Starting phenix.real_space_refine on Thu Sep 26 05:03:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0z_0585/09_2024/6o0z_0585.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0z_0585/09_2024/6o0z_0585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0z_0585/09_2024/6o0z_0585.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0z_0585/09_2024/6o0z_0585.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0z_0585/09_2024/6o0z_0585.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0z_0585/09_2024/6o0z_0585.cif" } resolution = 3.3 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= -0.001 sd= 0.043 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 134 5.49 5 S 15 5.16 5 C 7080 2.51 5 N 2132 2.21 5 O 2551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11912 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9063 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 1288, 9063 Classifications: {'peptide': 1288} Incomplete info: {'truncation_to_alanine': 391} Link IDs: {'PTRANS': 34, 'TRANS': 1253} Chain breaks: 11 Unresolved non-hydrogen bonds: 1545 Unresolved non-hydrogen angles: 1919 Unresolved non-hydrogen dihedrals: 1252 Unresolved non-hydrogen chiralities: 106 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 3, 'TYR:plan': 12, 'ASN:plan1': 32, 'TRP:plan': 1, 'ASP:plan': 45, 'PHE:plan': 16, 'GLU:plan': 61, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 883 Chain: "B" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 2058 Classifications: {'RNA': 96} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 51, 'rna3p_pyr': 34} Link IDs: {'rna2p': 11, 'rna3p': 84} Chain: "C" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 563 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "D" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 228 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Time building chain proxies: 8.34, per 1000 atoms: 0.70 Number of scatterers: 11912 At special positions: 0 Unit cell: (140.448, 127.072, 98.648, 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 15 16.00 P 134 15.00 O 2551 8.00 N 2132 7.00 C 7080 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 - 3.00 Amino acid : True - 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: 3.06 Conformation dependent library (CDL) restraints added in 1.4 seconds 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 7 sheets defined 52.7% alpha, 6.3% beta 49 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 5.22 Creating SS restraints... Processing helix chain 'A' and resid 59 through 86 Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.960A pdb=" N ALA A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 4.018A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.608A pdb=" N PHE A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 196 removed outlier: 3.592A pdb=" N ILE A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLN A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 218 through 227 Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'A' and resid 269 through 281 removed outlier: 4.594A pdb=" N ASP A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 302 Processing helix chain 'A' and resid 315 through 342 removed outlier: 3.557A pdb=" N ALA A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.520A pdb=" N ILE A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.352A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.628A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.572A pdb=" N ILE A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.618A pdb=" N VAL A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.676A pdb=" N SER A 487 " --> pdb=" O ASP A 483 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 543 through 556 removed outlier: 4.275A pdb=" N ALA A 547 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A 553 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 573 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 605 through 609 removed outlier: 3.524A pdb=" N ASP A 608 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN A 609 " --> pdb=" O PHE A 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 605 through 609' Processing helix chain 'A' and resid 610 through 626 removed outlier: 4.013A pdb=" N ASP A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 621 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 638 Processing helix chain 'A' and resid 644 through 653 Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 678 through 685 removed outlier: 3.602A pdb=" N SER A 685 " --> pdb=" O ASP A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 703 through 711 removed outlier: 3.690A pdb=" N ASP A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.798A pdb=" N ASN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.545A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 792 removed outlier: 3.562A pdb=" N GLY A 792 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 817 removed outlier: 3.974A pdb=" N TYR A 812 " --> pdb=" O ASN A 808 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TYR