Starting phenix.real_space_refine on Sat Oct 11 02:55:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jmn_36424/10_2025/8jmn_36424.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jmn_36424/10_2025/8jmn_36424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jmn_36424/10_2025/8jmn_36424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jmn_36424/10_2025/8jmn_36424.map" model { file = "/net/cci-nas-00/data/ceres_data/8jmn_36424/10_2025/8jmn_36424.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jmn_36424/10_2025/8jmn_36424.cif" } resolution = 2.26 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.004 sd= 0.082 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: 9 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 65 5.16 5 Cl 1 4.86 5 Be 1 3.05 5 C 6529 2.51 5 N 1653 2.21 5 O 2233 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10491 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7633 Classifications: {'peptide': 983} Link IDs: {'PTRANS': 47, 'TRANS': 935} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Chain: "B" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2142 Classifications: {'peptide': 268} Link IDs: {'PCIS': 4, 'PTRANS': 18, 'TRANS': 245} Chain: "A" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 219 Unusual residues: {' MG': 1, 'PCW': 4, 'UOU': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 124 Unusual residues: {'CLR': 1, 'NAG': 3, 'PCW': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 260 Classifications: {'water': 260} Link IDs: {None: 259} Chain: "B" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Time building chain proxies: 2.11, per 1000 atoms: 0.20 Number of scatterers: 10491 At special positions: 0 Unit cell: (81.968, 102.272, 171.456, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Cl 1 17.00 S 65 16.00 P 5 15.00 Mg 1 11.99 F 3 9.00 O 2233 8.00 N 1653 7.00 C 6529 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 178 " distance=2.04 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 262 " distance=2.03 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 Links applied NAG-ASN " NAG B 302 " - " ASN B 99 " " NAG B 303 " - " ASN B 130 " " NAG B 304 " - " ASN B 161 " Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 369.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2340 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 9 sheets defined 50.1% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 73 through 84 Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 107 through 130 Processing helix chain 'A' and resid 135 through 169 removed outlier: 3.818A pdb=" N LEU A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 274 through 286 removed outlier: 3.504A pdb=" N VAL A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 322 Processing helix chain 'A' and resid 325 through 341 removed outlier: 3.808A pdb=" N VAL A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 362 Processing helix chain 'A' and resid 371 through 379 removed outlier: 4.265A pdb=" N THR A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLY A 377 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 437 Processing helix chain 'A' and resid 450 through 454 Processing helix chain 'A' and resid 459 through 473 Processing helix chain 'A' and resid 475 through 482 removed outlier: 3.622A pdb=" N ARG A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 removed outlier: 3.786A pdb=" N ARG A 526 " --> pdb=" O ARG A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 557 Processing helix chain 'A' and resid 607 through 618 Processing helix chain 'A' and resid 629 through 640 Processing helix chain 'A' and resid 649 through 658 Processing helix chain 'A' and resid 660 through 664 Processing helix chain 'A' and resid 665 through 669 removed outlier: 3.570A pdb=" N ALA A 669 " --> pdb=" O ARG A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 681 removed outlier: 3.670A pdb=" N ASP A 681 " --> pdb=" O MET A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 694 Processing helix chain 'A' and resid 703 through 717 Processing helix chain 'A' and resid 727 through 729 No H-bonds generated for 'chain 'A' and resid 727 through 729' Processing helix chain 'A' and resid 730 through 737 Processing helix chain 'A' and resid 748 through 755 Processing helix chain 'A' and resid 765 through 791 removed outlier: 3.546A pdb=" N THR A 769 " --> pdb=" O ALA A 765 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 805 Proline residue: A 798 - end of helix Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 824 through 831 removed outlier: 3.603A pdb=" N