Starting phenix.real_space_refine on Wed Feb 14 17:12:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/02_2024/6pza_20530_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/02_2024/6pza_20530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/02_2024/6pza_20530.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/02_2024/6pza_20530.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/02_2024/6pza_20530_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pza_20530/02_2024/6pza_20530_neut_updated.pdb" } resolution = 3.74 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 3 5.49 5 S 34 5.16 5 Cl 1 4.86 5 C 6209 2.51 5 N 1717 2.21 5 O 1695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 16": "NH1" <-> "NH2" Residue "C TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 258": "NH1" <-> "NH2" Residue "C ARG 285": "NH1" <-> "NH2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C ARG 298": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 598": "NH1" <-> "NH2" Residue "C ARG 702": "NH1" <-> "NH2" Residue "C ARG 837": "NH1" <-> "NH2" Residue "C ARG 1104": "NH1" <-> "NH2" Residue "C ARG 1218": "NH1" <-> "NH2" Residue "C ARG 1300": "NH1" <-> "NH2" 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: 9659 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 9501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1422, 9501 Classifications: {'peptide': 1422} Incomplete info: {'truncation_to_alanine': 543} Link IDs: {'CIS': 1, 'PTRANS': 48, 'TRANS': 1372} Chain breaks: 4 Unresolved non-hydrogen bonds: 1768 Unresolved non-hydrogen angles: 2233 Unresolved non-hydrogen dihedrals: 1378 Unresolved non-hydrogen chiralities: 225 Planarities with less than four sites: {'GLN:plan1': 32, 'ASP:plan': 41, 'TYR:plan': 2, 'ASN:plan1': 21, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 17, 'GLU:plan': 44, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 833 Chain: "D" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 94 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 17} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'ATP': 1, 'GBM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.73, per 1000 atoms: 0.59 Number of scatterers: 9659 At special positions: 0 Unit cell: (96.615, 110.295, 140.22, 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 34 16.00 P 3 15.00 O 1695 8.00 N 1717 7.00 C 6209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 26 " distance=2.02 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: 4.09 Conformation dependent library (CDL) restraints added in 2.0 seconds 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2730 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 6 sheets defined 60.5% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.07 Creating SS restraints... Processing helix chain 'C' and resid 13 through 15 No H-bonds generated for 'chain 'C' and resid 13 through 15' Processing helix chain 'C' and resid 27 through 54 removed outlier: 3.885A pdb=" N VAL C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) Proline residue: C 35 - end of helix Proline residue: C 45 - end of helix Processing helix chain 'C' and resid 59 through 62 removed outlier: 4.448A pdb=" N HIS C 62 " --> pdb=" O HIS C 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 59 through 62' Processing helix chain 'C' and resid 72 through 96 Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 109 through 128 removed outlier: 3.599A pdb=" N TYR C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 159 removed outlier: 3.651A pdb=" N ILE C 137 " --> pdb=" O LYS C 134 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA C 138 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 139 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE C 141 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR C 144 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 146 " --> pdb=" O TRP C 143 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE C 147 " --> pdb=" O THR C 144 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C 149 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C 150 " --> pdb=" O PHE C 147 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 155 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 193 Processing helix chain 'C' and resid 208 through 211 No H-bonds generated for 'chain 'C' and resid 208 through 211' Processing helix chain 'C' and resid 224 through 229 Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 255 through 257 No H-bonds generated for 'chain 'C' and resid 255 through 257' Processing helix chain 'C' and resid 259 through 276 Processing helix chain 'C' and resid 284 through 327 removed outlier: 5.732A pdb=" N ARG C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ARG C 298 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY C 316 " --> pdb=" O LEU C 312 " (cutoff:3.500A) Proline residue: C 317 - end of helix Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 348 through 352 Processing helix chain 'C' and resid 356 through 397 removed outlier: 3.505A pdb=" N LEU C 368 " --> pdb=" O LEU C 364 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLN C 374 " --> pdb=" O ARG C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 433 removed outlier: 3.554A pdb=" N ASP C 424 