Starting phenix.real_space_refine on Thu Feb 15 07:34:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lcr_0873/02_2024/6lcr_0873_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lcr_0873/02_2024/6lcr_0873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lcr_0873/02_2024/6lcr_0873.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lcr_0873/02_2024/6lcr_0873.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lcr_0873/02_2024/6lcr_0873_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lcr_0873/02_2024/6lcr_0873_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 4 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 7395 2.51 5 N 1931 2.21 5 O 2168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 347": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A GLU 617": "OE1" <-> "OE2" Residue "A GLU 656": "OE1" <-> "OE2" Residue "A GLU 681": "OE1" <-> "OE2" Residue "A GLU 692": "OE1" <-> "OE2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A GLU 722": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A GLU 818": "OE1" <-> "OE2" Residue "A GLU 836": "OE1" <-> "OE2" Residue "A GLU 871": "OE1" <-> "OE2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A GLU 955": "OE1" <-> "OE2" Residue "A GLU 963": "OE1" <-> "OE2" Residue "A GLU 964": "OE1" <-> "OE2" Residue "A GLU 1077": "OE1" <-> "OE2" Residue "A PHE 1216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1340": "OE1" <-> "OE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11561 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8280 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 35, 'TRANS': 1008} Chain breaks: 4 Chain: "B" Number of atoms: 3061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3061 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 26, 'TRANS': 349} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {' MG': 1, 'ACP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.00, per 1000 atoms: 0.61 Number of scatterers: 11561 At special positions: 0 Unit cell: (143.48, 118.16, 128.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 62 16.00 P 4 15.00 Mg 1 11.99 O 2168 8.00 N 1931 7.00 C 7395 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG B 508 " - " ASN B 241 " " NAG E 1 " - " ASN B 189 " " NAG F 1 " - " ASN B 314 " Time building additional restraints: 4.84 Conformation dependent library (CDL) restraints added in 2.2 seconds 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2676 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 8 sheets defined 40.3% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'A' and resid 161 through 183 removed outlier: 4.365A pdb=" N ILE A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 469 through 472 No H-bonds generated for 'chain 'A' and resid 469 through 472' Processing helix chain 'A' and resid 484 through 487 No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 489 through 513 removed outlier: 3.873A pdb=" N ILE A 512 " --> pdb=" O ILE A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 3.707A pdb=" N PHE A 524 " --> pdb=" O SER A 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 524' Processing helix chain 'A' and resid 533 through 551 removed outlier: 3.935A pdb=" N PHE A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN A 549 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ASN A 550 " --> pdb=" O ILE A 546 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU A 551 " --> pdb=" O VAL A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 572 removed outlier: 4.116A pdb=" N TYR A 557 " --> pdb=" O ILE A 554 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE A 558 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU A 561 " --> pdb=" O ILE A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 593 No H-bonds generated for 'chain 'A' and resid 591 through 593' Processing helix chain 'A' and resid 596 through 599 Processing helix chain 'A' and resid 634 through 641 Processing helix chain 'A' and resid 649 through 670 removed outlier: 4.319A pdb=" N ARG A 655 " --> pdb=" O ALA A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 695 Processing helix chain 'A' and resid 701 through 714 removed outlier: 3.505A pdb=" N ALA A 714 " --> pdb=" O MET A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 750 removed outlier: 3.595A pdb=" N VAL A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET A 750 " --> pdb=" O THR