LEU A 831 " --> pdb=" O PRO A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 834 No H-bonds generated for 'chain 'A' and resid 832 through 834' Processing helix chain 'A' and resid 839 through 843 removed outlier: 3.534A pdb=" N LEU A 843 " --> pdb=" O ILE A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 865 Processing helix chain 'A' and resid 865 through 885 Processing helix chain 'A' and resid 888 through 893 Processing helix chain 'A' and resid 895 through 901 Processing helix chain 'A' and resid 916 through 946 removed outlier: 3.612A pdb=" N ALA A 941 " --> pdb=" O MET A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 957 Processing helix chain 'A' and resid 961 through 981 Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 994 through 1000 removed outlier: 3.797A pdb=" N TRP A 998 " --> pdb=" O ARG A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1022 Processing helix chain 'A' and resid 1025 through 1032 removed outlier: 3.548A pdb=" N TYR A1032 " --> pdb=" O ASP A1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 66 Processing helix chain 'B' and resid 102 through 119 removed outlier: 4.103A pdb=" N TRP B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 163 removed outlier: 6.542A pdb=" N ASN B 161 " --> pdb=" O MET B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 removed outlier: 4.042A pdb=" N THR B 223 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 190 removed outlier: 11.758A pdb=" N GLN A 177 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N LYS A 203 " --> pdb=" O GLN A 177 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR A 179 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N CYS A 258 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LYS A 221 " --> pdb=" O CYS A 258 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLU A 260 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLY A 219 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR A 262 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA A 217 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLN A 264 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP A 211 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS A 220 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 207 removed outlier: 3.807A pdb=" N ASP A 206 " --> pdb=" O CYS A 258 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N CYS A 258 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LYS A 221 " --> pdb=" O CYS A 258 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLU A 260 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLY A 219 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR A 262 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA A 217 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLN A 264 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP A 211 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 367 removed outlier: 6.322A pdb=" N GLY A 740 " --> pdb=" O MET A 757 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU A 759 " --> pdb=" O GLY A 740 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA A 742 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A 721 " --> pdb=" O ILE A 739 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL A 741 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL A 723 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N MET A 743 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLY A 725 " --> pdb=" O MET A 743 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL A 622 " --> pdb=" O MET A 697 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N PHE A 699 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N MET A 624 " --> pdb=" O PHE A 699 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 405 through 408 removed outlier: 5.156A pdb=" N VAL A 397 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE A 601 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS A 399 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N PHE A 594 " --> pdb=" O GLN A 566 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN A 566 " --> pdb=" O PHE A 594 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A 503 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS A 485 " --> pdb=" O THR A 503 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 408 removed outlier: 5.156A pdb=" N VAL A 397 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE A 601 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS A 399 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N SER A 529 " --> pdb=" O PHE A 594 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLY A 596 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N LEU A 531 " --> pdb=" O GLY A 596 " (cutoff:3.500A) removed outlier: 12.189A pdb=" N VAL A 598 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 441 through 442 removed outlier: 3.527A pdb=" N ALA A 441 " --> pdb=" O ILE A 457 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 908 Processing sheet with id=AA8, first strand: chain 'B' and resid 82 through 85 Processing sheet with id=AA9, first strand: chain 'B' and resid 94 through 99 removed outlier: 4.524A pdb=" N LEU B 94 " --> pdb=" O GLU B 283 " (cutoff:3.500A) 522 hydrogen bonds defined for protein. 