729 (m-80) REVERT: D 140 ASP cc_start: 0.6811 (OUTLIER) cc_final: 0.6287 (t0) REVERT: E 932 MET cc_start: 0.5176 (ptt) cc_final: 0.2431 (mmt) REVERT: E 996 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7391 (tp) REVERT: E 1018 MET cc_start: 0.6978 (tpp) cc_final: 0.6735 (tpp) REVERT: E 1024 MET cc_start: 0.7121 (ptp) cc_final: 0.6848 (ptt) REVERT: E 1175 PHE cc_start: 0.9331 (t80) cc_final: 0.8766 (t80) REVERT: E 1207 TRP cc_start: 0.6903 (m100) cc_final: 0.6168 (m100) REVERT: E 1593 TRP cc_start: 0.7494 (OUTLIER) cc_final: 0.6434 (p90) REVERT: E 1607 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.8455 (m-80) outliers start: 25 outliers final: 15 residues processed: 92 average time/residue: 0.2059 time to fit residues: 30.0340 Evaluate side-chains 86 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 66 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain D residue 42 PHE Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 1011 SER Chi-restraints excluded: chain E residue 1117 VAL Chi-restraints excluded: chain E residue 1194 VAL Chi-restraints excluded: chain E residue 1313 ASP Chi-restraints excluded: chain E residue 1401 ASP Chi-restraints excluded: chain E residue 1403 ASP Chi-restraints excluded: chain E residue 1418 LEU Chi-restraints excluded: chain E residue 1473 SER Chi-restraints excluded: chain E residue 1583 TYR Chi-restraints excluded: chain E residue 1593 TRP Chi-restraints excluded: chain E residue 1607 TYR Chi-restraints excluded: chain E residue 1659 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.4980 chunk 127 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12222 Z= 0.192 Angle : 0.568 11.432 16598 Z= 0.286 Chirality : 0.043 0.152 1810 Planarity : 0.004 0.065 2145 Dihedral : 7.948 167.280 1637 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.48 % Favored : 96.32 % Rotamer: Outliers : 1.71 % Allowed : 9.87 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.22), residues: 1466 helix: 1.09 (0.24), residues: 515 sheet: 0.17 (0.31), residues: 285 loop : 0.24 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E1518 HIS 0.006 0.001 HIS E 998 PHE 0.012 0.001 PHE A 162 TYR 0.015 0.001 TYR E1036 ARG 0.003 0.000 ARG E1168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8347 (m-30) cc_final: 0.8137 (m-30) REVERT: A 153 MET cc_start: 0.6117 (ttp) cc_final: 0.5851 (ppp) REVERT: D 16 MET cc_start: 0.8361 (mtt) cc_final: 0.8015 (mtt) REVERT: D 42 PHE cc_start: 0.6175 (OUTLIER) cc_final: 0.5644 (m-80) REVERT: E 932 MET cc_start: 0.4811 (ptt) cc_final: 0.1902 (mmt) REVERT: E 984 MET cc_start: 0.2810 (ppp) cc_final: 0.2401 (ppp) REVERT: E 1018 MET cc_start: 0.6964 (tpp) cc_final: 0.6729 (tpp) REVERT: E 1024 MET cc_start: 0.7214 (ptp) cc_final: 0.6979 (ptt) REVERT: E 1175 PHE cc_start: 0.9300 (t80) cc_final: 0.8701 (t80) REVERT: E 1185 MET cc_start: 0.7909 (tpp) cc_final: 0.7402 (ttm) REVERT: E 1252 MET cc_start: 0.7153 (tpt) cc_final: 0.6901 (tpt) REVERT: E 1593 TRP cc_start: 0.7607 (OUTLIER) cc_final: 0.6490 (p90) REVERT: E 1607 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.8483 (m-80) outliers start: 22 outliers final: 16 residues processed: 96 average time/residue: 0.2001 time to fit residues: 30.6456 Evaluate side-chains 91 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 72 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 TRP Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain D residue 42 PHE Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 1011 SER Chi-restraints excluded: chain E residue 1111 LEU Chi-restraints excluded: chain E residue 1117 VAL Chi-restraints excluded: chain E residue 1194 VAL Chi-restraints excluded: chain E residue 1401 ASP Chi-restraints excluded: chain E residue 1418 LEU Chi-restraints excluded: chain E residue 1473 SER Chi-restraints excluded: chain E residue 1583 TYR Chi-restraints excluded: chain E residue 1593 TRP Chi-restraints excluded: chain E residue 1607 TYR Chi-restraints excluded: chain E residue 1659 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 140 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 64 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.5374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12222 Z= 0.169 Angle : 0.560 10.101 16598 Z= 0.280 Chirality : 0.043 0.152 1810 Planarity : 0.004 0.064 2145 Dihedral : 7.833 167.829 1637 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.62 % Favored : 96.18 % Rotamer: Outliers : 1.94 % Allowed : 10.41 % Favored : 87.65 % 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: 0.67 (0.23), residues: 1466 helix: 1.11 (0.24), residues: 514 sheet: 0.14 (0.31), residues: 285 loop : 0.21 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E1518 HIS 0.005 0.001 HIS E 998 PHE 0.016 0.001 PHE E 977 TYR 0.014 0.001 TYR E1036 ARG 0.003 0.000 ARG E1168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 76 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 MET cc_start: 0.8438 (mtt) cc_final: 0.8074 (mtt) REVERT: D 42 PHE cc_start: 0.6328 (OUTLIER) cc_final: 0.5791 (m-80) REVERT: E 932 MET cc_start: 0.4604 (ptt) cc_final: 0.1740 (mmt) REVERT: E 948 MET cc_start: 0.4030 (tpt) cc_final: 0.3632 (tpp) REVERT: E 977 PHE cc_start: 0.5802 (p90) cc_final: 0.5397 (p90) REVERT: E 984 MET cc_start: 0.2638 (ppp) cc_final: 0.2218 (ppp) REVERT: E 1018 MET cc_start: 0.6998 (tpp) cc_final: 0.6773 (tpp) REVERT: E 1024 MET cc_start: 0.7273 (ptp) cc_final: 0.7072 (ptt) REVERT: E 1175 PHE cc_start: 0.9266 (t80) cc_final: 0.8668 (t80) REVERT: E 1185 MET cc_start: 0.7953 (tpp) cc_final: 0.7476 (ttm) REVERT: E 1191 MET cc_start: 0.9047 (mmm) cc_final: 0.8715 (mmm) REVERT: E 1207 TRP cc_start: 0.6820 (m100) cc_final: 0.6189 (m100) REVERT: E 1252 MET cc_start: 0.7040 (tpt) cc_final: 0.6822 (tpt) REVERT: E 1593 TRP cc_start: 0.7672 (OUTLIER) cc_final: 0.6643 (p90) outliers start: 25 outliers final: 19 residues processed: 96 average time/residue: 0.2025 time to fit residues: 31.1413 Evaluate side-chains 90 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 69 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 TRP Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain D residue 42 PHE Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 1011 SER Chi-restraints excluded: chain E residue 1117 VAL Chi-restraints excluded: chain E residue 1194 VAL Chi-restraints excluded: chain E residue 1313 ASP Chi-restraints excluded: chain E residue 1396 CYS Chi-restraints excluded: chain E residue 1401 ASP Chi-restraints excluded: chain E residue 1404 LEU Chi-restraints excluded: chain E residue 1418 LEU Chi-restraints excluded: chain E residue 1473 SER Chi-restraints excluded: chain E residue 1476 CYS Chi-restraints excluded: chain E residue 1583 TYR Chi-restraints excluded: chain E residue 1593 TRP Chi-restraints excluded: chain E residue 1659 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12222 Z= 0.398 Angle : 0.735 12.417 16598 Z= 0.381 Chirality : 0.047 0.154 1810 Planarity : 0.005 0.071 2145 Dihedral : 8.177 163.531 1637 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.91 % Favored : 94.88 % Rotamer: Outliers : 2.02 % Allowed : 11.11 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.07 (0.22), residues: 1466 helix: 0.65 (0.23), residues: 500 sheet: -0.03 (0.32), residues: 273 loop : -0.24 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP E1518 HIS 0.008 0.002 HIS E 900 PHE 0.023 0.002 PHE D 39 TYR 0.022 0.002 TYR E 999 ARG 0.008 0.001 ARG E1168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 69 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 16 MET cc_start: 0.8462 (mtt) cc_final: 0.8132 (mtt) REVERT: D 42 PHE cc_start: 0.6383 (OUTLIER) cc_final: 0.5762 (m-80) REVERT: D 56 PHE cc_start: 0.8462 (m-80) cc_final: 0.7951 (m-80) REVERT: E 1018 MET cc_start: 0.6944 (tpp) cc_final: 0.6687 (tpp) REVERT: E 1024 MET cc_start: 0.7338 (ptp) cc_final: 0.7117 (ptt) REVERT: E 1175 PHE cc_start: 0.9274 (t80) cc_final: 0.8720 (t80) REVERT: E 1252 MET cc_start: 0.7521 (tpt) cc_final: 0.7223 (tpt) REVERT: E 1593 TRP cc_start: 0.7892 (OUTLIER) cc_final: 0.6686 (p90) outliers start: 26 outliers final: 24 residues processed: 91 average time/residue: 0.2037 time to fit residues: 29.9749 Evaluate side-chains 89 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 63 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain D residue 42 PHE Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain E residue 1011 SER Chi-restraints excluded: chain E residue 1111 LEU Chi-restraints excluded: chain E residue 1117 VAL Chi-restraints excluded: chain E residue 1194 VAL Chi-restraints excluded: chain E residue 1313 ASP Chi-restraints excluded: chain E residue 1396 CYS Chi-restraints excluded: chain E residue 1401 ASP Chi-restraints excluded: chain E residue 1404 LEU Chi-restraints excluded: chain E residue 1418 LEU Chi-restraints excluded: chain E residue 1473 SER Chi-restraints excluded: chain E residue 1476 CYS Chi-restraints excluded: chain E residue 1532 VAL Chi-restraints excluded: chain E residue 1583 TYR Chi-restraints excluded: chain E residue 1593 TRP Chi-restraints excluded: chain E residue 1659 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.5885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12222 Z= 0.187 Angle : 0.578 12.296 16598 Z= 0.293 Chirality : 0.043 0.151 1810 Planarity : 0.004 0.068 2145 Dihedral : 7.974 167.647 1637 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.48 % Favored : 96.18 % Rotamer: Outliers : 1.71 % Allowed : 11.81 % Favored : 86.48 % 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: 0.37 (0.23), residues: 1466 helix: 1.00 (0.24), residues: 506 sheet: -0.06 (0.32), residues: 281 loop : -0.08 (0.25), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E1076 HIS 0.005 0.001 HIS E 998 PHE 0.028 0.001 PHE E1151 TYR 0.016 0.001 TYR E1036 ARG 0.006 0.000 ARG E1504 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 68 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 16 MET cc_start: 0.8476 (mtt) cc_final: 0.8157 (mtt) REVERT: D 42 PHE cc_start: 0.6318 (OUTLIER) cc_final: 0.5676 (m-80) REVERT: D 56 PHE cc_start: 0.8404 (m-80) cc_final: 0.8029 (m-80) REVERT: D 279 LEU cc_start: 0.8610 (tp) cc_final: 0.8389 (tp) REVERT: E 932 MET cc_start: 0.4641 (ptt) cc_final: 0.1964 (mmt) REVERT: E 948 MET cc_start: 0.4703 (tpp) cc_final: 0.4385 (tpp) REVERT: E 1018 MET cc_start: 0.6762 (tpp) cc_final: 0.6482 (tpp) REVERT: E 1175 PHE cc_start: 0.9235 (t80) cc_final: 0.8646 (t80) REVERT: E 1185 MET cc_start: 0.7983 (tpp) cc_final: 0.7530 (ttm) REVERT: E 1191 MET cc_start: 0.8976 (mmm) cc_final: 0.8621 (mmm) REVERT: E 1252 MET cc_start: 0.7197 (tpt) cc_final: 0.6926 (tpt) REVERT: E 1593 TRP cc_start: 0.7796 (OUTLIER) cc_final: 0.6738 (p90) outliers start: 22 outliers final: 18 residues processed: 85 average time/residue: 0.1998 time to fit residues: 27.8960 Evaluate side-chains 86 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 66 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain D residue 42 PHE Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 1011 SER Chi-restraints excluded: chain E residue 1111 LEU Chi-restraints excluded: chain E residue 1117 VAL Chi-restraints excluded: chain E residue 1183 HIS Chi-restraints excluded: chain E residue 1194 VAL Chi-restraints excluded: chain E residue 1396 CYS Chi-restraints excluded: chain E residue 1401 ASP Chi-restraints excluded: chain E residue 1404 LEU Chi-restraints excluded: chain E residue 1418 LEU Chi-restraints excluded: chain E residue 1583 TYR Chi-restraints excluded: chain E residue 1593 TRP Chi-restraints excluded: chain E residue 1659 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 0.0050 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 145 