A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 768 No H-bonds generated for 'chain 'A' and resid 766 through 768' Processing helix chain 'A' and resid 807 through 810 No H-bonds generated for 'chain 'A' and resid 807 through 810' Processing helix chain 'A' and resid 820 through 836 removed outlier: 4.179A pdb=" N GLU A 825 " --> pdb=" O ASP A 821 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 865 removed outlier: 4.276A pdb=" N GLU A 859 " --> pdb=" O GLU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 877 removed outlier: 4.123A pdb=" N GLU A 875 " --> pdb=" O GLU A 871 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU A 876 " --> pdb=" O GLU A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 882 No H-bonds generated for 'chain 'A' and resid 879 through 882' Processing helix chain 'A' and resid 901 through 911 removed outlier: 3.978A pdb=" N ALA A 906 " --> pdb=" O PRO A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 932 Processing helix chain 'A' and resid 955 through 971 Processing helix chain 'A' and resid 979 through 987 removed outlier: 4.668A pdb=" N LYS A 987 " --> pdb=" O LYS A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'A' and resid 1014 through 1023 Processing helix chain 'A' and resid 1034 through 1046 removed outlier: 4.152A pdb=" N ALA A1038 " --> pdb=" O PRO A1034 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A1041 " --> pdb=" O LYS A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1066 removed outlier: 4.910A pdb=" N ALA A1063 " --> pdb=" O ASN A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1135 removed outlier: 4.604A pdb=" N VAL A1100 " --> pdb=" O GLN A1097 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A1101 " --> pdb=" O ARG A1098 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N HIS A1103 " --> pdb=" O VAL A1100 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLY A1104 " --> pdb=" O LEU A1101 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A1105 " --> pdb=" O VAL A1102 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TRP A1106 " --> pdb=" O HIS A1103 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG A1110 " --> pdb=" O SER A1107 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS A1121 " --> pdb=" O PHE A1118 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TRP A1127 " --> pdb=" O ILE A1124 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TRP A1131 " --> pdb=" O SER A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1151 Processing helix chain 'A' and resid 1159 through 1166 Processing helix chain 'A' and resid 1175 through 1178 No H-bonds generated for 'chain 'A' and resid 1175 through 1178' Processing helix chain 'A' and resid 1180 through 1187 Processing helix chain 'A' and resid 1194 through 1217 Proline residue: A1215 - end of helix Processing helix chain 'A' and resid 1237 through 1256 Proline residue: A1245 - end of helix removed outlier: 3.745A pdb=" N ASN A1251 " --> pdb=" O VAL A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1284 removed outlier: 3.851A pdb=" N ILE A1276 " --> pdb=" O SER A1272 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE A1277 " --> pdb=" O ASP A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1300 Processing helix chain 'A' and resid 1304 through 1330 Proline residue: A1313 - end of helix Proline residue: A1319 - end of helix removed outlier: 3.924A pdb=" N VAL A1323 " --> pdb=" O PRO A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1344 removed outlier: 3.590A pdb=" N ARG A1344 " --> pdb=" O GLU A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1346 through 1355 removed outlier: 3.516A pdb=" N ALA A1349 " --> pdb=" O ASP A1346 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP A1351 " --> pdb=" O ALA A1348 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 54 No H-bonds generated for 'chain 'B' and resid 51 through 54' Processing helix chain 'B' and resid 57 through 74 Processing helix chain 'B' and resid 85 through 88 No H-bonds generated for 'chain 'B' and resid 85 through 88' Processing helix chain 'B' and resid 167 through 170 No H-bonds generated for 'chain 'B' and resid 167 through 170' Processing helix chain 'B' and resid 175 through 178 No H-bonds generated for 'chain 'B' and resid 175 through 178' Processing helix chain 'B' and resid 186 through 189 No H-bonds generated for 'chain 'B' and resid 186 through 