1497 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: 2.14 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1622 1.31 - 1.43: 2697 1.43 - 1.56: 5916 1.56 - 1.69: 10 1.69 - 1.82: 98 Bond restraints: 10343 Sorted by residual: bond pdb=" F3 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.529 1.764 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" F2 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.535 1.752 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" F1 BFD A 385 " pdb="BE BFD A 385 " ideal model delta sigma weight residual 1.542 1.750 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" CG BFD A 385 " pdb=" OD1 BFD A 385 " ideal model delta sigma weight residual 1.269 1.446 -0.177 2.00e-02 2.50e+03 7.87e+01 bond pdb=" C11 PCW A1103 " pdb=" O3 PCW A1103 " ideal model delta sigma weight residual 1.326 1.455 -0.129 2.00e-02 2.50e+03 4.19e+01 ... (remaining 10338 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.07: 13943 5.07 - 10.14: 65 10.14 - 15.21: 4 15.21 - 20.28: 2 20.28 - 25.35: 3 Bond angle restraints: 14017 Sorted by residual: angle pdb=" C5 PCW A1104 " pdb=" N PCW A1104 " pdb=" C8 PCW A1104 " ideal model delta sigma weight residual 111.64 86.29 25.35 3.00e+00 1.11e-01 7.14e+01 angle pdb=" C6 PCW A1104 " pdb=" N PCW A1104 " pdb=" C8 PCW A1104 " ideal model delta sigma weight residual 109.11 86.09 23.02 3.00e+00 1.11e-01 5.89e+01 angle pdb=" C7 PCW A1104 " pdb=" N PCW A1104 " pdb=" C8 PCW A1104 " ideal model delta sigma weight residual 108.24 86.90 21.34 3.00e+00 1.11e-01 5.06e+01 angle pdb=" OD1 BFD A 385 " pdb="BE BFD A 385 " pdb=" F1 BFD A 385 " ideal model delta sigma weight residual 102.38 119.00 -16.62 3.00e+00 1.11e-01 3.07e+01 angle pdb=" F2 BFD A 385 " pdb="BE BFD A 385 " pdb=" F3 BFD A 385 " ideal model delta sigma weight residual 112.60 96.08 16.52 3.00e+00 1.11e-01 3.03e+01 ... (remaining 14012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 6048 35.45 - 70.90: 274 70.90 - 106.35: 18 106.35 - 141.80: 3 141.80 - 177.25: 2 Dihedral angle restraints: 6345 sinusoidal: 2712 harmonic: 3633 Sorted by residual: dihedral pdb=" N PCW A1104 " pdb=" C4 PCW A1104 " pdb=" C5 PCW A1104 " pdb=" O4P PCW A1104 " ideal model delta sinusoidal sigma weight residual 293.34 116.09 177.25 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW A1104 " pdb=" C31 PCW A1104 " pdb=" C32 PCW A1104 " pdb=" O2 PCW A1104 " ideal model delta sinusoidal sigma weight residual 191.83 39.31 152.52 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" N PCW A1105 " pdb=" C4 PCW A1105 " pdb=" C5 PCW A1105 " pdb=" O4P PCW A1105 " ideal model delta sinusoidal sigma weight residual 293.34 151.86 141.48 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 6342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1266 0.054 - 0.108: 255 0.108 - 0.162: 36 0.162 - 0.215: 5 0.215 - 0.269: 4 Chirality restraints: 1566 Sorted by residual: chirality pdb=" C1 NAG B 302 " pdb=" ND2 ASN B 99 " pdb=" C2 NAG B 302 " pdb=" O5 NAG B 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C2 PCW A1101 " pdb=" C1 PCW A1101 " pdb=" C3 PCW A1101 " pdb=" O2 PCW A1101 " both_signs ideal model delta sigma weight residual False -2.32 -2.57 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" C2 PCW A1103 " pdb=" C1 PCW A1103 " pdb=" C3 PCW A1103 " pdb=" O2 PCW A1103 " both_signs ideal model delta sigma weight residual False -2.32 -2.56 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 1563 not shown) Planarity restraints: 1782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 304 " -0.348 2.00e-02 2.50e+03 2.99e-01 1.11e+03 pdb=" C7 NAG B 304 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG B 304 " -0.152 2.00e-02 2.50e+03 pdb=" N2 NAG B 304 " 0.530 2.00e-02 2.50e+03 pdb=" O7 NAG B 304 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 303 " -0.311 2.00e-02 2.50e+03 2.69e-01 9.04e+02 pdb=" C7 NAG B 303 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG B 303 " -0.017 2.00e-02 2.50e+03 pdb=" N2 NAG B 303 " 0.465 2.00e-02 2.50e+03 pdb=" O7 NAG B 303 " -0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 302 " 0.048 2.00e-02 2.50e+03 3.94e-02 1.94e+01 pdb=" C7 NAG B 302 " -0.014 2.00e-02 2.50e+03 pdb=" C8 NAG B 302 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG B 302 " -0.062 2.00e-02 2.50e+03 pdb=" O7 NAG B 302 " -0.008 2.00e-02 2.50e+03 ... (remaining 1779 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 105 2.49 - 3.09: 7309 3.09 - 3.70: 17563 3.70 - 4.30: 26881 4.30 - 4.90: 41347 Nonbonded interactions: 93205 Sorted by model distance: nonbonded pdb="MG MG A1102 " pdb=" O HOH A1225 " model vdw 1.890 2.170 nonbonded pdb=" O THR A 387 " pdb="MG MG A1102 " model vdw 1.984 2.170 nonbonded pdb=" OD2 ASP A 877 " pdb=" O HOH A1201 " model vdw 2.143 3.040 nonbonded pdb=" O PRO B 145 " pdb=" OG1 THR B 148 " model vdw 2.144 3.040 nonbonded pdb=" OD2 BFD A 385 " pdb="MG MG A1102 " model vdw 2.162 2.170 ... (remaining 93200 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=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: 7.050 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.190 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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: 0.000 Load rotamer database and sin/cos tables:9.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 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 : 0.007 0.235 10349 Z= 0.337 Angle : 0.915 25.350 14032 Z= 0.378 Chirality : 0.045 0.269 1566 Planarity : 0.011 0.299 1779 Dihedral : 18.686 177.253 3996 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.29 % Allowed : 19.45 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.24), residues: 1244 helix: 1.68 (0.21), residues: 584 sheet: 0.07 (0.40), residues: 157 loop : -0.03 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 850 TYR 0.013 0.001 TYR B 136 PHE 0.017 0.002 PHE A 970 TRP 0.012 0.002 TRP A 427 HIS 0.003 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00680 (10343) covalent geometry : angle 0.91189 (14017) SS BOND : bond 0.00273 ( 3) SS BOND : angle 0.75041 ( 6) hydrogen bonds : bond 0.11269 ( 511) hydrogen bonds : angle 5.20411 ( 1497) link_NAG-ASN : bond 0.00828 ( 3) link_NAG-ASN : angle 2.93391 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 540 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6874 (p0) REVERT: A 850 ARG cc_start: 0.7689 (mtm110) cc_final: 0.7474 (mtm110) REVERT: B 135 LYS cc_start: 0.7565 (tptp) cc_final: 0.7183 (tttm) outliers start: 35 outliers final: 28 residues processed: 150 average time/residue: 0.7324 time to fit residues: 116.0557 Evaluate side-chains 143 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 974 ILE Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 194 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 446 GLN B 76 GLN B 160 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.153967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.108549 restraints weight = 9142.754| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.33 r_work: 0.2998 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.0588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10349 Z= 0.152 Angle : 0.594 10.963 14032 Z= 0.302 Chirality : 0.045 0.267 1566 Planarity : 0.005 0.057 1779 Dihedral : 13.927 160.427 1743 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.01 % Allowed : 17.95 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.24), residues: 1244 helix: 1.62 (0.21), residues: 591 sheet: 0.07 (0.40), residues: 155 loop : 0.10 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 946 TYR 0.013 0.002 TYR A 802 PHE 0.018 0.002 PHE A 300 TRP 0.012 0.002 TRP A 427 HIS 0.004 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00336 (10343) covalent geometry : angle 0.58820 (14017) SS BOND : bond 0.00429 ( 3) SS BOND : angle 0.95962 ( 6) hydrogen bonds : bond 0.04958 ( 511) hydrogen bonds : angle 4.42886 ( 1497) link_NAG-ASN : bond 0.00816 ( 3) link_NAG-ASN : angle 3.30897 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 143 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8352 (tp) REVERT: A 453 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7499 (ttmm) REVERT: A 516 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7528 (tpp) REVERT: A 540 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7164 (p0) REVERT: B 78 LYS cc_start: 0.8765 (mppt) cc_final: 0.8538 (mppt) REVERT: B 135 LYS cc_start: 0.7575 (tptp) cc_final: 0.7227 (tttm) outliers start: 32 outliers final: 14 residues processed: 137 average time/residue: 0.7739 time to