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR C 425 " --> pdb=" O VAL C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 455 removed outlier: 3.822A pdb=" N TRP C 439 " --> pdb=" O CYS C 435 " (cutoff:3.500A) Proline residue: C 442 - end of helix Processing helix chain 'C' and resid 458 through 469 Processing helix chain 'C' and resid 471 through 503 removed outlier: 4.128A pdb=" N GLU C 494 " --> pdb=" O GLU C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 511 Processing helix chain 'C' and resid 516 through 563 removed outlier: 4.277A pdb=" N THR C 525 " --> pdb=" O ARG C 521 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER C 543 " --> pdb=" O TYR C 539 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 544 " --> pdb=" O THR C 540 " (cutoff:3.500A) Proline residue: C 551 - end of helix Processing helix chain 'C' and resid 573 through 614 Proline residue: C 589 - end of helix removed outlier: 3.972A pdb=" N LEU C 592 " --> pdb=" O THR C 588 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 594 " --> pdb=" O LEU C 590 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 595 " --> pdb=" O PHE C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 726 Processing helix chain 'C' and resid 786 through 789 No H-bonds generated for 'chain 'C' and resid 786 through 789' Processing helix chain 'C' and resid 796 through 805 Processing helix chain 'C' and resid 809 through 814 Processing helix chain 'C' and resid 832 through 845 Processing helix chain 'C' and resid 863 through 878 Processing helix chain 'C' and resid 914 through 917 No H-bonds generated for 'chain 'C' and resid 914 through 917' Processing helix chain 'C' and resid 997 through 1008 Processing helix chain 'C' and resid 1010 through 1042 removed outlier: 4.494A pdb=" N LEU C1015 " --> pdb=" O LEU C1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 1061 through 1106 removed outlier: 3.906A pdb=" N LEU C1074 " --> pdb=" O LEU C1070 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU C1087 " --> pdb=" O SER C1083 " (cutoff:3.500A) Processing helix chain 'C' and resid 1110 through 1115 Processing helix chain 'C' and resid 1118 through 1134 removed outlier: 4.733A pdb=" N ASP C1128 " --> pdb=" O ARG C1124 " (cutoff:3.500A) Processing helix chain 'C' and resid 1136 through 1160 removed outlier: 4.000A pdb=" N LEU C1148 " --> pdb=" O SER C1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 1164 through 1209 Proline residue: C1170 - end of helix removed outlier: 3.720A pdb=" N ASP C1188 " --> pdb=" O VAL C1184 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C1196 " --> pdb=" O LEU C1192 " (cutoff:3.500A) Proline residue: C1199 - end of helix removed outlier: 3.587A pdb=" N VAL C1208 " --> pdb=" O PHE C1204 " (cutoff:3.500A) Processing helix chain 'C' and resid 1211 through 1216 Processing helix chain 'C' and resid 1220 through 1272 removed outlier: 3.666A pdb=" N ALA C1237 " --> pdb=" O SER C1233 " (cutoff:3.500A) Processing helix chain 'C' and resid 1279 through 1291 removed outlier: 3.914A pdb=" N TYR C1287 " --> pdb=" O LEU C1283 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N MET C1290 " --> pdb=" O THR C1286 " (cutoff:3.500A) Processing helix chain 'C' and resid 1295 through 1319 removed outlier: 3.806A pdb=" N ALA C1311 " --> pdb=" O ILE C1307 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL C1312 " --> pdb=" O GLN C1308 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE C1315 " --> pdb=" O ALA C1311 " (cutoff:3.500A) Processing helix chain 'C' and resid 1386 through 1393 removed outlier: 4.668A pdb=" N PHE C1393 " --> pdb=" O SER C1389 " (cutoff:3.500A) Processing helix chain 'C' and resid 1415 through 1418 No H-bonds generated for 'chain 'C' and resid 1415 through 1418' Processing helix chain 'C' and resid 1436 through 1441 Processing helix chain 'C' and resid 1448 through 1457 Processing helix chain 'C' and resid 1461 through 1464 No H-bonds generated for 'chain 'C' and resid 1461 through 1464' Processing helix chain 'C' and resid 1485 through 1497 Processing helix chain 'C' and resid 1513 through 1529 Processing helix chain 'C' and resid 1540 through 1542 No H-bonds generated for 'chain 'C' and resid 1540 through 1542' Processing helix chain 'C' and resid 1565 through 1569 Processing helix chain 'C' and resid 1572 through 1577 Processing sheet with id= A, first strand: chain 'C' and resid 338 through 340 removed outlier: 4.227A pdb=" N THR C 338 " --> pdb=" O PHE C 345 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 679 through 681 Processing sheet with id= C, first strand: chain 'C' and resid 708 through 711 removed outlier: 6.611A pdb=" N VAL C 884 " --> pdb=" O THR C 709 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE C 711 " --> pdb=" O VAL C 884 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU C 886 " --> pdb=" O ILE C 711 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 1346 through 1348 Processing sheet with id= E, first strand: chain 'C' and resid 1422 through 1424 removed outlier: 6.435A pdb=" N ILE C1502 " --> pdb=" O SER C1423 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 1549 through 1551 616 hydrogen bonds defined for protein. 