189' Processing helix chain 'B' and resid 252 through 254 No H-bonds generated for 'chain 'B' and resid 252 through 254' Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 356 through 382 Processing sheet with id= A, first strand: chain 'A' and resid 327 through 330 removed outlier: 3.738A pdb=" N PHE A 339 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 378 through 381 Processing sheet with id= C, first strand: chain 'A' and resid 1088 through 1090 removed outlier: 3.690A pdb=" N PHE A1088 " --> pdb=" O GLY A1071 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR A 602 " --> pdb=" O LEU A1053 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE A1055 " --> pdb=" O TYR A 602 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N PHE A 604 " --> pdb=" O ILE A1055 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS A 914 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N SER A 605 " --> pdb=" O LYS A 914 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N TRP A 916 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A 998 " --> pdb=" O LEU A1028 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N CYS A1030 " --> pdb=" O LEU A 998 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE A1000 " --> pdb=" O CYS A1030 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU A 943 " --> pdb=" O VAL A 999 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N ASP A1001 " --> pdb=" O LEU A 943 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N LEU A 945 " --> pdb=" O ASP A1001 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 626 through 628 removed outlier: 3.657A pdb=" N ALA A 621 " --> pdb=" O TYR A 628 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA A 892 " --> pdb=" O LYS A 619 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA A 621 " --> pdb=" O GLY A 890 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY A 890 " --> pdb=" O ALA A 621 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ILE A 623 " --> pdb=" O LEU A 888 " (cutoff:3.500A) removed outlier: 9.022A pdb=" N LEU A 888 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE A 843 " --> pdb=" O LEU A 888 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ARG A 793 " --> pdb=" O VAL A 775 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL A 775 " --> pdb=" O ARG A 793 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 720 through 723 Processing sheet with id= F, first strand: chain 'A' and resid 763 through 766 Processing sheet with id= G, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.733A pdb=" N ARG B 340 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR B 157 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU B 310 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU B 159 " --> pdb=" O TYR B 308 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N TYR B 308 " --> pdb=" O LEU B 159 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 119 through 126 419 hydrogen bonds defined for protein. 1038 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: 3.67 Time building geometry restraints manager: 5.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1898 1.31 - 1.44: 3230 1.44 - 1.56: 6586 1.56 - 1.69: 9 1.69 - 1.81: 100 Bond restraints: 11823 Sorted by residual: bond pdb=" C17 P5S A2003 " pdb=" O19 P5S A2003 " ideal model delta sigma weight residual 1.328 1.449 -0.121 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C38 P5S A2003 " pdb=" O37 P5S A2003 " ideal model delta sigma weight residual 1.331 1.451 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" O2B ACP A2002 " pdb=" PB ACP A2002 " ideal model delta sigma weight residual 1.507 1.610 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" O15 P5S A2003 " pdb=" P12 P5S A2003 " ideal model delta sigma weight residual 1.502 1.600 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" O3A ACP A2002 " pdb=" PB ACP A2002 " ideal model delta sigma weight residual 1.698 1.610 0.088 2.00e-02 2.50e+03 1.96e+01 ... (remaining 11818 not shown) Histogram of bond angle deviations from ideal: 96.46 - 104.40: 205 104.40 - 112.33: 5900 112.33 - 120.27: 5251 120.27 - 128.20: 4596 128.20 - 136.13: 100 Bond angle restraints: 16052 Sorted by residual: angle pdb=" C GLN A 408 " pdb=" N PRO A 409 " pdb=" CA PRO A 409 " ideal model delta sigma weight residual 119.84 127.83 -7.99 1.25e+00 6.40e-01 4.09e+01 angle pdb=" C4 