fit residues: 111.8613 Evaluate side-chains 131 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 140 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 112 optimal weight: 0.0980 chunk 22 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 446 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.152870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107462 restraints weight = 9160.099| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.33 r_work: 0.2984 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10349 Z= 0.160 Angle : 0.586 9.234 14032 Z= 0.301 Chirality : 0.045 0.269 1566 Planarity : 0.005 0.054 1779 Dihedral : 13.379 163.383 1717 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.01 % Allowed : 17.01 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.23), residues: 1244 helix: 1.58 (0.21), residues: 590 sheet: -0.05 (0.38), residues: 165 loop : 0.16 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 844 TYR 0.015 0.002 TYR A 802 PHE 0.016 0.002 PHE A 497 TRP 0.012 0.002 TRP A 427 HIS 0.004 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00358 (10343) covalent geometry : angle 0.58230 (14017) SS BOND : bond 0.00449 ( 3) SS BOND : angle 0.84053 ( 6) hydrogen bonds : bond 0.05013 ( 511) hydrogen bonds : angle 4.37862 ( 1497) link_NAG-ASN : bond 0.00695 ( 3) link_NAG-ASN : angle 2.65491 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 453 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7493 (ttmm) REVERT: A 540 ASP cc_start: 0.7124 (OUTLIER) cc_final: 0.6875 (p0) REVERT: B 78 LYS cc_start: 0.8786 (mppt) cc_final: 0.8515 (mppt) REVERT: B 135 LYS cc_start: 0.7565 (tptp) cc_final: 0.7230 (tttm) outliers start: 32 outliers final: 13 residues processed: 134 average time/residue: 0.8955 time to fit residues: 126.2110 Evaluate side-chains 127 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 103 optimal weight: 0.0980 chunk 112 optimal weight: 0.0370 chunk 105 optimal weight: 0.7980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 446 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.155968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111474 restraints weight = 9319.923| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.35 r_work: 0.3046 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10349 Z= 0.104 Angle : 0.502 7.728 14032 Z= 0.257 Chirality : 0.042 0.257 1566 Planarity : 0.004 0.052 1779 Dihedral : 12.789 167.828 1713 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.63 % Allowed : 17.76 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.24), residues: 1244 helix: 1.86 (0.22), residues: 589 sheet: 0.09 (0.38), residues: 160 loop : 0.27 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 850 TYR 0.010 0.001 TYR A 802 PHE 0.021 0.001 PHE A 300 TRP 0.010 0.001 TRP A 427 HIS 0.003 0.001 HIS A 502 Details of bonding type rmsd covalent geometry : bond 0.00220 (10343) covalent geometry : angle 0.49881 (14017) SS BOND : bond 0.00207 ( 3) SS BOND : angle 0.46468 ( 6) hydrogen bonds : bond 0.03914 ( 511) hydrogen bonds : angle 4.12062 ( 1497) link_NAG-ASN : bond 0.00660 ( 3) link_NAG-ASN : angle 2.16700 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8348 (tp) REVERT: A 192 ASP cc_start: 0.7562 (m-30) cc_final: 0.6829 (p0) REVERT: A 960 ARG cc_start: 0.7888 (mtt180) cc_final: 0.7252 (mtt180) REVERT: B 135 LYS cc_start: 0.7306 (tptp) cc_final: 0.7036 (tttm) outliers start: 28 outliers final: 11 residues processed: 135 average time/residue: 0.8621 time to fit residues: 122.6494 Evaluate side-chains 124 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 97 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 116 optimal weight: 0.0570 chunk 91 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 405 HIS A 446 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.155495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110098 restraints weight = 9216.523| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.37 r_work: 0.3027 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10349 Z= 0.116 Angle : 0.522 6.675 14032 Z= 0.265 Chirality : 0.043 0.271 1566 Planarity : 0.004 0.050 1779 Dihedral : 12.671 169.835 1711 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.63 % Allowed : 17.67 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.24), residues: 1244 helix: 1.85 (0.21), residues: 589 sheet: 0.18 (0.38), residues: 160 loop : 0.32 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 850 TYR 0.012 0.001 TYR A 802 PHE 0.021 0.001 PHE A 300 TRP 0.010 0.001 TRP A 427 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.00249 (10343) covalent