1791 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: 3.57 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1543 1.31 - 1.43: 2702 1.43 - 1.56: 5567 1.56 - 1.68: 7 1.68 - 1.81: 53 Bond restraints: 9872 Sorted by residual: bond pdb=" O5 GBM C1601 " pdb=" S2 GBM C1601 " ideal model delta sigma weight residual 1.448 1.648 -0.200 2.00e-02 2.50e+03 9.97e+01 bond pdb=" O4 GBM C1601 " pdb=" S2 GBM C1601 " ideal model delta sigma weight residual 1.453 1.647 -0.194 2.00e-02 2.50e+03 9.43e+01 bond pdb=" C4 ATP C1602 " pdb=" C5 ATP C1602 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.26e+01 bond pdb=" C5 ATP C1602 " pdb=" C6 ATP C1602 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.31e+01 bond pdb=" C17 GBM C1601 " pdb=" N8 GBM C1601 " ideal model delta sigma weight residual 1.340 1.443 -0.103 2.00e-02 2.50e+03 2.65e+01 ... (remaining 9867 not shown) Histogram of bond angle deviations from ideal: 98.60 - 106.00: 216 106.00 - 113.41: 5478 113.41 - 120.81: 4781 120.81 - 128.22: 3000 128.22 - 135.62: 101 Bond angle restraints: 13576 Sorted by residual: angle pdb=" PB ATP C1602 " pdb=" O3B ATP C1602 " pdb=" PG ATP C1602 " ideal model delta sigma weight residual 139.87 117.67 22.20 1.00e+00 1.00e+00 4.93e+02 angle pdb=" PA ATP C1602 " pdb=" O3A ATP C1602 " pdb=" PB ATP C1602 " ideal model delta sigma weight residual 136.83 117.58 19.25 1.00e+00 1.00e+00 3.70e+02 angle pdb=" C5 ATP C1602 " pdb=" C4 ATP C1602 " pdb=" N3 ATP C1602 " ideal model delta sigma weight residual 126.80 119.13 7.67 1.00e+00 1.00e+00 5.88e+01 angle pdb=" C LEU C 571 " pdb=" N SER C 572 " pdb=" CA SER C 572 " ideal model delta sigma weight residual 121.70 134.37 -12.67 1.80e+00 3.09e-01 4.95e+01 angle pdb=" N3 ATP C1602 " pdb=" C4 ATP C1602 " pdb=" N9 ATP C1602 " ideal model delta sigma weight residual 127.04 135.10 -8.06 1.15e+00 7.59e-01 4.93e+01 ... (remaining 13571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 5444 16.79 - 33.58: 219 33.58 - 50.37: 47 50.37 - 67.16: 6 67.16 - 83.95: 5 Dihedral angle restraints: 5721 sinusoidal: 1521 harmonic: 4200 Sorted by residual: dihedral pdb=" CA LYS C 252 " pdb=" C LYS C 252 " pdb=" N LEU C 253 " pdb=" CA LEU C 253 " ideal model delta harmonic sigma weight residual 180.00 132.03 47.97 0 5.00e+00 4.00e-02 9.20e+01 dihedral pdb=" CA ILE C 996 " pdb=" C ILE C 996 " pdb=" N PRO C 997 " pdb=" CA PRO C 997 " ideal model delta harmonic sigma weight residual -180.00 -137.86 -42.14 0 5.00e+00 4.00e-02 7.10e+01 dihedral pdb=" CA LYS C1562 " pdb=" C LYS C1562 " pdb=" N PRO C1563 " pdb=" CA PRO C1563 " ideal model delta harmonic sigma weight residual 180.00 151.85 28.15 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 5718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1144 0.056 - 0.111: 416 0.111 - 0.167: 75 0.167 - 0.222: 7 0.222 - 0.278: 4 Chirality restraints: 1646 Sorted by residual: chirality pdb=" CG LEU C1248 " pdb=" CB LEU C1248 " pdb=" CD1 LEU C1248 " pdb=" CD2 LEU C1248 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA LEU C 175 " pdb=" N LEU C 175 " pdb=" C LEU C 175 " pdb=" CB LEU C 175 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C1' ATP C1602 " pdb=" C2' ATP C1602 " pdb=" N9 ATP C1602 " pdb=" O4' ATP C1602 " both_signs ideal model delta sigma weight residual False 2.41 2.64 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1643 not shown) Planarity restraints: 1752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 420 " -0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C LEU C 420 " 0.058 2.00e-02 2.50e+03 pdb=" O LEU C 420 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL C 421 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET C 441 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO C 442 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 442 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 442 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1037 " 0.023 2.00e-02 2.50e+03 1.62e-02 6.53e+00 pdb=" CG TRP C1037 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP C1037 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP C1037 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C1037 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C1037 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C1037 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1037 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1037 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C1037 " 0.000 2.00e-02 2.50e+03 ... (remaining 1749 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2266 2.78 - 3.31: 9221 3.31 - 3.84: 15515 3.84 - 4.37: 16416 4.37 - 4.90: 28420 Nonbonded interactions: 71838 Sorted by model distance: nonbonded pdb=" OH TYR C 123 " pdb=" O LEU C 135 " model vdw 2.252 2.440 nonbonded pdb=" OD2 ASP C1128 " pdb=" NH1 ARG C1314 " model vdw 2.271 2.520 nonbonded pdb=" O GLU C 791 " pdb=" OH TYR C1219 " model vdw 2.287 2.440 nonbonded pdb=" OG1 THR C 338 " pdb=" O PHE C 345 " model vdw 2.291 2.440 nonbonded pdb=" O THR C 789 " pdb=" OG SER C 792 " model vdw 2.308 2.440 ... (remaining 71833 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 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: 0.000 Extract box with map and model: 2.650 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 30.680 Find NCS groups from input model: 0.290 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5080 