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 chunk 89 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.5966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12222 Z= 0.139 Angle : 0.545 13.098 16598 Z= 0.271 Chirality : 0.042 0.151 1810 Planarity : 0.004 0.064 2145 Dihedral : 7.759 169.473 1637 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.48 % Favored : 96.25 % Rotamer: Outliers : 1.40 % Allowed : 12.43 % Favored : 86.17 % 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: 0.62 (0.23), residues: 1466 helix: 1.19 (0.24), residues: 507 sheet: 0.13 (0.32), residues: 278 loop : 0.06 (0.25), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E1076 HIS 0.004 0.001 HIS E 998 PHE 0.018 0.001 PHE E1150 TYR 0.012 0.001 TYR E1036 ARG 0.005 0.000 ARG E1504 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.5738 (tpt90) cc_final: 0.5091 (tpt90) REVERT: D 16 MET cc_start: 0.8529 (mtt) cc_final: 0.8192 (mtt) REVERT: D 42 PHE cc_start: 0.6319 (OUTLIER) cc_final: 0.5716 (m-80) REVERT: D 56 PHE cc_start: 0.8412 (m-80) cc_final: 0.8148 (m-80) REVERT: D 257 MET cc_start: 0.8963 (tpp) cc_final: 0.8446 (mmm) REVERT: D 279 LEU cc_start: 0.8607 (tp) cc_final: 0.8396 (tp) REVERT: E 932 MET cc_start: 0.4706 (ptt) cc_final: 0.1823 (mmt) REVERT: E 948 MET cc_start: 0.4283 (tpp) cc_final: 0.3806 (tpp) REVERT: E 984 MET cc_start: 0.2951 (ppp) cc_final: 0.2436 (ppp) REVERT: E 1018 MET cc_start: 0.6272 (tpp) cc_final: 0.6028 (tpp) REVERT: E 1024 MET cc_start: 0.8056 (ptt) cc_final: 0.7822 (mmt) REVERT: E 1175 PHE cc_start: 0.9235 (t80) cc_final: 0.8605 (t80) REVERT: E 1185 MET cc_start: 0.7936 (tpp) cc_final: 0.7461 (ttm) REVERT: E 1191 MET cc_start: 0.9015 (mmm) cc_final: 0.8756 (mmm) REVERT: E 1593 TRP cc_start: 0.7750 (OUTLIER) cc_final: 0.6710 (p90) outliers start: 18 outliers final: 14 residues processed: 87 average time/residue: 0.1979 time to fit residues: 27.6055 Evaluate side-chains 83 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 67 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 TRP Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain D residue 42 PHE Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 1011 SER Chi-restraints excluded: chain E residue 1111 LEU Chi-restraints excluded: chain E residue 1117 VAL Chi-restraints excluded: chain E residue 1194 VAL Chi-restraints excluded: chain E residue 1396 CYS Chi-restraints excluded: chain E residue 1401 ASP Chi-restraints excluded: chain E residue 1418 LEU Chi-restraints excluded: chain E residue 1583 TYR Chi-restraints excluded: chain E residue 1593 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 119 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 913 GLN ** 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 = 0.3751 r_free = 0.3751 target = 0.084528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.071544 restraints weight = 49548.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.073200 restraints weight = 26861.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.074273 restraints weight = 17860.884| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.6045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12222 Z= 0.158 Angle : 0.557 12.672 16598 Z= 0.277 Chirality : 0.042 0.152 1810 Planarity : 0.004 0.064 2145 Dihedral : 7.704 168.954 1637 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.41 % Favored : 96.32 % Rotamer: Outliers : 1.40 % Allowed : 12.43 % Favored : 86.17 % 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: 0.66 (0.23), residues: 1466 helix: 1.22 (0.24), residues: 507 sheet: 0.12 (0.32), residues: 278 loop : 0.11 (0.25), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E1076 HIS 0.003 0.001 HIS E 998 PHE 0.025 0.001 PHE E1151 TYR 0.020 0.001 TYR D 113 ARG 0.004 0.000 ARG E1504 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2373.75 seconds wall clock time: 44 minutes 37.88 seconds (2677.88 seconds total)