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" O3 NAG D 2 " ideal model delta sigma weight residual 112.02 96.46 15.56 3.00e+00 1.11e-01 2.69e+01 angle pdb=" C4 NAG F 1 " pdb=" C5 NAG F 1 " pdb=" C6 NAG F 1 " ideal model delta sigma weight residual 113.89 99.50 14.39 3.00e+00 1.11e-01 2.30e+01 angle pdb=" C ALA A 952 " pdb=" CA ALA A 952 " pdb=" CB ALA A 952 " ideal model delta sigma weight residual 116.54 111.05 5.49 1.15e+00 7.56e-01 2.28e+01 angle pdb=" N PHE A 548 " pdb=" CA PHE A 548 " pdb=" C PHE A 548 " ideal model delta sigma weight residual 112.97 108.13 4.84 1.06e+00 8.90e-01 2.08e+01 ... (remaining 16047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.08: 6834 29.08 - 58.16: 322 58.16 - 87.24: 34 87.24 - 116.32: 12 116.32 - 145.39: 3 Dihedral angle restraints: 7205 sinusoidal: 3057 harmonic: 4148 Sorted by residual: dihedral pdb=" CA SER A1233 " pdb=" C SER A1233 " pdb=" N GLU A1234 " pdb=" CA GLU A1234 " ideal model delta harmonic sigma weight residual 180.00 152.35 27.65 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA ASP A1231 " pdb=" C ASP A1231 " pdb=" N VAL A1232 " pdb=" CA VAL A1232 " ideal model delta harmonic sigma weight residual 180.00 152.63 27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA ASN A 990 " pdb=" C ASN A 990 " pdb=" N ALA A 991 " pdb=" CA ALA A 991 " ideal model delta harmonic sigma weight residual 180.00 153.90 26.10 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 7202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.223: 1800 0.223 - 0.446: 4 0.446 - 0.670: 3 0.670 - 0.893: 1 0.893 - 1.116: 2 Chirality restraints: 1810 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.31 -1.09 2.00e-02 2.50e+03 2.98e+03 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.87 0.47 2.00e-02 2.50e+03 5.60e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.79 0.39 2.00e-02 2.50e+03 3.72e+02 ... (remaining 1807 not shown) Planarity restraints: 2039 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " 0.255 2.00e-02 2.50e+03 2.14e-01 5.70e+02 pdb=" C7 NAG E 2 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.173 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " -0.359 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.230 2.00e-02 2.50e+03 1.85e-01 4.29e+02 pdb=" C7 NAG E 1 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " 0.169 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.289 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.181 2.00e-02 2.50e+03 1.52e-01 2.87e+02 pdb=" C7 NAG D 1 " -0.049 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.131 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.250 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.014 2.00e-02 2.50e+03 ... (remaining 2036 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 118 2.51 - 3.11: 9256 3.11 - 3.71: 17854 3.71 - 4.30: 26154 4.30 - 4.90: 43463 Nonbonded interactions: 96845 Sorted by model distance: nonbonded pdb=" OD2 ASP A 606 " pdb="MG MG A2001 " model vdw 1.914 2.170 nonbonded pdb=" O3 NAG E 1 " pdb=" O7 NAG E 1 " model vdw 2.035 2.440 nonbonded pdb=" O3 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.044 2.440 nonbonded pdb=" O3 NAG F 1 " pdb=" O7 NAG F 1 " model vdw 2.103 2.440 nonbonded pdb=" OE1 GLU A1234 " pdb=" OG1 THR A1236 " model vdw 2.105 2.440 ... (remaining 96840 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.200 Check model and map are aligned: 0.190 Set scattering table: 0.100 Process input model: 35.070 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 : 0.009 0.121 11823 Z= 0.563 Angle : 0.984 15.559 16052 Z= 0.496 Chirality : 0.070 1.116 1810 Planarity : 0.009 0.214 2036 Dihedral : 17.155 145.395 4529 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.58 % Favored : 88.21 % Rotamer: Outliers : 0.49 % Allowed : 10.33 % Favored : 89.18 % 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: -4.30 (0.19), residues: 1408 helix: -2.74 (0.17), residues: 578 sheet: -1.82 (0.37), residues: 174 loop : -3.22 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 120 HIS 0.003 0.001 HIS A 717 PHE 0.023 0.002 PHE A1017 TYR 0.025 0.002 TYR B 132 ARG 0.017 0.001 ARG A1260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 151 time to evaluate : 1.378 Fit side-chains revert: symmetry clash REVERT: A 408 GLN cc_start: 0.3650 (OUTLIER) cc_final: 0.0394 (pt0) REVERT: A 683 MET cc_start: 0.1248 (mtt) cc_final: 