Starting phenix.real_space_refine on Tue Jul 29 06:37:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jmn_36424/07_2025/8jmn_36424.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jmn_36424/07_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_36424/07_2025/8jmn_36424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jmn_36424/07_2025/8jmn_36424.map" model { file = "/net/cci-nas-00/data/ceres_data/8jmn_36424/07_2025/8jmn_36424.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jmn_36424/07_2025/8jmn_36424.cif" } resolution = 2.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.22, per 1000 atoms: 0.88 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: 2.97 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.48 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: 4.13 Time building geometry restraints manager: 3.43 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: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.090 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.930 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (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 TRP 0.012 0.002 TRP A 427 HIS 0.003 0.001 HIS A 53 PHE 0.017 0.002 PHE A 970 TYR 0.013 0.001 TYR B 136 ARG 0.013 0.001 ARG A 850 Details of bonding type rmsd link_NAG-ASN : bond 0.00828 ( 3) link_NAG-ASN : angle 2.93391 ( 9) hydrogen bonds : bond 0.11269 ( 511) hydrogen bonds : angle 5.20411 ( 1497) SS BOND : bond 0.00273 ( 3) SS BOND : angle 0.75041 ( 6) covalent geometry : bond 0.00680 (10343) covalent geometry : angle 0.91189 (14017) *********************** 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 : 1.075 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: 1.6896 time to fit residues: 268.8296 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 : 1.166 ------------------------------------------------------------------------------- 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 104 optimal weight: 0.0470 chunk 93 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 0.0970 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 112 optimal weight: 0.0050 overall best weight: 0.3090 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.157029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.112489 restraints weight = 9116.627| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.34 r_work: 0.3059 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.0687 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= 0.109 Angle : 0.534 10.596 14032 Z= 0.268 Chirality : 0.042 0.261 1566 Planarity : 0.004 0.057 1779 Dihedral : 13.589 160.651 1747 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.29 % Allowed : 17.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.24), residues: 1244 helix: 1.81 (0.21), residues: 593 sheet: 0.06 (0.40), residues: 160 loop : 0.23 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 39 HIS 0.002 0.001 HIS A 502 PHE 0.017 0.001 PHE A 300 TYR 0.009 0.001 TYR A 878 ARG 0.006 0.000 ARG A 850 Details of bonding type rmsd link_NAG-ASN : bond 0.00778 ( 3) link_NAG-ASN : angle 3.25014 ( 9) hydrogen bonds : bond 0.04064 ( 511) hydrogen bonds : angle 4.24143 ( 1497) SS BOND : bond 0.00248 ( 3) SS BOND : angle 0.78632 ( 6) covalent geometry : bond 0.00221 (10343) covalent geometry : angle 0.52761 (14017) *********************** 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 158 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 1.176 Fit side-chains revert: symmetry clash REVERT: A 143 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8338 (tp) REVERT: A 192 ASP cc_start: 0.7535 (m-30) cc_final: 0.6868 (p0) REVERT: A 453 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7471 (ttmm) REVERT: A 540 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.7036 (p0) REVERT: B 135 LYS cc_start: 0.7359 (tptp) cc_final: 0.7009 (tttm) outliers start: 35 outliers final: 13 residues processed: 147 average time/residue: 1.6352 time to fit residues: 255.1846 Evaluate side-chains 131 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 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 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 71 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 GLN B 160 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 = 0.154458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109089 restraints weight = 9235.523| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.34 r_work: 0.3007 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.0720 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= 0.136 Angle : 0.551 8.871 14032 Z= 0.282 Chirality : 0.044 0.256 1566 Planarity : 0.005 0.053 1779 Dihedral : 13.225 162.852 1718 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.35 % Allowed : 17.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1244 helix: 1.75 (0.21), residues: 591 sheet: 0.08 (0.39), residues: 162 loop : 0.20 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 427 HIS 0.004 0.001 HIS B 227 PHE 0.018 0.002 PHE A 300 TYR 0.014 0.002 TYR A 802 ARG 0.005 0.000 ARG A 946 Details of bonding type rmsd link_NAG-ASN : bond 0.00688 ( 3) link_NAG-ASN : angle 2.43058 ( 9) hydrogen bonds : bond 0.04614 ( 511) hydrogen bonds : angle 4.27288 ( 1497) SS BOND : bond 0.00335 ( 3) SS BOND : angle 0.71131 ( 6) covalent geometry : bond 0.00300 (10343) covalent geometry : angle 0.54788 (14017) *********************** 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 139 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8366 (tp) REVERT: A 192 ASP cc_start: 0.7515 (m-30) cc_final: 0.6840 (p0) REVERT: A 849 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7749 (mttt) REVERT: B 135 LYS cc_start: 0.7501 (tptp) cc_final: 0.7178 (tttm) outliers start: 25 outliers final: 11 residues processed: 127 average time/residue: 1.8580 time to fit residues: 249.0801 Evaluate side-chains 125 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 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 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 849 LYS 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 2 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.151970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.106599 restraints weight = 9193.307| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.32 r_work: 0.2971 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10349 