geometry : angle 0.51172 (14017) SS BOND : bond 0.00398 ( 3) SS BOND : angle 1.17364 ( 6) hydrogen bonds : bond 0.04138 ( 511) hydrogen bonds : angle 4.11667 ( 1497) link_NAG-ASN : bond 0.00377 ( 3) link_NAG-ASN : angle 3.92523 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 143 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8359 (tp) REVERT: A 192 ASP cc_start: 0.7569 (m-30) cc_final: 0.6824 (p0) REVERT: A 216 GLN cc_start: 0.7982 (mt0) cc_final: 0.7722 (tt0) REVERT: A 477 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7382 (mtm) REVERT: A 572 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.6914 (mppt) REVERT: A 946 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.7945 (mpt90) REVERT: B 29 MET cc_start: 0.7656 (ttt) cc_final: 0.7328 (ttp) REVERT: B 135 LYS cc_start: 0.7475 (tptp) cc_final: 0.7198 (tttm) outliers start: 28 outliers final: 11 residues processed: 129 average time/residue: 0.8739 time to fit residues: 118.6494 Evaluate side-chains 124 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain A residue 974 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 6 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 446 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.154026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.108424 restraints weight = 9255.310| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.35 r_work: 0.3000 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10349 Z= 0.143 Angle : 0.553 8.478 14032 Z= 0.283 Chirality : 0.044 0.252 1566 Planarity : 0.005 0.049 1779 Dihedral : 12.696 170.180 1710 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.35 % Allowed : 18.33 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.24), residues: 1244 helix: 1.80 (0.21), residues: 587 sheet: 0.17 (0.39), residues: 160 loop : 0.25 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 850 TYR 0.015 0.002 TYR A 802 PHE 0.018 0.002 PHE A 300 TRP 0.011 0.002 TRP A 427 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.00320 (10343) covalent geometry : angle 0.54255 (14017) SS BOND : bond 0.00390 ( 3) SS BOND : angle 0.66799 ( 6) hydrogen bonds : bond 0.04609 ( 511) hydrogen bonds : angle 4.21391 ( 1497) link_NAG-ASN : bond 0.00779 ( 3) link_NAG-ASN : angle 4.19426 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 143 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8341 (tp) REVERT: A 192 ASP cc_start: 0.7575 (m-30) cc_final: 0.6843 (p0) REVERT: A 216 GLN cc_start: 0.7987 (mt0) cc_final: 0.7728 (tt0) REVERT: A 453 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7469 (ttmm) REVERT: A 572 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6914 (mppt) REVERT: A 946 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.7994 (mpt90) REVERT: B 29 MET cc_start: 0.7681 (ttt) cc_final: 0.7409 (ttp) outliers start: 25 outliers final: 13 residues processed: 131 average time/residue: 0.8774 time to fit residues: 121.2091 Evaluate side-chains 129 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 75 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 84 optimal weight: 0.0980 chunk 78 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 446 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.154371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109130 restraints weight = 9277.767| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.36 r_work: 0.3011 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10349 Z= 0.134 Angle : 0.538 6.551 14032 Z= 0.277 Chirality : 0.044 0.255 1566 Planarity : 0.005 0.049 1779 Dihedral : 12.606 172.134 1710 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.44 % Allowed : 18.42 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.24), residues: 1244 helix: 1.78 (0.21), residues: 587 sheet: 0.16 (0.39), residues: 160 loop : 0.26 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 850 TYR 0.013 0.002 TYR A 802 PHE 0.018 0.002 PHE A 300 TRP 0.011 0.001 TRP A 427 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.00296 (10343) covalent geometry : angle 0.53032 (14017) SS BOND : bond 0.00365 ( 3) SS BOND : angle 0.60887 ( 6) hydrogen bonds : bond 0.04460 ( 511) hydrogen bonds : angle 4.17604 ( 1497) link_NAG-ASN : bond 0.00965 ( 3) link_NAG-ASN : angle 3.56316 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 143 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8327 (tp) REVERT: A 192 ASP cc_start: 0.7555 (m-30) cc_final: 0.6822 (p0) REVERT: A 216 GLN cc_start: 0.7912 (mt0) cc_final: 0.7645 (tt0) REVERT: A 453 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7459 (ttmm) REVERT: A 572 