Starting phenix.real_space_refine on Fri Jul 3 00:17:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jmn_36424/07_2026/8jmn_36424.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jmn_36424/07_2026/8jmn_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_36424/07_2026/8jmn_36424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jmn_36424/07_2026/8jmn_36424.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8jmn_36424/07_2026/8jmn_36424.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jmn_36424/07_2026/8jmn_36424.cif" model { file = "/net/cci-nas-00/data/ceres_data/8jmn_36424/07_2026/8jmn_36424.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jmn_36424/07_2026/8jmn_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-dev-6108/lib/python3.11/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 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: 2.35, per 1000 atoms: 0.22 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: 0.94 Conformation dependent library (CDL) restraints added in 421.7 milliseconds 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: 0.29 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: 1.95 Time building geometry restraints manager: 1.22 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: 5899 35.45 - 70.90: 258 70.90 - 106.35: 14 106.35 - 141.80: 3 141.80 - 177.25: 2 Dihedral angle restraints: 6176 sinusoidal: 2543 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 6173 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: 9.140 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.590 Find NCS groups from input model: 0.060 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:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 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 : 18.475 177.253 3827 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 are 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/Z covalent geometry : bond 0.00680 / 0.34 (10343) covalent geometry : angle 0.91189 / 0.38 (14017) SS BOND : bond 0.00273 / 0.13 ( 3) SS BOND : angle 0.75041 / 0.71 ( 6) hydrogen bonds : bond 0.11269 / 7.28 ( 511) hydrogen bonds : angle 5.20411 / 3.75 ( 1497) link_NAG-ASN : bond 0.00828 / 0.40 ( 3) link_NAG-ASN : angle 2.93391 / 2.19 ( 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 : 0.403 Fit side-chains revert: symmetry clash 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: 29 residues processed: 150 average time/residue: 0.6779 time to fit residues: 108.1396 Evaluate side-chains 144 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 70 LYS 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: 0.9980 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: 0.1980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3758 r_free = 0.3758 target = 0.153809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.108395 restraints weight = 9134.534| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.33 r_work: 0.2996 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.0612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10349 Z= 0.152 Angle : 0.598 11.204 14032 Z= 0.303 Chirality : 0.045 0.293 1566 Planarity : 0.005 0.057 1779 Dihedral : 12.783 159.483 1578 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.38 % Allowed : 17.29 % 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 are not related in a simple way. whole: 1.17 (0.24), residues: 1244 helix: 1.60 (0.21), residues: 591 sheet: 0.01 (0.39), residues: 165 loop : 0.15 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 946 TYR 0.013 0.002 TYR B 43 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/Z covalent geometry : bond 0.00336 / 0.15 (10343) covalent geometry : angle 0.59170 / 0.30 (14017) SS BOND : bond 0.00497 / 0.24 ( 3) SS BOND : angle 1.04384 / 1.01 ( 6) hydrogen bonds : bond 0.04990 / 3.39 ( 511) hydrogen bonds : angle 4.42025 / 3.23 ( 1497) link_NAG-ASN : bond 0.00689 / 0.34 ( 3) link_NAG-ASN : angle 3.37729 / 2.45 ( 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 152 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 143 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8346 (tp) REVERT: A 453 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7494 (ttmm) REVERT: A 516 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7539 (tpp) REVERT: A 540 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.7171 (p0) REVERT: B 78 LYS cc_start: 0.8769 (mppt) cc_final: 0.8535 (mppt) REVERT: B 135 LYS cc_start: 0.7561 (tptp) cc_final: 0.7223 (tttm) outliers start: 36 outliers final: 15 residues processed: 138 average time/residue: 0.7423 time to fit residues: 108.4883 Evaluate side-chains 131 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR 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 196 VAL 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 chunk 109 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 93 optimal weight: 0.0870 chunk 112 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 GLN A 404 ASN A 405 HIS A 446 