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 : 0.008 0.200 9872 Z= 0.530 Angle : 1.063 22.204 13576 Z= 0.612 Chirality : 0.058 0.278 1646 Planarity : 0.008 0.065 1752 Dihedral : 11.133 83.951 2988 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: -4.29 (0.17), residues: 1429 helix: -2.33 (0.12), residues: 915 sheet: -3.78 (0.52), residues: 60 loop : -3.46 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP C1037 HIS 0.012 0.002 HIS C1098 PHE 0.040 0.003 PHE C 432 TYR 0.033 0.003 TYR C 179 ARG 0.014 0.002 ARG C1145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: C 112 MET cc_start: 0.6739 (mtm) cc_final: 0.6412 (mtp) REVERT: C 301 LEU cc_start: 0.6998 (tp) cc_final: 0.6398 (tt) REVERT: C 393 THR cc_start: 0.5310 (m) cc_final: 0.5049 (t) REVERT: C 1163 VAL cc_start: 0.6894 (t) cc_final: 0.6651 (t) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.2208 time to fit residues: 68.3033 Evaluate side-chains 143 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 50.0000 chunk 108 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 0.1980 chunk 57 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 83 optimal weight: 50.0000 chunk 129 optimal weight: 50.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 160 HIS C 219 GLN C 262 ASN C 374 GLN ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 707 GLN ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1197 GLN ** C1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5797 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9872 Z= 0.254 Angle : 0.720 10.541 13576 Z= 0.373 Chirality : 0.045 0.261 1646 Planarity : 0.006 0.049 1752 Dihedral : 6.788 77.421 1561 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.76 % Allowed : 10.95 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: -1.88 (0.21), residues: 1429 helix: -0.17 (0.16), residues: 920 sheet: -3.54 (0.55), residues: 60 loop : -3.12 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 288 HIS 0.006 0.001 HIS C1098 PHE 0.020 0.002 PHE C 432 TYR 0.028 0.002 TYR C 123 ARG 0.011 0.001 ARG C 289 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 188 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.6532 (mpp) cc_final: 0.6322 (mpp) REVERT: C 424 ASP cc_start: 0.5944 (m-30) cc_final: 0.5701 (m-30) REVERT: C 1030 ILE cc_start: 0.6590 (tp) cc_final: 0.5933 (pt) outliers start: 33 outliers final: 18 residues processed: 208 average time/residue: 0.2015 time to fit residues: 59.7401 Evaluate side-chains 179 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 161 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 435 CYS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1192 LEU Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1242 THR Chi-restraints excluded: chain C residue 1269 SER Chi-restraints excluded: chain C residue 1272 LEU Chi-restraints excluded: chain C residue 1298 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 0.0370 chunk 108 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 140 optimal weight: 0.0870 chunk 115 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 ASN C 125 HIS ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1245 ASN C1301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6053 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9872 Z= 0.184 Angle : 0.603 8.544 13576 Z= 0.308 Chirality : 0.042 0.163 1646 Planarity : 0.004 0.044 1752 Dihedral : 6.256 75.871 1561 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.76 % Allowed : 15.99 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.22), residues: 1429 helix: 0.76 (0.17), residues: 925 sheet: -3.26 (0.58), residues: 60 loop : -2.91 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 430 HIS 0.004 0.001 HIS C 326 PHE 0.017 0.002 PHE C 433 TYR 0.016 0.002 TYR C 845 ARG 0.006 0.001 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 175 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 134 LYS cc_start: 0.8741 (tptm) cc_final: 0.8508 (tppp) REVERT: C 1030 ILE cc_start: 0.6462 (tp) cc_final: 0.6051 (pt) outliers start: 40 outliers final: 21 residues processed: 192 average time/residue: 0.1789 time to fit residues: 51.1242 Evaluate side-chains 172 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1154 LEU Chi-restraints excluded: chain C residue 1192 LEU Chi-restraints excluded: chain C residue 1242 THR Chi-restraints excluded: chain C residue 1253 GLU Chi-restraints excluded: chain C residue 1283 LEU Chi-restraints excluded: chain C residue 1293 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 67 optimal weight: 50.0000 chunk 14 optimal weight: 7.9990 chunk 62 optimal weight: 30.0000 chunk 87 optimal weight: 10.0000 chunk 130 optimal weight: 40.0000 chunk 138 optimal weight: 50.0000 chunk 68 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 HIS C 105 HIS ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1301 ASN C1316 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.8531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 9872 Z= 0.404 Angle : 0.841 13.570 13576 Z= 0.434 Chirality : 0.050 0.249 1646 Planarity : 0.006 0.083 1752 Dihedral : 7.043 79.592 1561 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 8.79 % Allowed : 17.00 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: -1.10 (0.22), residues: 1429 helix: 0.51 (0.17), residues: 901 sheet: -3.59 (0.59), residues: 45 loop : -2.87 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 65 HIS 0.010 0.002 HIS C1024 PHE 0.033 0.003 PHE C 591 TYR 0.032 0.003 TYR C1254 ARG 0.011 0.001 ARG C1099 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 201 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 134 LYS cc_start: 0.8965 (tptm) cc_final: 0.8633 (tppp) REVERT: C 158 TYR cc_start: 0.8016 (t80) cc_final: 0.7289 (t80) REVERT: C 170 CYS cc_start: 0.7597 (m) cc_final: 0.7178 (p) REVERT: C 369 GLN cc_start: 0.8434 (tt0) cc_final: 0.8225 (tt0) REVERT: C 426 ASN cc_start: 0.8664 (t0) cc_final: 0.8377 (t0) REVERT: C 434 LEU cc_start: 0.8735 (mm) cc_final: 0.8497 (mm) REVERT: C 452 LEU cc_start: 0.8180 (tp) cc_final: 0.7915 (tp) REVERT: C 483 GLN cc_start: 0.8549 (tt0) cc_final: 0.7845 (tm-30) REVERT: C 528 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7071 (mtpt) REVERT: C 602 LYS cc_start: 0.8339 (mttt) cc_final: 0.8107 (mtpt) REVERT: C 1091 LEU cc_start: 0.8105 (tp) cc_final: 0.7789 (tt) REVERT: C 1191 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7311 (mm110) REVERT: C 1229 GLU cc_start: 0.8197 (tp30) cc_final: 0.7836 (tm-30) outliers start: 61 outliers final: 33 residues processed: 238 average time/residue: 0.2050 time to fit residues: 69.1524 Evaluate side-chains 195 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 160 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1165 LEU Chi-restraints excluded: chain C residue 1173 VAL Chi-restraints excluded: chain C residue 1191 GLN Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1231 THR Chi-restraints excluded: chain C residue 1250 VAL Chi-restraints excluded: chain C residue 1253 GLU Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1266 THR Chi-restraints excluded: chain C residue 1272 LEU Chi-restraints excluded: chain C residue 1298 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 8.9990 chunk 78 optimal weight: 50.0000 chunk 2 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 20.0000 chunk 124 optimal weight: 50.0000 chunk 34 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 HIS ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS C 547 ASN C 896 HIS ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1203 HIS ** C1224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1301 ASN C1316 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.9330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9872 Z= 0.307 Angle : 0.659 9.975 13576 Z= 0.342 Chirality : 0.045 0.148 1646 Planarity : 0.005 0.074 1752 Dihedral : 6.538 72.514 1561 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 8.07 % Allowed : 23.78 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -0.47 (0.23), residues: 1429 helix: 1.01 (0.17), residues: 910 sheet: -3.26 (0.62), residues: 55 loop : -2.68 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 288 HIS 0.012 0.002 HIS C 125 PHE 0.023 0.002 PHE C 154 TYR 0.024 0.002 TYR C 195 ARG 0.009 0.001 ARG C 289 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 174 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 41 PHE cc_start: 0.8399 (m-80) cc_final: 0.8005 (m-80) REVERT: C 88 GLU cc_start: 0.7752 (tp30) cc_final: 0.7137 (tp30) REVERT: C 108 MET cc_start: 0.8506 (tpp) cc_final: 0.7919 (tpp) REVERT: C 112 MET cc_start: 0.7993 (mtm) cc_final: 0.7739 (mtp) REVERT: C 134 LYS cc_start: 0.8901 (tptm) cc_final: 0.8612 (tppp) REVERT: C 158 TYR cc_start: 0.8122 (t80) cc_final: 0.7290 (t80) REVERT: C 426 ASN cc_start: 0.8613 (t0) cc_final: 0.8401 (t0) REVERT: C 434 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8535 (mm) REVERT: C 483 GLN cc_start: 0.8532 (tt0) cc_final: 0.7944 (tm-30) REVERT: C 574 SER cc_start: 0.7750 (p) cc_final: 0.7425 (p) REVERT: C 602 LYS cc_start: 0.8509 (mttt) cc_final: 0.7910 (mtpt) REVERT: C 1030 ILE cc_start: 0.7589 (tt) cc_final: 0.7191 (pt) REVERT: C 1091 LEU cc_start: 0.8277 (tp) cc_final: 0.7897 (tt) REVERT: C 1191 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7390 (mm110) REVERT: C 1197 GLN cc_start: 0.8448 (tt0) cc_final: 0.8163 (tm-30) REVERT: C 1209 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8293 (mm-30) REVERT: C 1229 GLU cc_start: 0.8223 (tp30) cc_final: 0.7962 (tm-30) outliers start: 56 outliers final: 35 residues processed: 204 average time/residue: 0.1762 time to fit residues: 53.8284 Evaluate side-chains 182 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 145 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1151 VAL Chi-restraints excluded: chain C residue 1158 SER Chi-restraints excluded: chain C residue 1165 LEU Chi-restraints excluded: chain C residue 1173 VAL Chi-restraints excluded: chain C residue 1188 ASP Chi-restraints excluded: chain C residue 1191 GLN Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1227 LEU Chi-restraints excluded: chain C residue 1234 ASN Chi-restraints excluded: chain C residue 1242 THR Chi-restraints excluded: chain C residue 1272 LEU Chi-restraints excluded: chain C residue 1283 LEU Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1315 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 8.9990 chunk 124 optimal weight: 50.0000 chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 