A 814 " --> pdb=" O LYS A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 872 through 879 Processing helix chain 'A' and resid 881 through 889 Processing helix chain 'A' and resid 893 through 902 Processing helix chain 'A' and resid 903 through 905 No H-bonds generated for 'chain 'A' and resid 903 through 905' Processing helix chain 'A' and resid 909 through 922 Processing helix chain 'A' and resid 925 through 940 removed outlier: 3.857A pdb=" N LYS A 929 " --> pdb=" O ARG A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 971 removed outlier: 4.131A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1001 Processing helix chain 'A' and resid 1004 through 1009 removed outlier: 3.870A pdb=" N PHE A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 3.747A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1186 removed outlier: 3.690A pdb=" N PHE A1181 " --> pdb=" O ASN A1177 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A1186 " --> pdb=" O LEU A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1195 removed outlier: 4.029A pdb=" N ILE A1195 " --> pdb=" O LYS A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 removed outlier: 3.592A pdb=" N HIS A1241 " --> pdb=" O TYR A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1261 Processing helix chain 'A' and resid 1264 through 1280 removed outlier: 3.906A pdb=" N GLU A1268 " --> pdb=" O HIS A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1302 through 1312 removed outlier: 4.172A pdb=" N GLU A1307 " --> pdb=" O ARG A1303 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN A1308 " --> pdb=" O GLU A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1315 No H-bonds generated for 'chain 'A' and resid 1313 through 1315' Processing helix chain 'A' and resid 1341 through 1344 Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 6.201A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A1095 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 32 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 6.251A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 839 through 840 Processing sheet with id=AA5, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA6, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA7, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.760A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 122 hydrogen bonds 240 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 7.00 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2133 1.33 - 1.45: 3597 1.45 - 1.57: 6375 1.57 - 1.69: 266 1.69 - 1.81: 28 Bond restraints: 12399 Sorted by residual: bond pdb=" C LEU A1198 " pdb=" O LEU A1198 " ideal model delta sigma weight residual 1.249 1.236 0.013 8.50e-03 1.38e+04 2.41e+00 bond pdb=" O5' DC C 20 " pdb=" C5' DC C 20 " ideal model delta sigma weight residual 1.423 1.379 0.044 3.00e-02 1.11e+03 2.11e+00 bond pdb=" CG LYS A1334 " pdb=" CD LYS A1334 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.61e+00 bond pdb=" C1' DC C 20 " pdb=" N1 DC C 20 " ideal model delta sigma weight residual 1.490 1.527 -0.037 3.00e-02 1.11e+03 1.49e+00 bond pdb=" C ILE A1110 " pdb=" N LEU A1111 " ideal model delta sigma weight residual 1.339 1.273 0.067 5.57e-02 3.22e+02 1.44e+00 ... (remaining 12394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 16848 1.65 - 3.30: 536 3.30 - 4.95: 59 4.95 - 6.60: 20 6.60 - 8.25: 8 Bond angle restraints: 17471 Sorted by residual: angle pdb=" C3' A B 68 " pdb=" O3' A B 68 " pdb=" P A B 69 " ideal model delta sigma weight residual 120.20 126.75 -6.55 1.50e+00 4.44e-01 1.90e+01 angle pdb=" C LYS A 862 " pdb=" N ASN A 863 " pdb=" CA ASN A 863 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 angle pdb=" O3' A B 68 " pdb=" C3' A B 68 " pdb=" C2' A B 68 " ideal model delta sigma weight residual 113.70 119.68 -5.98 1.50e+00 4.44e-01 1.59e+01 angle pdb=" CA LYS A1334 " pdb=" CB LYS A1334 " pdb=" CG LYS A1334 " ideal model delta sigma weight residual 114.10 107.11 6.99 2.00e+00 2.50e-01 1.22e+01 angle pdb=" C3' A B 42 " pdb=" O3' A B 42 " pdb=" P G B 43 " ideal model delta sigma weight residual 120.20 125.37 -5.17 1.50e+00 4.44e-01 1.19e+01 ... (remaining 17466 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.56: 6972 34.56 - 69.13: 393 69.13 - 103.69: 27 103.69 - 138.25: 0 138.25 - 172.81: 3 Dihedral angle restraints: 7395 sinusoidal: 3618 harmonic: 3777 Sorted by residual: dihedral pdb=" O4' C B 70 " pdb=" C1' C B 70 " pdb=" N1 C B 70 " pdb=" C2 C B 70 " ideal model delta sinusoidal sigma weight residual 200.00 43.08 156.92 1 1.50e+01 4.44e-03 8.19e+01 dihedral pdb=" CA ASP A 861 " pdb=" C ASP A 861 " pdb=" N LYS A 862 " pdb=" CA LYS A 862 " ideal model delta harmonic sigma weight residual 180.00 157.81 22.19 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA SER A1040 " pdb=" C SER A1040 " pdb=" N ASN A1041 " pdb=" CA ASN A1041 " ideal model delta harmonic sigma weight residual -180.00 -159.30 -20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 7392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1835 0.062 - 0.123: 261 0.123 - 