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.155264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.110228 restraints weight = 9198.645| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.35 r_work: 0.3029 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10349 Z= 0.116 Angle : 0.523 8.279 14032 Z= 0.268 Chirality : 0.043 0.242 1566 Planarity : 0.004 0.054 1779 Dihedral : 11.963 158.329 1549 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.10 % Allowed : 17.01 % Favored : 79.89 % 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 are not related in a simple way. whole: 1.36 (0.24), residues: 1244 helix: 1.77 (0.21), residues: 593 sheet: -0.01 (0.38), residues: 165 loop : 0.28 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 850 TYR 0.011 0.001 TYR A 802 PHE 0.019 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/Z covalent geometry : bond 0.00249 / 0.12 (10343) covalent geometry : angle 0.52037 / 0.27 (14017) SS BOND : bond 0.00261 / 0.12 ( 3) SS BOND : angle 0.59929 / 0.59 ( 6) hydrogen bonds : bond 0.04203 / 2.85 ( 511) hydrogen bonds : angle 4.18627 / 3.07 ( 1497) link_NAG-ASN : bond 0.00649 / 0.32 ( 3) link_NAG-ASN : angle 2.23906 / 1.80 ( 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 153 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8343 (tp) REVERT: A 192 ASP cc_start: 0.7535 (m-30) cc_final: 0.6846 (p0) REVERT: A 453 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7470 (ttmm) REVERT: A 960 ARG cc_start: 0.7848 (mtt180) cc_final: 0.7211 (mtt180) REVERT: B 78 LYS cc_start: 0.8734 (mppt) cc_final: 0.8496 (mppt) REVERT: B 135 LYS cc_start: 0.7400 (tptp) cc_final: 0.7111 (tttm) outliers start: 33 outliers final: 12 residues processed: 138 average time/residue: 0.6852 time to fit residues: 100.0801 Evaluate side-chains 128 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 203 LYS 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 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: 6.9990 chunk 24 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 74 optimal weight: 0.2980 chunk 5 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.154569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109165 restraints weight = 9208.612| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.34 r_work: 0.3010 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.0848 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= 0.128 Angle : 0.532 6.646 14032 Z= 0.274 Chirality : 0.043 0.240 1566 Planarity : 0.005 0.052 1779 Dihedral : 11.691 160.222 1542 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.73 % Allowed : 17.48 % Favored : 79.79 % 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 are not related in a simple way. whole: 1.37 (0.24), residues: 1244 helix: 1.80 (0.21), residues: 587 sheet: 0.08 (0.38), residues: 162 loop : 0.24 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 850 TYR 0.013 0.001 TYR A 802 PHE 0.021 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/Z covalent geometry : bond 0.00282 / 0.13 (10343) covalent geometry : angle 0.52941 / 0.27 (14017) SS BOND : bond 0.00321 / 0.15 ( 3) SS BOND : angle 0.60187 / 0.57 ( 6) hydrogen bonds : bond 0.04429 / 3.00 ( 511) hydrogen bonds : angle 4.20352 / 3.08 ( 1497) link_NAG-ASN : bond 0.00581 / 0.28 ( 3) link_NAG-ASN : angle 2.12654 / 1.69 ( 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 139 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8361 (tp) REVERT: A 192 ASP cc_start: 0.7533 (m-30) cc_final: 0.6781 (p0) REVERT: A 477 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7433 (mtm) REVERT: B 78 LYS cc_start: 0.8751 (mppt) cc_final: 0.8545 (mppt) REVERT: B 135 LYS cc_start: 0.7514 (tptp) cc_final: 0.7203 (tttm) outliers start: 29 outliers final: 12 residues processed: 127 average time/residue: 0.7902 time to fit residues: 105.5770 Evaluate side-chains 126 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 203 LYS 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 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 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: 0.9990 chunk 106 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3765 r_free = 0.3765 target = 0.154362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.108832 restraints weight = 9196.525| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.36 r_work: 0.3006 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10349 Z= 0.132 Angle : 0.544 6.449 14032 Z= 0.278 Chirality : 0.044 0.240 1566 Planarity : 0.005 0.050 1779 Dihedral : 11.536 162.933 1542 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.73 % Allowed : 17.67 % 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 are not related in a simple way. whole: 1.39 (0.24), residues: 1244 helix: 1.79 (0.21), residues: 587 sheet: 0.12 (0.38), residues: 162 loop : 0.26 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 850 TYR 0.014 0.001 TYR A 802 PHE 0.017 0.002 PHE A 300 TRP 0.011 0.001 TRP A 427 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (10343) covalent