40.0000 chunk 34 optimal weight: 6.9990 chunk 138 optimal weight: 50.0000 chunk 114 optimal weight: 8.9990 chunk 64 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 HIS C 397 ASN C 491 HIS ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1224 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.9857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9872 Z= 0.281 Angle : 0.653 9.659 13576 Z= 0.336 Chirality : 0.044 0.138 1646 Planarity : 0.005 0.067 1752 Dihedral : 6.404 74.224 1561 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 7.93 % Allowed : 26.08 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: -0.09 (0.23), residues: 1429 helix: 1.33 (0.17), residues: 904 sheet: -3.58 (0.64), residues: 46 loop : -2.51 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C1297 HIS 0.018 0.002 HIS C 125 PHE 0.020 0.002 PHE C 154 TYR 0.024 0.002 TYR C 195 ARG 0.011 0.001 ARG C 289 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 161 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 41 PHE cc_start: 0.8277 (m-80) cc_final: 0.7979 (m-80) REVERT: C 54 GLN cc_start: 0.6627 (OUTLIER) cc_final: 0.5941 (mp-120) REVERT: C 88 GLU cc_start: 0.7820 (tp30) cc_final: 0.7198 (tp30) REVERT: C 112 MET cc_start: 0.7995 (mtm) cc_final: 0.7722 (mtp) REVERT: C 158 TYR cc_start: 0.8303 (t80) cc_final: 0.7426 (t80) REVERT: C 170 CYS cc_start: 0.7700 (m) cc_final: 0.7286 (p) REVERT: C 289 ARG cc_start: 0.8710 (mtt90) cc_final: 0.8329 (ptp90) REVERT: C 426 ASN cc_start: 0.8593 (t0) cc_final: 0.8384 (t0) REVERT: C 434 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8537 (mm) REVERT: C 483 GLN cc_start: 0.8412 (tt0) cc_final: 0.7943 (tm-30) REVERT: C 574 SER cc_start: 0.7919 (p) cc_final: 0.7577 (p) REVERT: C 1030 ILE cc_start: 0.7609 (tt) cc_final: 0.7343 (mt) REVERT: C 1091 LEU cc_start: 0.8413 (tp) cc_final: 0.8008 (tt) REVERT: C 1191 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7494 (mm110) REVERT: C 1209 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8266 (mm-30) REVERT: C 1227 LEU cc_start: 0.8708 (tt) cc_final: 0.8437 (tp) REVERT: C 1229 GLU cc_start: 0.8257 (tp30) cc_final: 0.7993 (tm-30) outliers start: 55 outliers final: 41 residues processed: 198 average time/residue: 0.1711 time to fit residues: 51.0682 Evaluate side-chains 189 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 145 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1151 VAL Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain C residue 1161 THR Chi-restraints excluded: chain C residue 1165 LEU Chi-restraints excluded: chain C residue 1173 VAL Chi-restraints excluded: chain C residue 1191 GLN Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1224 GLN Chi-restraints excluded: chain C residue 1242 THR Chi-restraints excluded: chain C residue 1272 LEU Chi-restraints excluded: chain C residue 1283 LEU Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1315 ILE Chi-restraints excluded: chain C residue 1325 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 78 optimal weight: 30.0000 chunk 101 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 77 optimal weight: 40.0000 chunk 137 optimal weight: 50.0000 chunk 86 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 85 optimal weight: 0.0770 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 HIS C 397 ASN C 491 HIS ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1197 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 1.0163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9872 Z= 0.290 Angle : 0.643 9.352 13576 Z= 0.331 Chirality : 0.043 0.139 1646 Planarity : 0.005 0.064 1752 Dihedral : 6.366 73.710 1561 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 8.21 % Allowed : 25.36 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.02 (0.23), residues: 1429 helix: 1.42 (0.17), residues: 905 sheet: -3.57 (0.66), residues: 46 loop : -2.47 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C1297 HIS 0.006 0.001 HIS C1203 PHE 0.026 0.002 PHE C 577 TYR 0.020 0.002 TYR C 195 ARG 0.008 0.001 ARG C 289 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 147 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 41 PHE cc_start: 0.8329 (m-80) cc_final: 0.8022 (m-80) REVERT: C 54 GLN cc_start: 0.6488 (OUTLIER) cc_final: 0.5814 (mp-120) REVERT: C 88 GLU cc_start: 0.7744 (tp30) cc_final: 0.7093 (tp30) REVERT: C 112 MET cc_start: 0.7939 (mtm) cc_final: 0.7639 (mtp) REVERT: C 158 TYR cc_start: 0.8385 (t80) cc_final: 0.7538 (t80) REVERT: C 167 LEU cc_start: 0.6908 (tp) cc_final: 0.5890 (tp) REVERT: C 170 CYS cc_start: 0.7761 (m) cc_final: 0.7377 (p) REVERT: C 289 ARG cc_start: 0.8764 (mtt90) cc_final: 0.8503 (mtt180) REVERT: C 426 ASN cc_start: 0.8554 (t0) cc_final: 0.8350 (t0) REVERT: C 434 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8548 (mm) REVERT: C 483 GLN cc_start: 0.8427 (tt0) cc_final: 0.7986 (tm-30) REVERT: C 574 SER cc_start: 0.7928 (p) cc_final: 0.7603 (p) REVERT: C 1030 ILE cc_start: 0.7595 (tt) cc_final: 0.7349 (pt) REVERT: C 1209 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8316 (mm-30) REVERT: C 1229 GLU cc_start: 0.8291 (tp30) cc_final: 0.8011 (tm-30) outliers start: 57 outliers final: 43 residues processed: 183 average time/residue: 0.1798 time to fit residues: 