0.1021 (mtt) REVERT: A 1019 LEU cc_start: 0.7888 (mt) cc_final: 0.7641 (mp) REVERT: B 188 ILE cc_start: 0.8628 (tp) cc_final: 0.8391 (tp) outliers start: 6 outliers final: 4 residues processed: 157 average time/residue: 0.3350 time to fit residues: 72.7734 Evaluate side-chains 123 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 118 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 1304 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 110 optimal weight: 0.0010 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 128 optimal weight: 0.8980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS A 466 HIS A 489 ASN A 510 ASN A 550 ASN A 626 GLN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 ASN A 898 GLN A 969 ASN A 990 ASN A1023 GLN A1092 GLN ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1251 ASN B 73 HIS ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN B 166 HIS B 177 GLN B 312 GLN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11823 Z= 0.221 Angle : 0.697 9.407 16052 Z= 0.358 Chirality : 0.047 0.289 1810 Planarity : 0.006 0.054 2036 Dihedral : 11.774 118.511 1851 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.81 % Favored : 92.12 % Rotamer: Outliers : 1.97 % Allowed : 15.41 % Favored : 82.62 % 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: -3.30 (0.21), residues: 1408 helix: -1.87 (0.19), residues: 591 sheet: -1.45 (0.39), residues: 170 loop : -2.67 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 120 HIS 0.014 0.002 HIS A 829 PHE 0.021 0.002 PHE B 94 TYR 0.018 0.002 TYR B 132 ARG 0.005 0.000 ARG A 944 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.252 Fit side-chains revert: symmetry clash REVERT: A 408 GLN cc_start: 0.3591 (OUTLIER) cc_final: 0.3081 (mt0) REVERT: A 675 ASN cc_start: 0.3687 (OUTLIER) cc_final: 0.3479 (t0) REVERT: A 1183 TYR cc_start: 0.8671 (t80) cc_final: 0.8342 (t80) REVERT: B 78 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8654 (tt) REVERT: B 94 PHE cc_start: 0.8613 (m-80) cc_final: 0.7767 (m-10) REVERT: B 161 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8193 (t0) REVERT: B 188 ILE cc_start: 0.8510 (tp) cc_final: 0.8290 (tp) outliers start: 24 outliers final: 13 residues processed: 153 average time/residue: 0.2545 time to fit residues: 55.6577 Evaluate side-chains 131 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 675 ASN Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1308 CYS Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 336 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 128 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 chunk 127 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1103 HIS ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11823 Z= 0.230 Angle : 0.656 8.006 16052 Z= 0.338 Chirality : 0.045 0.280 1810 Planarity : 0.005 0.056 2036 Dihedral : 10.399 113.066 1849 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.74 % Favored : 92.19 % Rotamer: Outliers : 3.03 % Allowed : 17.30 % Favored : 79.67 % 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: -2.77 (0.22), residues: 1408 helix: -1.43 (0.20), residues: 580 sheet: -1.14 (0.40), residues: 175 loop : -2.39 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 120 HIS 0.006 0.001 HIS A 717 PHE 0.019 0.002 PHE A1197 TYR 0.019 0.001 TYR B 375 ARG 0.006 0.000 ARG B 167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 122 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 GLN cc_start: 0.3309 (OUTLIER) cc_final: 0.2106 (pt0) REVERT: A 1183 TYR cc_start: 0.8620 (t80) cc_final: 0.8230 (t80) REVERT: B 78 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8622 (tt) REVERT: B 161 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8210 (t0) outliers start: 37 outliers final: 19 residues processed: 153 average time/residue: 0.2391 time to fit residues: 54.4008 Evaluate side-chains 132 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1308 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 336 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 66 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 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 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11823 Z= 0.216 Angle : 0.631 7.426 16052 Z= 0.325 Chirality : 0.044 0.253 1810 Planarity : 0.005 0.056 2036 Dihedral : 9.343 106.636 1849 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.67 % Favored : 92.26 % Rotamer: Outliers : 3.69 % Allowed : 18.20 % Favored : 78.11 % 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: -2.50 (0.22), residues: 1408 helix: -1.23 (0.21), residues: 592 sheet: -0.98 (0.40), residues: 175 loop : -2.23 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1279 HIS 0.011 0.001 HIS B 73 PHE 0.015 0.002 PHE A1197 TYR 0.019 0.001 TYR B 375 ARG 0.003 0.000 ARG A1260 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 128 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 GLN cc_start: 0.2889 (OUTLIER) cc_final: 0.2077 (pt0) REVERT: A 710 MET cc_start: 0.6208 (tpt) cc_final: 0.5826 (tpt) REVERT: A 803 CYS cc_start: 0.4470 (OUTLIER) cc_final: 0.3891 (m) REVERT: A 1124 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8251 (tt) REVERT: A 1183 TYR cc_start: 0.8601 (t80) cc_final: 0.8209 (t80) REVERT: A 1265 MET cc_start: 0.8001 (tpp) cc_final: 0.7773 (tpt) REVERT: B 78 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8596 (tt) outliers start: 45 outliers final: 29 residues processed: 167 average time/residue: 0.2460 time to fit residues: 59.1021 Evaluate side-chains 149 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1308 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 336 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.9980 chunk 77 optimal weight: 0.3980 chunk 1 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 56 optimal weight: 0.0060 chunk 116 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 122 optimal weight: 0.0980 chunk 34 optimal weight: 7.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 ASN ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11823 Z= 0.179 Angle : 0.606 7.195 16052 Z= 0.311 Chirality : 0.044 0.230 1810 Planarity : 0.005 0.057 2036 Dihedral : 8.365 88.441 1849 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.32 % Favored : 92.61 % Rotamer: Outliers : 3.44 % Allowed : 20.25 % Favored : 76.31 % 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: -2.20 (0.22), residues: 1408 helix: -0.93 (0.21), residues: 592 sheet: -1.08 (0.38), residues: 186 loop : -2.04 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1279 HIS 0.006 0.001 HIS A 717 PHE 0.015 0.001 PHE A1197 TYR 0.020 0.001 TYR B 375 ARG 0.004 0.000 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 135 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 GLN cc_start: 0.2572 (OUTLIER) cc_final: 0.2150 (mt0) REVERT: A 803 CYS cc_start: 0.4072 (OUTLIER) cc_final: 0.3701 (m) REVERT: A 960 GLN cc_start: 0.7435 (mp10) cc_final: 0.7171 (mp10) REVERT: A 1067 GLU cc_start: 0.7311 (mm-30) cc_final: 0.7070 (mm-30) REVERT: A 1183 TYR cc_start: 0.8624 (t80) cc_final: 0.8299 (t80) REVERT: B 78 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8558 (tt) REVERT: B 161 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8429 (t0) outliers start: 42 outliers final: 26 residues processed: 172 average time/residue: 0.2258 time to fit residues: 57.1998 Evaluate side-chains 155 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1308 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 336 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 33 optimal weight: 7.9990 chunk 136 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN B 177 GLN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11823 Z= 0.217 Angle : 0.615 10.024 16052 Z= 0.315 Chirality : 0.044 0.230 1810 Planarity : 0.005 0.057 2036 Dihedral : 7.917 83.645 1849 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.60 % Favored : 92.33 % Rotamer: Outliers : 4.10 % Allowed : 19.92 % Favored : 75.98 % 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: -2.06 (0.23), residues: 1408 helix: -0.80 (0.21), residues: 592 sheet: -0.99 (0.39), residues: 186 loop : -1.98 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1279 HIS 0.013 0.001 HIS B 73 PHE 0.020 0.002 PHE A 833 TYR 0.020 0.001 TYR B 375 ARG 0.004 0.000 ARG A 655 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 129 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 803 CYS cc_start: 0.4122 (OUTLIER) cc_final: 0.3715 (m) REVERT: A 1067 GLU cc_start: 0.7291 (mm-30) cc_final: 0.7065 (mm-30) REVERT: A 1124 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8203 (tt) REVERT: A 1183 TYR cc_start: 0.8650 (t80) cc_final: 0.8316 (t80) REVERT: B 119 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7516 (mt0) REVERT: B 161 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.7993 (t0) REVERT: B 220 ASP cc_start: 0.8043 (m-30) cc_final: 0.7762 (m-30) outliers start: 50 outliers final: 37 residues processed: 171 average time/residue: 0.2393 time to fit residues: 59.3494 Evaluate side-chains 164 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 124 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1030 CYS Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1308 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 336 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 chunk 114 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 84 optimal weight: 0.0970 chunk 54 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11823 Z= 0.190 Angle : 0.602 9.527 16052 Z= 0.308 Chirality : 0.044 0.218 1810 Planarity : 0.005 0.057 2036 Dihedral : 7.491 81.051 1846 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.60 % Favored : 92.33 % Rotamer: Outliers : 4.43 % Allowed : 20.41 % Favored : 75.16 % 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: -1.94 (0.23), residues: 1408 helix: -0.70 (0.22), residues: 591 sheet: -0.92 (0.39), residues: 186 loop : -1.92 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1279 HIS 0.005 0.001 HIS A 829 PHE 0.018 0.002 PHE A 833 TYR 0.021 0.001 TYR B 375 ARG 0.003 0.000 ARG A1260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 130 time to evaluate : 1.144 Fit side-chains revert: symmetry clash REVERT: A 803 CYS cc_start: 0.4078 (OUTLIER) cc_final: 0.3688 (m) REVERT: A 960 GLN cc_start: 0.7461 (mp10) cc_final: 0.7225 (mp10) REVERT: A 1031 ARG cc_start: 0.7749 (tpp80) cc_final: 0.7371 (mtt-85) REVERT: A 1067 GLU cc_start: 0.7291 (mm-30) cc_final: 0.7052 (mm-30) REVERT: A 1124 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8182 (tt) REVERT: A 1183 TYR cc_start: 0.8646 (t80) cc_final: 0.8306 (t80) REVERT: B 119 GLN cc_start: 0.7801 (mm-40) cc_final: 0.7576 (mt0) REVERT: B 220 ASP cc_start: 0.8045 (m-30) cc_final: 0.7767 (m-30) outliers start: 54 outliers final: 37 residues processed: 175 average time/residue: 0.2254 time to fit residues: 57.0834 Evaluate side-chains 166 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 127 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1030 CYS Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1308 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 336 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 123 optimal weight: 0.0980 chunk 130 optimal weight: 0.6980 chunk 118 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11823 Z= 0.180 Angle : 0.604 9.020 16052 Z= 0.308 Chirality : 0.043 0.211 1810 Planarity : 0.005 0.057 2036 Dihedral : 7.264 76.306 1846 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.17 % Favored : 92.76 % Rotamer: Outliers : 3.85 % Allowed : 20.98 % Favored : 75.16 % 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: -1.79 (0.23), residues: 1408 helix: -0.55 (0.22), residues: 585 sheet: -0.91 (0.39), residues: 186 loop : -1.84 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1279 HIS 0.006 0.001 HIS A 829 PHE 0.019 0.001 PHE A 833 TYR 0.022 0.001 TYR B 375 ARG 0.004 0.000 ARG A 870 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 131 time to evaluate : 1.321 Fit side-chains revert: symmetry clash REVERT: A 596 ASP cc_start: 0.7877 (t0) cc_final: 0.7636 (t70) REVERT: A 803 CYS cc_start: 0.4031 (OUTLIER) cc_final: 0.3666 (m) REVERT: A 1031 ARG cc_start: 0.7739 (tpp80) cc_final: 0.7356 (mtt-85) REVERT: A 1067 GLU cc_start: 0.7285 (mm-30) cc_final: 0.7029 (mm-30) REVERT: A 1124 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8148 (tt) REVERT: A 1183 TYR cc_start: 0.8642 (t80) cc_final: 0.8387 (t80) REVERT: B 119 GLN cc_start: 0.7820 (mm-40) cc_final: 0.7575 (mt0) REVERT: B 220 ASP cc_start: 0.8019 (m-30) cc_final: 0.7733 (m-30) outliers start: 47 outliers final: 32 residues processed: 169 average time/residue: 0.2470 time to fit residues: 60.1410 Evaluate side-chains 161 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1030 CYS Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1308 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 336 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 99 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 ASN ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11823 Z= 0.269 Angle : 0.643 8.641 16052 Z= 0.329 Chirality : 0.045 