geometry : angle 0.53698 / 0.28 (14017) SS BOND : bond 0.00559 / 0.28 ( 3) SS BOND : angle 1.32933 / 0.89 ( 6) hydrogen bonds : bond 0.04469 / 3.03 ( 511) hydrogen bonds : angle 4.18798 / 3.07 ( 1497) link_NAG-ASN : bond 0.00346 / 0.18 ( 3) link_NAG-ASN : angle 3.43601 / 2.29 ( 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 145 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 143 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8359 (tp) REVERT: A 192 ASP cc_start: 0.7560 (m-30) cc_final: 0.6820 (p0) REVERT: A 216 GLN cc_start: 0.8026 (mt0) cc_final: 0.7769 (tt0) REVERT: A 453 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7515 (ttmm) REVERT: A 477 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7439 (mtm) REVERT: A 572 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.6886 (mppt) REVERT: A 946 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.7995 (mpt90) REVERT: B 78 LYS cc_start: 0.8757 (mppt) cc_final: 0.8549 (mppt) outliers start: 29 outliers final: 12 residues processed: 134 average time/residue: 0.7822 time to fit residues: 110.8172 Evaluate side-chains 127 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 6 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 0.0060 chunk 62 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3764 r_free = 0.3764 target = 0.154175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.108572 restraints weight = 9238.550| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.36 r_work: 0.3002 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.0958 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= 0.136 Angle : 0.542 7.538 14032 Z= 0.279 Chirality : 0.044 0.241 1566 Planarity : 0.005 0.049 1779 Dihedral : 11.454 166.830 1541 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.26 % Allowed : 18.33 % Favored : 79.42 % 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 are not related in a simple way. whole: 1.37 (0.24), residues: 1244 helix: 1.77 (0.21), residues: 587 sheet: 0.11 (0.38), residues: 162 loop : 0.26 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 850 TYR 0.014 0.002 TYR A 802 PHE 0.021 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/Z covalent geometry : bond 0.00301 / 0.14 (10343) covalent geometry : angle 0.53378 / 0.28 (14017) SS BOND : bond 0.00407 / 0.20 ( 3) SS BOND : angle 0.76373 / 0.64 ( 6) hydrogen bonds : bond 0.04532 / 3.07 ( 511) hydrogen bonds : angle 4.19774 / 3.08 ( 1497) link_NAG-ASN : bond 0.00415 / 0.21 ( 3) link_NAG-ASN : angle 3.69055 / 2.35 ( 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: 24 poor density : 115 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 143 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8351 (tp) REVERT: A 192 ASP cc_start: 0.7539 (m-30) cc_final: 0.6797 (p0) REVERT: A 216 GLN cc_start: 0.7928 (mt0) cc_final: 0.7669 (tt0) REVERT: A 453 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7495 (ttmm) REVERT: A 572 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.6948 (mppt) REVERT: A 946 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.7997 (mpt90) REVERT: B 29 MET cc_start: 0.7656 (ttt) cc_final: 0.7356 (ttp) REVERT: B 135 LYS cc_start: 0.7527 (tptp) cc_final: 0.7212 (tttm) outliers start: 24 outliers final: 12 residues processed: 131 average time/residue: 0.8156 time to fit residues: 112.7934 Evaluate side-chains 127 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 84 optimal weight: 0.0980 chunk 78 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3750 r_free = 0.3750 target = 0.152863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.107469 restraints weight = 9221.197| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.33 r_work: 0.2984 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 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 : 0.004 0.043 10349 Z= 0.170 Angle : 0.596 10.054 14032 Z= 0.304 Chirality : 0.046 0.245 1566 Planarity : 0.005 0.048 1779 Dihedral : 11.616 168.191 1541 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.54 % Allowed : 17.95 % Favored : 79.51 % 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 are not related in a simple way. whole: 1.23 (0.23), residues: 1244 helix: 1.65 (0.21), residues: 586 sheet: -0.02 (0.37), residues: 165 loop : 0.23 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 850 TYR 0.016 0.002 TYR A 802 PHE 0.019 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/Z covalent geometry : bond 0.00386 / 0.17 (10343) covalent geometry : angle 0.58151 / 0.30 (14017) SS BOND : bond 0.00508 / 0.24 ( 3) SS BOND : angle 0.77586 / 0.69 ( 6) hydrogen bonds : bond 0.05005 / 3.39 ( 511) hydrogen bonds : angle 4.30177 / 3.15 ( 1497) link_NAG-ASN : bond 0.00596 / 0.29 ( 3) link_NAG-ASN : angle 5.17210 / 3.12 ( 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: 27 poor density : 114 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 143 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8356 (tp) REVERT: A 453 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7523 (ttmm) REVERT: A 849 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7707 (mttt) REVERT: A 946 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8027 (mpt90) REVERT: B 29 MET cc_start: 0.7646 (ttt) cc_final: 0.7394 (ttp) REVERT: B 135 LYS cc_start: 0.7605 (tptp) cc_final: 0.7270 (tttm) outliers start: 27 outliers final: 12 residues processed: 132 average time/residue: 0.7966 time to fit residues: 111.2928 Evaluate side-chains 129 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 235 THR 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 494 THR 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 849 LYS 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: 0.8980 chunk 84 optimal weight: 0.1980 chunk 91 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 95 optimal weight: 0.0670 chunk 22 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.154350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108931 restraints weight = 9142.065| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.36 r_work: 0.3008 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10349 Z= 0.129 Angle : 0.554 9.858 14032 Z= 0.281 Chirality : 0.044 0.247 1566 Planarity : 0.005 0.049 1779 Dihedral : 11.324 169.264 1537 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.07 % Allowed : 18.42 % Favored : 79.51 % 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 are not related in a simple way. whole: 1.34 (0.24), residues: 1244 helix: 1.75 (0.21), residues: 587 sheet: 0.06 (0.38), residues: 163 loop : 0.26 (0.28), residues: 494 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 0.019 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/Z covalent geometry : bond 0.00283 / 0.13 (10343) covalent geometry : angle 0.53670 / 0.28 (14017) SS BOND : bond 0.00398 / 0.20 ( 3) SS BOND : angle 1.02895 / 0.76 ( 6) hydrogen bonds : bond 0.04408 / 2.99 ( 511) hydrogen bonds : angle 4.17887 / 3.06 ( 1497) link_NAG-ASN : bond 0.00291 / 0.15 ( 3) link_NAG-ASN : angle 5.32996 / 3.27 ( 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 137 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.285 Fit side-chains REVERT: A 143 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8326 (tp) REVERT: A 192 ASP cc_start: 0.7549 (m-30) cc_final: 0.6811 (p0) REVERT: A 216 GLN cc_start: 0.7930 (mt0) cc_final: 0.7674 (tt0) REVERT: A 453 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7497 (ttmm) REVERT: A 572 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6916 (mppt) REVERT: A 849 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7676 (mttt) REVERT: A 946 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.7980 (mpt90) REVERT: B 29 MET cc_start: 0.7681 (ttt) cc_final: 0.7389 (ttp) REVERT: B 135 LYS cc_start: 0.7483 (tptp) cc_final: 0.7166 (tttm) outliers start: 22 outliers final: 12 residues processed: 130 average time/residue: 0.7826 time to fit residues: 107.4785 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 : 0.397 ------------------------------------------------------------------------------- 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 235 THR 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 494 THR 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 849 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 chunk 74 optimal weight: 0.0980 chunk 1 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 112 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.155783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110720 restraints weight = 9132.190| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.35 r_work: 0.3033 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1126 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= 0.111 Angle : 0.525 8.894 14032 Z= 0.267 Chirality : 0.043 0.242 1566 Planarity : 0.004 0.052 1779 Dihedral : 11.056 169.918 1537 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.88 % Allowed : 18.70 % Favored : 79.42 % 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 are not related in a simple way. whole: 1.47 (0.24), residues: 1244 helix: 1.84 (0.21), residues: 589 sheet: 0.13 (0.38), residues: 160 loop : 0.34 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 850 TYR 0.011 0.001 TYR A 802 PHE 0.023 0.001 PHE A 300 TRP 0.011 0.001 TRP A 427 HIS 0.003 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (10343) covalent geometry : angle 0.51449 / 0.26 (14017) SS BOND : bond 0.00306 / 0.15 ( 3) SS BOND : angle 0.92517 / 0.70 ( 6) hydrogen bonds : bond 0.03988 / 2.71 ( 511) hydrogen bonds : angle 4.06170 / 2.98 ( 1497) link_NAG-ASN : bond 0.00449 / 0.22 ( 3) link_NAG-ASN : angle 4.11548 / 2.73 ( 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 134 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.361 Fit side-chains REVERT: A 84 ASP cc_start: 0.7305 (m-30) cc_final: 0.6874 (m-30) REVERT: A 143 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8372 (tp) REVERT: A 192 ASP cc_start: 0.7549 (m-30) cc_final: 0.6830 (p0) REVERT: A 216 