49.1659 Evaluate side-chains 186 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 141 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 491 HIS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1151 VAL Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain C residue 1158 SER Chi-restraints excluded: chain C residue 1161 THR Chi-restraints excluded: chain C residue 1165 LEU Chi-restraints excluded: chain C residue 1173 VAL Chi-restraints excluded: chain C residue 1188 ASP Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1242 THR Chi-restraints excluded: chain C residue 1269 SER Chi-restraints excluded: chain C residue 1272 LEU Chi-restraints excluded: chain C residue 1283 LEU Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1315 ILE Chi-restraints excluded: chain C residue 1325 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 4.9990 chunk 82 optimal weight: 0.0030 chunk 41 optimal weight: 5.9990 chunk 27 optimal weight: 0.2980 chunk 26 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 HIS ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 1.0249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9872 Z= 0.164 Angle : 0.603 8.677 13576 Z= 0.303 Chirality : 0.041 0.280 1646 Planarity : 0.004 0.065 1752 Dihedral : 5.999 74.522 1561 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.60 % Allowed : 30.12 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.41 (0.24), residues: 1429 helix: 1.67 (0.18), residues: 919 sheet: -3.11 (0.68), residues: 55 loop : -2.30 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C1297 HIS 0.026 0.002 HIS C 491 PHE 0.027 0.001 PHE C 577 TYR 0.021 0.001 TYR C 195 ARG 0.009 0.001 ARG C 289 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 163 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 41 PHE cc_start: 0.8271 (m-80) cc_final: 0.7977 (m-80) REVERT: C 54 GLN cc_start: 0.6472 (OUTLIER) cc_final: 0.5828 (mp-120) REVERT: C 88 GLU cc_start: 0.7564 (tp30) cc_final: 0.6867 (tp30) REVERT: C 112 MET cc_start: 0.7855 (mtm) cc_final: 0.7546 (mtp) REVERT: C 158 TYR cc_start: 0.8359 (t80) cc_final: 0.7500 (t80) REVERT: C 257 MET cc_start: 0.9019 (mpp) cc_final: 0.8457 (mtt) REVERT: C 289 ARG cc_start: 0.8746 (mtt90) cc_final: 0.8454 (mtt180) REVERT: C 434 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8409 (mm) REVERT: C 483 GLN cc_start: 0.8406 (tt0) cc_final: 0.8004 (tm-30) REVERT: C 574 SER cc_start: 0.7728 (p) cc_final: 0.7394 (p) REVERT: C 1229 GLU cc_start: 0.8249 (tp30) cc_final: 0.7929 (tm-30) REVERT: C 1230 TYR cc_start: 0.8904 (m-80) cc_final: 0.8636 (m-80) REVERT: C 1305 MET cc_start: 0.7859 (tpp) cc_final: 0.7614 (tpp) outliers start: 25 outliers final: 21 residues processed: 177 average time/residue: 0.1926 time to fit residues: 50.4165 Evaluate side-chains 171 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 491 HIS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 792 SER Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain C residue 1158 SER Chi-restraints excluded: chain C residue 1188 ASP Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1228 LEU Chi-restraints excluded: chain C residue 1283 LEU Chi-restraints excluded: chain C residue 1296 ASN Chi-restraints excluded: chain C residue 1315 ILE Chi-restraints excluded: chain C residue 1325 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 50.0000 chunk 120 optimal weight: 40.0000 chunk 128 optimal weight: 30.0000 chunk 77 optimal weight: 30.0000 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 116 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 84 optimal weight: 0.8980 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 HIS C 293 HIS C 491 HIS ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 1.0549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9872 Z= 0.288 Angle : 0.640 9.691 13576 Z= 0.329 Chirality : 0.044 0.228 1646 Planarity : 0.005 0.062 1752 Dihedral : 6.112 71.567 1561 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 5.33 % Allowed : 28.67 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.24), residues: 1429 helix: 1.67 (0.18), residues: 913 sheet: -3.53 (0.67), residues: 46 loop : -2.28 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C1037 HIS 0.010 0.002 HIS C 293 PHE 0.023 0.002 PHE C 433 TYR 0.028 0.002 TYR C 845 ARG 0.007 0.001 ARG C 289 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 145 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 41 PHE cc_start: 0.8343 (m-80) cc_final: 0.8042 (m-80) REVERT: C 54 GLN cc_start: 0.6451 (OUTLIER) cc_final: 0.5783 (mp-120) REVERT: C 88 GLU cc_start: 0.7721 (tp30) cc_final: 0.7116 (tp30) REVERT: C 112 MET cc_start: 0.7931 (mtm) cc_final: 0.7616 (mtp) REVERT: C 158 TYR cc_start: 0.8402 (t80) cc_final: 0.7539 (t80) REVERT: C 167 LEU cc_start: 0.6932 (tp) cc_final: 0.5879 (tp) REVERT: C 170 CYS cc_start: 0.7932 (m) cc_final: 0.7498 (p) REVERT: C 266 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8366 (tt) REVERT: C 289 ARG cc_start: 0.8779 (mtt90) cc_final: 0.8531 (mtt90) REVERT: C 426 ASN cc_start: 0.8525 (t0) cc_final: 0.8313 (m-40) REVERT: C 434 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8530 (mm) REVERT: C 483 GLN cc_start: 0.8454 (tt0) cc_final: 0.8072 (tm-30) REVERT: C 574 SER cc_start: 0.8065 (p) cc_final: 