0.228 1810 Planarity : 0.005 0.058 2036 Dihedral : 7.368 79.018 1846 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.03 % Favored : 91.90 % Rotamer: Outliers : 4.10 % Allowed : 21.07 % Favored : 74.84 % 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: -1.85 (0.23), residues: 1408 helix: -0.68 (0.22), residues: 591 sheet: -0.89 (0.40), residues: 180 loop : -1.79 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 120 HIS 0.007 0.001 HIS A 829 PHE 0.019 0.002 PHE A 833 TYR 0.020 0.002 TYR B 375 ARG 0.004 0.000 ARG A1260 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 123 time to evaluate : 1.297 Fit side-chains REVERT: A 803 CYS cc_start: 0.4126 (OUTLIER) cc_final: 0.3713 (m) REVERT: A 1124 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8150 (tt) REVERT: A 1183 TYR cc_start: 0.8654 (t80) cc_final: 0.8249 (t80) REVERT: B 119 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7546 (mt0) outliers start: 50 outliers final: 39 residues processed: 163 average time/residue: 0.2419 time to fit residues: 57.7625 Evaluate side-chains 159 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 118 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1030 CYS Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1308 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 378 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 140 optimal weight: 0.0770 chunk 129 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 11 optimal weight: 0.0170 chunk 86 optimal weight: 0.8980 chunk 68 optimal weight: 0.0270 chunk 88 optimal weight: 0.5980 chunk 119 optimal weight: 0.0370 chunk 34 optimal weight: 8.9990 overall best weight: 0.1512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1117 ASN ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1257 ASN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11823 Z= 0.153 Angle : 0.605 8.657 16052 Z= 0.308 Chirality : 0.043 0.193 1810 Planarity : 0.005 0.057 2036 Dihedral : 6.988 66.231 1846 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.46 % Favored : 93.47 % Rotamer: Outliers : 2.13 % Allowed : 23.03 % Favored : 74.84 % 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: -1.68 (0.23), residues: 1408 helix: -0.45 (0.22), residues: 589 sheet: -0.80 (0.39), residues: 187 loop : -1.81 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1279 HIS 0.007 0.001 HIS A 829 PHE 0.016 0.001 PHE A 833 TYR 0.022 0.001 TYR B 375 ARG 0.005 0.000 ARG A1031 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 1.241 Fit side-chains REVERT: A 731 MET cc_start: 0.2687 (ttm) cc_final: 0.2423 (ttm) REVERT: A 803 CYS cc_start: 0.4042 (OUTLIER) cc_final: 0.3644 (m) REVERT: A 1124 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8128 (tt) REVERT: A 1183 TYR cc_start: 0.8646 (t80) cc_final: 0.8335 (t80) REVERT: B 220 ASP cc_start: 0.7893 (m-30) cc_final: 0.7685 (m-30) outliers start: 26 outliers final: 22 residues processed: 153 average time/residue: 0.2387 time to fit residues: 53.1857 Evaluate side-chains 146 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1030 CYS Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1124 ILE Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 230 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 115 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 98 optimal weight: 0.1980 chunk 6 optimal weight: 30.0000 chunk 80 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.201003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.152515 restraints weight = 13812.266| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 4.02 r_work: 0.3352 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11823 Z= 0.197 Angle : 0.619 8.996 16052 Z= 0.314 Chirality : 0.044 0.202 1810 Planarity : 0.005 0.058 2036 Dihedral : 6.904 65.964 1845 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.24 % Favored : 92.68 % Rotamer: Outliers : 2.46 % Allowed : 22.79 % Favored : 74.75 % 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: -1.64 (0.23), residues: 1408 helix: -0.46 (0.22), residues: 597 sheet: -0.81 (0.39), residues: 187 loop : -1.75 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 120 HIS 0.006 0.001 HIS A 829 PHE 0.018 0.002 PHE A 833 TYR 0.021 0.001 TYR B 375 ARG 0.004 0.000 ARG A1260 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2671.53 seconds wall clock time: 49 minutes 33.23 seconds (2973.23 seconds total)