0.185: 28 0.185 - 0.247: 2 0.247 - 0.309: 2 Chirality restraints: 2128 Sorted by residual: chirality pdb=" C3' A B 42 " pdb=" C4' A B 42 " pdb=" O3' A B 42 " pdb=" C2' A B 42 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C3' A B 38 " pdb=" C4' A B 38 " pdb=" O3' A B 38 " pdb=" C2' A B 38 " both_signs ideal model delta sigma weight residual False -2.48 -2.22 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB VAL A1149 " pdb=" CA VAL A1149 " pdb=" CG1 VAL A1149 " pdb=" CG2 VAL A1149 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.10e-01 ... (remaining 2125 not shown) Planarity restraints: 1752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 474 " -0.035 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO A 475 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 475 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 475 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1228 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO A1229 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A1229 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1229 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1342 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C VAL A1342 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL A1342 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A1343 " -0.011 2.00e-02 2.50e+03 ... (remaining 1749 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3643 2.82 - 3.34: 9736 3.34 - 3.86: 20451 3.86 - 4.38: 21925 4.38 - 4.90: 35065 Nonbonded interactions: 90820 Sorted by model distance: nonbonded pdb=" OG SER A 469 " pdb=" OE1 GLU A 471 " model vdw 2.302 3.040 nonbonded pdb=" O TYR A 521 " pdb=" OG1 THR A 525 " model vdw 2.308 3.040 nonbonded pdb=" O LYS A 141 " pdb=" OG SER A 145 " model vdw 2.328 3.040 nonbonded pdb=" OG SER A1109 " pdb=" OP2 DG C 11 " model vdw 2.334 3.040 nonbonded pdb=" N2 G B 73 " pdb=" OP2 A B 76 " model vdw 2.337 3.120 ... (remaining 90815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.100 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 37.530 Find NCS groups from input model: 0.140 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: 0.020 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 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 : 0.006 0.067 12399 Z= 0.364 Angle : 0.716 8.255 17471 Z= 0.395 Chirality : 0.044 0.309 2128 Planarity : 0.005 0.052 1752 Dihedral : 18.936 172.814 4935 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.27 % Allowed : 8.34 % Favored : 91.38 % 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: -4.11 (0.18), residues: 1264 helix: -2.68 (0.15), residues: 608 sheet: -0.72 (0.46), residues: 127 loop : -3.20 (0.21), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 476 HIS 0.005 0.001 HIS A 167 PHE 0.016 0.002 PHE A1324 TYR 0.014 0.002 TYR A 325 ARG 0.005 0.000 ARG A1084 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 1.243 Fit side-chains REVERT: A 518 PHE cc_start: 0.9042 (t80) cc_final: 0.8744 (t80) REVERT: A 927 ILE cc_start: 0.9262 (mt) cc_final: 0.9034 (tp) REVERT: A 933 GLN cc_start: 0.9239 (tt0) cc_final: 0.9036 (tm-30) REVERT: A 961 LYS cc_start: 0.8817 (tptp) cc_final: 0.8564 (tptp) REVERT: A 1183 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8333 (tm-30) outliers start: 2 outliers final: 1 residues processed: 72 average time/residue: 0.2693 time to fit residues: 27.7671 Evaluate side-chains 52 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1098 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 50.0000 chunk 81 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 113 HIS ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 HIS A 426 GLN A 990 ASN A1272 GLN A1308 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12399 Z= 0.225 Angle : 0.507 5.943 17471 Z= 0.280 Chirality : 0.036 0.202 2128 Planarity : 0.004 0.059 1752 Dihedral : 19.835 177.699 3226 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.37 % Allowed : 9.71 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.22), residues: 1264 helix: -0.63 (0.20), residues: 625 sheet: -0.48 (0.47), residues: 127 loop : -2.87 (0.23), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1074 HIS 0.003 0.001 HIS A 160 PHE 0.009 0.001 PHE A 432 TYR 0.010 0.001 TYR A 325 ARG 0.006 0.000 ARG A 976 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 1.135 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 64 average time/residue: 0.2027 time to fit residues: 21.4557 Evaluate side-chains 52 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1146 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 127 optimal weight: 0.6980 chunk 137 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 12399 Z= 0.356 Angle : 0.560 6.557 17471 Z= 0.302 Chirality : 0.038 0.200 2128 Planarity : 0.003 0.059 1752 Dihedral : 19.818 173.896 3226 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.37 % Allowed : 12.45 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.23), residues: 1264 helix: 0.29 (0.21), residues: 617 sheet: -0.69 (0.46), residues: 137 loop : -2.56 