GLN cc_start: 0.7957 (mt0) cc_final: 0.7700 (tt0) REVERT: A 453 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7460 (ttmm) REVERT: A 477 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7385 (mtm) REVERT: A 572 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.6903 (mppt) REVERT: A 844 ARG cc_start: 0.8243 (mmp80) cc_final: 0.7880 (mmm160) REVERT: A 849 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7686 (mttt) REVERT: A 850 ARG cc_start: 0.7765 (mtm110) cc_final: 0.7275 (ttm170) REVERT: A 946 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.7922 (mpt90) REVERT: B 29 MET cc_start: 0.7727 (ttt) cc_final: 0.7413 (ttp) REVERT: B 135 LYS cc_start: 0.7421 (tptp) cc_final: 0.7114 (tttm) REVERT: B 285 LYS cc_start: 0.8197 (tptp) cc_final: 0.7899 (mtmm) outliers start: 20 outliers final: 8 residues processed: 125 average time/residue: 0.7936 time to fit residues: 104.7229 Evaluate side-chains 124 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 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 477 MET Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 849 LYS 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: 1.9990 chunk 13 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 chunk 2 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3766 r_free = 0.3766 target = 0.154068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.108647 restraints weight = 9037.646| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.33 r_work: 0.3004 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10349 Z= 0.143 Angle : 0.575 11.772 14032 Z= 0.292 Chirality : 0.044 0.242 1566 Planarity : 0.005 0.054 1779 Dihedral : 11.137 170.236 1535 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.41 % Allowed : 19.17 % Favored : 79.42 % 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 are not related in a simple way. whole: 1.34 (0.23), residues: 1244 helix: 1.74 (0.21), residues: 587 sheet: 0.05 (0.37), residues: 163 loop : 0.28 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 850 TYR 0.015 0.002 TYR A 802 PHE 0.021 0.002 PHE A 300 TRP 0.012 0.002 TRP A 427 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10343) covalent geometry : angle 0.55884 / 0.29 (14017) SS BOND : bond 0.00410 / 0.20 ( 3) SS BOND : angle 1.09807 / 0.81 ( 6) hydrogen bonds : bond 0.04627 / 3.14 ( 511) hydrogen bonds : angle 4.18439 / 3.06 ( 1497) link_NAG-ASN : bond 0.00287 / 0.15 ( 3) link_NAG-ASN : angle 5.28598 / 3.26 ( 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 127 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 84 ASP cc_start: 0.7291 (m-30) cc_final: 0.6845 (m-30) REVERT: A 143 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8353 (tp) REVERT: A 192 ASP cc_start: 0.7542 (m-30) cc_final: 0.6825 (p0) REVERT: A 216 GLN cc_start: 0.7984 (mt0) cc_final: 0.7725 (tt0) REVERT: A 453 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7496 (ttmm) REVERT: A 849 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7677 (mttt) REVERT: A 850 ARG cc_start: 0.7761 (mtm110) cc_final: 0.7256 (ttm170) REVERT: A 946 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.7958 (mpt90) REVERT: B 29 MET cc_start: 0.7751 (ttt) cc_final: 0.7396 (ttp) REVERT: B 135 LYS cc_start: 0.7545 (tptp) cc_final: 0.7220 (tttm) outliers start: 15 outliers final: 10 residues processed: 122 average time/residue: 0.7638 time to fit residues: 98.2623 Evaluate side-chains 127 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 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 849 LYS 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: 0.6980 chunk 122 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3777 r_free = 0.3777 target = 0.155062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110060 restraints weight = 9233.751| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.34 r_work: 0.3024 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1139 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= 0.118 Angle : 0.546 11.457 14032 Z= 0.276 Chirality : 0.043 0.241 1566 Planarity : 0.004 0.050 1779 Dihedral : 10.992 170.488 1535 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.69 % Allowed : 19.08 % Favored : 79.23 % 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 are not related in a simple way. whole: 1.44 (0.24), residues: 1244 helix: 1.83 (0.21), residues: 587 sheet: 0.13 (0.39), residues: 155 loop : 0.31 (0.27), residues: 502 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 0.022 0.001 PHE A 970 TRP 0.011 0.001 TRP A 427 HIS 0.003 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (10343) covalent geometry : angle 0.52698 / 0.27 (14017) SS BOND : bond 0.00333 / 0.16 ( 3) SS BOND : angle 0.89593 / 0.69 ( 6) hydrogen bonds : bond 0.04163 / 2.83 ( 511) hydrogen bonds : angle 4.08609 / 2.99 ( 1497) link_NAG-ASN : bond 0.00297 / 0.16 ( 3) link_NAG-ASN : angle 5.58223 / 3.17 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4987.19 seconds wall clock time: 85 minutes 25.99 seconds (5125.99 seconds total)