0.7718 (p) REVERT: C 591 PHE cc_start: 0.7893 (t80) cc_final: 0.7572 (t80) REVERT: C 1227 LEU cc_start: 0.8714 (tt) cc_final: 0.8359 (tp) REVERT: C 1229 GLU cc_start: 0.8308 (tp30) cc_final: 0.7997 (tm-30) REVERT: C 1305 MET cc_start: 0.7934 (tpp) cc_final: 0.7661 (tpp) outliers start: 37 outliers final: 28 residues processed: 172 average time/residue: 0.1755 time to fit residues: 45.8648 Evaluate side-chains 171 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 140 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 491 HIS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 792 SER Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain C residue 1158 SER Chi-restraints excluded: chain C residue 1161 THR Chi-restraints excluded: chain C residue 1165 LEU Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1228 LEU Chi-restraints excluded: chain C residue 1283 LEU Chi-restraints excluded: chain C residue 1296 ASN Chi-restraints excluded: chain C residue 1315 ILE Chi-restraints excluded: chain C residue 1325 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 50.0000 chunk 82 optimal weight: 0.0980 chunk 64 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 142 optimal weight: 50.0000 chunk 131 optimal weight: 30.0000 chunk 113 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 HIS C 293 HIS C 491 HIS ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 1.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9872 Z= 0.256 Angle : 0.633 9.486 13576 Z= 0.323 Chirality : 0.044 0.214 1646 Planarity : 0.004 0.062 1752 Dihedral : 6.104 70.486 1561 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 5.33 % Allowed : 28.39 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.40 (0.24), residues: 1429 helix: 1.68 (0.18), residues: 916 sheet: -3.47 (0.68), residues: 46 loop : -2.32 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 899 HIS 0.015 0.002 HIS C 125 PHE 0.022 0.002 PHE C 577 TYR 0.030 0.002 TYR C 845 ARG 0.007 0.001 ARG C 289 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 145 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 41 PHE cc_start: 0.8354 (m-80) cc_final: 0.8041 (m-80) REVERT: C 54 GLN cc_start: 0.6467 (OUTLIER) cc_final: 0.5800 (mp-120) REVERT: C 88 GLU cc_start: 0.7728 (tp30) cc_final: 0.7081 (tp30) REVERT: C 112 MET cc_start: 0.7877 (mtm) cc_final: 0.7567 (mtp) REVERT: C 158 TYR cc_start: 0.8407 (t80) cc_final: 0.7528 (t80) REVERT: C 167 LEU cc_start: 0.6929 (tp) cc_final: 0.5901 (tp) REVERT: C 170 CYS cc_start: 0.7922 (m) cc_final: 0.7500 (p) REVERT: C 266 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8364 (tt) REVERT: C 289 ARG cc_start: 0.8775 (mtt90) cc_final: 0.8540 (mtt90) REVERT: C 426 ASN cc_start: 0.8533 (t0) cc_final: 0.8321 (m-40) REVERT: C 434 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8524 (mm) REVERT: C 483 GLN cc_start: 0.8428 (tt0) cc_final: 0.8098 (tm-30) REVERT: C 574 SER cc_start: 0.7938 (p) cc_final: 0.7539 (p) REVERT: C 591 PHE cc_start: 0.7962 (t80) cc_final: 0.7680 (t80) REVERT: C 1227 LEU cc_start: 0.8676 (tt) cc_final: 0.8310 (tp) REVERT: C 1229 GLU cc_start: 0.8292 (tp30) cc_final: 0.7976 (tm-30) REVERT: C 1305 MET cc_start: 0.7939 (tpp) cc_final: 0.7654 (tpp) outliers start: 37 outliers final: 30 residues processed: 172 average time/residue: 0.1678 time to fit residues: 44.4468 Evaluate side-chains 172 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 491 HIS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 792 SER Chi-restraints excluded: chain C residue 1018 PHE Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain C residue 1158 SER Chi-restraints excluded: chain C residue 1161 THR Chi-restraints excluded: chain C residue 1165 LEU Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1228 LEU Chi-restraints excluded: chain C residue 1283 LEU Chi-restraints excluded: chain C residue 1296 ASN Chi-restraints excluded: chain C residue 1315 ILE Chi-restraints excluded: chain C residue 1325 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 116 optimal weight: 40.0000 chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 HIS C 293 HIS C 491 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.128465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.104083 restraints weight = 18726.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.106600 restraints weight = 9252.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.108282 restraints weight = 5687.055| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 1.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9872 Z= 0.193 Angle : 0.606 9.442 13576 Z= 0.307 Chirality : 0.042 0.213 1646 Planarity : 0.004 0.062 1752 Dihedral : 5.992 69.584 1561 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.47 % Allowed : 30.12 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: 0.54 (0.24), residues: 1429 helix: 1.81 (0.18), residues: 910 sheet: -3.44 (0.70), residues: 46 loop : -2.26 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 899 HIS 0.020 0.002 HIS C 125 PHE 0.024 0.001 PHE C 577 TYR 0.034 0.002 TYR C 845 ARG 0.007 0.001 ARG C 289 =============================================================================== Job complete usr+sys time: 1958.02 seconds wall clock time: 36 minutes 7.90 seconds (2167.90 seconds total)