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1074 HIS 0.004 0.001 HIS A 167 PHE 0.009 0.001 PHE A 518 TYR 0.012 0.001 TYR A 325 ARG 0.004 0.000 ARG A 976 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 1.097 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 56 average time/residue: 0.2024 time to fit residues: 18.6502 Evaluate side-chains 52 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1146 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 8.9990 chunk 95 optimal weight: 30.0000 chunk 66 optimal weight: 30.0000 chunk 14 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 112 optimal weight: 0.0970 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 HIS A 990 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12399 Z= 0.290 Angle : 0.523 6.264 17471 Z= 0.282 Chirality : 0.037 0.191 2128 Planarity : 0.003 0.057 1752 Dihedral : 19.768 172.012 3226 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.19 % Allowed : 13.95 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.24), residues: 1264 helix: 0.77 (0.22), residues: 616 sheet: -0.57 (0.47), residues: 137 loop : -2.40 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1074 HIS 0.003 0.001 HIS A 160 PHE 0.010 0.001 PHE A 432 TYR 0.014 0.001 TYR A 271 ARG 0.002 0.000 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 49 time to evaluate : 1.198 Fit side-chains REVERT: A 631 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8790 (pmm) outliers start: 16 outliers final: 12 residues processed: 62 average time/residue: 0.1927 time to fit residues: 19.3676 Evaluate side-chains 59 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 46 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1146 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 100 optimal weight: 0.2980 chunk 55 optimal weight: 20.0000 chunk 115 optimal weight: 3.9990 chunk 93 optimal weight: 0.0970 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 34 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12399 Z= 0.129 Angle : 0.457 5.970 17471 Z= 0.248 Chirality : 0.035 0.166 2128 Planarity : 0.003 0.053 1752 Dihedral : 19.597 172.550 3226 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.78 % Allowed : 15.05 % Favored : 83.17 % 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: -0.37 (0.25), residues: 1264 helix: 1.22 (0.22), residues: 613 sheet: -0.31 (0.48), residues: 137 loop : -2.12 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1074 HIS 0.002 0.000 HIS A 160 PHE 0.018 0.001 PHE A 518 TYR 0.009 0.001 TYR A 271 ARG 0.001 0.000 BARG A 437 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: A 631 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8672 (pmm) REVERT: A 1169 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7363 (mtp) outliers start: 13 outliers final: 8 residues processed: 64 average time/residue: 0.1874 time to fit residues: 19.4366 Evaluate side-chains 56 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1169 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 8.9990 chunk 26 optimal weight: 30.0000 chunk 79 optimal weight: 50.0000 chunk 33 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 0.0050 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 0.3980 chunk 71 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 overall best weight: 3.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN A 990 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12399 Z= 0.317 Angle : 0.528 6.467 17471 Z= 0.284 Chirality : 0.038 0.185 2128 Planarity : 0.003 0.055 1752 Dihedral : 19.674 170.468 3226 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.46 % Allowed : 14.64 % Favored : 82.90 % 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: -0.38 (0.25), residues: 1264 helix: 1.26 (0.22), residues: 617 sheet: -0.38 (0.48), residues: 137 loop : -2.19 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1074 HIS 0.003 0.001 HIS A 167 PHE 0.011 0.001 PHE A 432 TYR 0.012 0.001 TYR A 325 ARG 0.002 0.000 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 48 time to evaluate : 1.152 Fit side-chains REVERT: A 631 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8692 (pmm) outliers start: 18 outliers final: 13 residues processed: 63 average time/residue: 0.1973 time to fit residues: 20.2294 Evaluate side-chains 61 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1146 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 50.0000 chunk 98 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 75 optimal weight: 40.0000 chunk 134 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 82 optimal weight: 50.0000 chunk 62 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12399 Z= 0.413 Angle : 0.588 7.491 17471 Z= 0.313 Chirality : 0.040 0.196 2128 Planarity : 0.003 0.056 1752 Dihedral : 19.752 168.166 3226 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.74 % Allowed : 14.91 % Favored : 82.35 % 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: -0.50 (0.24), residues: 1264 helix: 1.14 (0.22), residues: 619 sheet: -0.48 (0.48), residues: 137 loop : -2.21 