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.6939 (mppt) REVERT: A 844 ARG cc_start: 0.8214 (mmp80) cc_final: 0.7741 (mmm160) REVERT: A 946 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.7993 (mpt90) REVERT: B 29 MET cc_start: 0.7680 (ttt) cc_final: 0.7341 (ttp) REVERT: B 135 LYS cc_start: 0.7510 (tptp) cc_final: 0.7188 (tttm) outliers start: 26 outliers final: 14 residues processed: 133 average time/residue: 0.9011 time to fit residues: 126.0136 Evaluate side-chains 130 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 122 optimal weight: 0.9990 chunk 84 optimal weight: 0.3980 chunk 91 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 120 optimal weight: 0.6980 chunk 95 optimal weight: 0.0070 chunk 22 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 404 ASN A 405 HIS A 446 GLN A 495 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.155584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110501 restraints weight = 9191.555| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.36 r_work: 0.3029 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10349 Z= 0.115 Angle : 0.516 6.620 14032 Z= 0.265 Chirality : 0.043 0.253 1566 Planarity : 0.004 0.048 1779 Dihedral : 12.383 174.438 1710 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.69 % Allowed : 19.45 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.24), residues: 1244 helix: 1.83 (0.22), residues: 589 sheet: 0.23 (0.40), residues: 155 loop : 0.34 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 850 TYR 0.012 0.001 TYR A 802 PHE 0.023 0.001 PHE A 300 TRP 0.010 0.001 TRP A 427 HIS 0.003 0.001 HIS A 502 Details of bonding type rmsd covalent geometry : bond 0.00251 (10343) covalent geometry : angle 0.50935 (14017) SS BOND : bond 0.00292 ( 3) SS BOND : angle 0.56055 ( 6) hydrogen bonds : bond 0.04129 ( 511) hydrogen bonds : angle 4.08170 ( 1497) link_NAG-ASN : bond 0.00793 ( 3) link_NAG-ASN : angle 3.27470 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.410 Fit side-chains REVERT: A 143 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8348 (tp) REVERT: A 192 ASP cc_start: 0.7552 (m-30) cc_final: 0.6811 (p0) REVERT: A 216 GLN cc_start: 0.7910 (mt0) cc_final: 0.7641 (tt0) REVERT: A 453 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7423 (ttmm) REVERT: A 477 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7393 (mtm) REVERT: A 572 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.6909 (mppt) REVERT: A 844 ARG cc_start: 0.8185 (mmp80) cc_final: 0.7740 (mmm160) REVERT: A 946 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.7940 (mpt90) REVERT: B 29 MET cc_start: 0.7696 (ttt) cc_final: 0.7327 (ttp) REVERT: B 135 LYS cc_start: 0.7443 (tptp) cc_final: 0.7132 (tttm) outliers start: 18 outliers final: 10 residues processed: 122 average time/residue: 0.9588 time to fit residues: 122.7256 Evaluate side-chains 123 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 74 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 112 optimal weight: 0.1980 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 404 ASN A 405 HIS A 446 GLN A 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.155688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.110622 restraints weight = 9190.947| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.36 r_work: 0.3031 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10349 Z= 0.115 Angle : 0.515 7.341 14032 Z= 0.264 Chirality : 0.043 0.247 1566 Planarity : 0.004 0.053 1779 Dihedral : 12.119 176.163 1704 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.69 % Allowed : 19.36 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.24), residues: 1244 helix: 1.82 (0.21), residues: 589 sheet: 0.24 (0.40), residues: 155 loop : 0.37 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 850 TYR 0.012 0.001 TYR A 802 PHE 0.023 0.001 PHE A 970 TRP 0.011 0.001 TRP A 427 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.00250 (10343) covalent geometry : angle 0.50956 (14017) SS BOND : bond 0.00288 ( 3) SS BOND : angle 0.56167 ( 6) hydrogen bonds : bond 0.04105 ( 511) hydrogen bonds : angle 4.05689 ( 1497) link_NAG-ASN : bond 0.00788 ( 3) link_NAG-ASN : angle 3.02032 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.364 Fit side-chains REVERT: A 143 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8348 (tp) REVERT: A 192 ASP cc_start: 0.7570 (m-30) cc_final: 0.6828 (p0) REVERT: A 216 GLN cc_start: 0.7952 (mt0) cc_final: 0.7693 (tt0) REVERT: A 447 ASP cc_start: 0.6584 (OUTLIER) cc_final: 0.6080 (m-30) REVERT: A 453 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7403 (ttmm) REVERT: A 572 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.6857 (mppt) REVERT: A 844 ARG cc_start: 0.8183 (mmp80) cc_final: 0.7738 (mmm160) REVERT: A 850 ARG cc_start: 0.7737 (mtm110) cc_final: 0.7252 (ttm170) REVERT: A 946 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.7936 (mpt90) REVERT: B 29 MET cc_start: 0.7739 (ttt) cc_final: 0.7360 (ttp) REVERT: B 135 LYS cc_start: 0.7450 (tptp) cc_final: 0.7136 (tttm) outliers start: 18 outliers final: 8 residues processed: 124 average time/residue: 0.9514 time to fit residues: 123.7765 Evaluate side-chains 122 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain B residue 30 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 405 HIS A 446 GLN A 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.155394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.110272 restraints weight = 9111.842| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.36 r_work: 0.3026 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10349 Z= 0.121 Angle : 0.526 8.774 14032 Z= 0.270 Chirality : 0.043 0.246 1566 Planarity : 0.004 0.054 1779 Dihedral : 12.062 176.764 1704 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.60 % Allowed : 19.27 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.24), residues: 1244 helix: 1.82 (0.21), residues: 587 sheet: 0.23 (0.40), residues: 155 loop : 0.34 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 850 TYR 0.013 0.001 TYR A 802 PHE 0.020 0.001 PHE A 300 TRP 0.011 0.001 TRP A 427 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.00266 (10343) covalent geometry : angle 0.52129 (14017) SS BOND : bond 0.00314 ( 3) SS BOND : angle 0.57571 ( 6) hydrogen bonds : bond 0.04219 ( 511) hydrogen bonds : angle 4.07493 ( 1497) link_NAG-ASN : bond 0.00762 ( 3) link_NAG-ASN : angle 2.94499 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.468 Fit side-chains REVERT: A 143 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8345 (tp) REVERT: A 192 ASP cc_start: 0.7566 (m-30) cc_final: 0.6806 (p0) REVERT: A 216 GLN cc_start: 0.7914 (mt0) cc_final: 0.7649 (tt0) REVERT: A 447 ASP cc_start: 0.6564 (OUTLIER) cc_final: 0.6069 (m-30) REVERT: A 453 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7414 (ttmm) REVERT: A 477 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7342 (mtm) REVERT: A 572 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.6840 (mppt) REVERT: A 844 ARG cc_start: 0.8196 (mmp80) cc_final: 0.7742 (mmm160) REVERT: A 850 ARG cc_start: 0.7743 (mtm110) cc_final: 0.7258 (ttm170) REVERT: A 946 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.7945 (mpt90) REVERT: B 29 MET cc_start: 0.7728 (ttt) cc_final: 0.7352 (ttp) REVERT: B 135 LYS cc_start: 0.7440 (tptp) cc_final: 0.7131 (tttm) REVERT: B 254 ARG cc_start: 0.8526 (mpt180) cc_final: 0.8268 (mpt180) outliers start: 17 outliers final: 8 residues processed: 122 average time/residue: 0.9569 time to fit residues: 122.4667 Evaluate side-chains 123 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain B residue 30 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 13 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 122 optimal weight: 0.0020 chunk 43 optimal weight: 0.0670 chunk 103 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 overall best weight: 0.5526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN A 405 HIS A 446 GLN A 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.156011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.110931 restraints weight = 9268.459| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.36 r_work: 0.3036 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10349 Z= 0.113 Angle : 0.517 8.907 14032 Z= 0.264 Chirality : 0.042 0.244 1566 Planarity : 0.004 0.050 1779 Dihedral : 11.931 178.391 1704 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.32 % Allowed : 19.74 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.24), residues: 1244 helix: 1.84 (0.21), residues: 589 sheet: 0.17 (0.39), residues: 158 loop : 0.42 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 850 TYR 0.012 0.001 TYR A 802 PHE 0.025 0.001 PHE A 970 TRP 0.010 0.001 TRP A 427 HIS 0.003 0.001 HIS A 502 Details of bonding type rmsd covalent geometry : bond 0.00247 (10343) covalent geometry : angle 0.51263 (14017) SS BOND : bond 0.00286 ( 3) SS BOND : angle 0.55220 ( 6) hydrogen bonds : bond 0.04044 ( 511) hydrogen bonds : angle 4.02276 ( 1497) link_NAG-ASN : bond 0.00767 ( 3) link_NAG-ASN : angle 2.82027 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5534.33 seconds wall clock time: 94 minutes 45.25 seconds (5685.25 seconds total)