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1074 HIS 0.004 0.001 HIS A 167 PHE 0.010 0.001 PHE A 432 TYR 0.016 0.001 TYR A 271 ARG 0.002 0.000 ARG A1084 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 50 time to evaluate : 1.152 Fit side-chains outliers start: 20 outliers final: 14 residues processed: 67 average time/residue: 0.1897 time to fit residues: 20.6637 Evaluate side-chains 57 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 43 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1149 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 40.0000 chunk 80 optimal weight: 40.0000 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12399 Z= 0.287 Angle : 0.526 6.337 17471 Z= 0.283 Chirality : 0.038 0.190 2128 Planarity : 0.003 0.054 1752 Dihedral : 19.704 168.649 3226 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.19 % Allowed : 15.73 % Favored : 82.08 % 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: -0.29 (0.25), residues: 1264 helix: 1.27 (0.22), residues: 619 sheet: -0.36 (0.48), residues: 136 loop : -2.07 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1074 HIS 0.004 0.001 HIS A 160 PHE 0.011 0.001 PHE A1174 TYR 0.013 0.001 TYR A 271 ARG 0.001 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 48 time to evaluate : 1.094 Fit side-chains REVERT: A 998 ILE cc_start: 0.8866 (tp) cc_final: 0.8662 (tp) outliers start: 16 outliers final: 13 residues processed: 61 average time/residue: 0.1930 time to fit residues: 19.0672 Evaluate side-chains 60 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 47 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1149 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.4980 chunk 125 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 50.0000 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 82 optimal weight: 50.0000 chunk 132 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12399 Z= 0.214 Angle : 0.494 8.574 17471 Z= 0.265 Chirality : 0.036 0.179 2128 Planarity : 0.003 0.053 1752 Dihedral : 19.624 169.417 3226 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.19 % Allowed : 15.87 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1264 helix: 1.51 (0.22), residues: 617 sheet: -0.29 (0.48), residues: 136 loop : -1.97 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1074 HIS 0.002 0.001 HIS A 160 PHE 0.011 0.001 PHE A 432 TYR 0.011 0.001 TYR A 155 ARG 0.001 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 48 time to evaluate : 1.263 Fit side-chains REVERT: A 271 TYR cc_start: 0.7096 (t80) cc_final: 0.6564 (t80) outliers start: 16 outliers final: 13 residues processed: 61 average time/residue: 0.2159 time to fit residues: 21.3896 Evaluate side-chains 58 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 45 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1149 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 30.0000 chunk 63 optimal weight: 0.0670 chunk 92 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 overall best weight: 4.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 12399 Z= 0.448 Angle : 0.610 9.047 17471 Z= 0.324 Chirality : 0.040 0.201 2128 Planarity : 0.003 0.057 1752 Dihedral : 19.765 167.345 3226 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.19 % Allowed : 16.42 % Favored : 81.40 % 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: -0.36 (0.24), residues: 1264 helix: 1.27 (0.22), residues: 617 sheet: -0.47 (0.48), residues: 137 loop : -2.15 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1074 HIS 0.005 0.001 HIS A 167 PHE 0.011 0.002 PHE A 518 TYR 0.015 0.001 TYR A 271 ARG 0.007 0.000 ARG A 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 47 time to evaluate : 1.082 Fit side-chains outliers start: 16 outliers final: 16 residues processed: 63 average time/residue: 0.2075 time to fit residues: 21.0518 Evaluate side-chains 60 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1190 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 0.0670 chunk 114 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 40.0000 chunk 97 optimal weight: 40.0000 chunk 6 optimal weight: 1.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.087809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.059294 restraints weight = 36013.942| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.92 r_work: 0.2771 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12399 Z= 0.128 Angle : 0.480 8.246 17471 Z= 0.257 Chirality : 0.036 0.172 2128 Planarity : 0.003 0.053 1752 Dihedral : 19.573 169.487 3226 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.92 % Allowed : 16.55 % Favored : 81.53 % 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: 0.12 (0.25), residues: 1264 helix: 1.62 (0.22), residues: 617 sheet: -0.21 (0.48), residues: 136 loop : -1.86 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 464 HIS 0.003 0.001 HIS A 982 PHE 0.012 0.001 PHE A1174 TYR 0.010 0.001 TYR A 155 ARG 0.002 0.000 ARG A 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2028.81 seconds wall clock time: 37 minutes 6.50 seconds (2226.50 seconds total)