Z= 0.193 Angle : 0.617 7.679 14032 Z= 0.319 Chirality : 0.047 0.266 1566 Planarity : 0.005 0.051 1779 Dihedral : 13.348 165.269 1711 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.23), residues: 1244 helix: 1.54 (0.21), residues: 590 sheet: -0.05 (0.38), residues: 165 loop : 0.17 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 427 HIS 0.005 0.001 HIS B 275 PHE 0.017 0.002 PHE A 300 TYR 0.016 0.002 TYR A 802 ARG 0.009 0.001 ARG A 946 Details of bonding type rmsd link_NAG-ASN : bond 0.00673 ( 3) link_NAG-ASN : angle 2.57374 ( 9) hydrogen bonds : bond 0.05378 ( 511) hydrogen bonds : angle 4.44659 ( 1497) SS BOND : bond 0.00547 ( 3) SS BOND : angle 0.89613 ( 6) covalent geometry : bond 0.00442 (10343) covalent geometry : angle 0.61311 (14017) *********************** 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: 32 poor density : 111 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 453 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7540 (ttmm) REVERT: B 135 LYS cc_start: 0.7654 (tptp) cc_final: 0.7271 (tttm) outliers start: 32 outliers final: 15 residues processed: 132 average time/residue: 1.7539 time to fit residues: 244.8770 Evaluate side-chains 126 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 1.169 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 93 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.154620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.109277 restraints weight = 9109.786| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.35 r_work: 0.3010 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10349 Z= 0.125 Angle : 0.535 6.315 14032 Z= 0.274 Chirality : 0.044 0.266 1566 Planarity : 0.004 0.050 1779 Dihedral : 12.936 168.604 1711 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.44 % Allowed : 17.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.24), residues: 1244 helix: 1.78 (0.21), residues: 587 sheet: 0.02 (0.37), residues: 163 loop : 0.26 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.003 0.001 HIS A 502 PHE 0.021 0.001 PHE A 300 TYR 0.012 0.001 TYR A 802 ARG 0.008 0.000 ARG A 850 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 3) link_NAG-ASN : angle 3.90899 ( 9) hydrogen bonds : bond 0.04368 ( 511) hydrogen bonds : angle 4.21349 ( 1497) SS BOND : bond 0.00458 ( 3) SS BOND : angle 1.00494 ( 6) covalent geometry : bond 0.00270 (10343) covalent geometry : angle 0.52572 (14017) *********************** 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: 26 poor density : 114 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 ASP cc_start: 0.7554 (m-30) cc_final: 0.6911 (p0) REVERT: A 216 GLN cc_start: 0.7980 (mt0) cc_final: 0.7727 (tt0) REVERT: A 453 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7505 (ttmm) REVERT: A 946 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8000 (mpt90) REVERT: B 29 MET cc_start: 0.7678 (ttt) cc_final: 0.7341 (ttp) REVERT: B 135 LYS cc_start: 0.7498 (tptp) cc_final: 0.7205 (tttm) outliers start: 26 outliers final: 15 residues processed: 130 average time/residue: 1.8060 time to fit residues: 248.0162 Evaluate side-chains 126 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain A residue 946 ARG Chi-restraints excluded: chain B residue 63 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 119 optimal weight: 0.2980 chunk 116 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3754 r_free = 0.3754 target = 0.153377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107790 restraints weight = 9173.222| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.34 r_work: 0.2989 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.0942 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= 0.151 Angle : 0.569 9.135 14032 Z= 0.291 Chirality : 0.045 0.264 1566 Planarity : 0.005 0.049 1779 Dihedral : 12.947 170.149 1711 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.73 % Allowed : 17.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.23), residues: 1244 helix: 1.72 (0.21), residues: 587 sheet: -0.00 (0.37), residues: 163 loop : 0.25 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 427 HIS 0.004 0.001 HIS B 275 PHE 0.018 0.002 PHE A 300 TYR 0.015 0.002 TYR A 802 ARG 0.008 0.001 ARG A 850 Details of bonding type rmsd link_NAG-ASN : bond 0.00710 ( 3) link_NAG-ASN : angle 4.45923 ( 9) hydrogen bonds : bond 0.04786 ( 511) hydrogen bonds : angle 4.26923 ( 1497) SS BOND : bond 0.00426 ( 3) SS BOND : angle 0.73280 ( 6) covalent geometry : bond 0.00337 (10343) covalent geometry : angle 0.55825 (14017) *********************** 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 138 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: A 143 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8321 (tp) REVERT: A 453 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7485 (ttmm) REVERT: A 572 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6919 (mppt) REVERT: A 946 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.8022 (mpt90) REVERT: B 29 MET cc_start: 0.7631 (ttt) cc_final: 0.7353 (ttp) REVERT: B 135 LYS cc_start: 0.7547 (tptp) cc_final: 0.7216 (tttm) outliers start: 29 outliers final: 14 residues processed: 129 average time/residue: 1.9961 time to fit residues: 272.1731 Evaluate side-chains 126 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 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 109 optimal weight: 0.0270 chunk 120 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 112 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 36 optimal weight: 0.0170 chunk 4 optimal weight: 0.0770 overall best weight: 0.3034 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.157435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.112834 restraints weight = 9380.531| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.37 r_work: 0.3067 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10349 Z= 0.099 Angle : 0.492 6.117 14032 Z= 0.250 Chirality : 0.042 0.258 1566 Planarity : 0.004 0.049 1779 Dihedral : 12.331 175.172 1710 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.79 % Allowed : 18.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.24), residues: 1244 helix: 1.97 (0.22), residues: 589 sheet: 0.11 (0.38), residues: 155 loop : 0.36 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 427 HIS 0.003 0.001 HIS A 502 PHE 0.021 0.001 PHE A 300 TYR 0.009 0.001 TYR A 878 ARG 0.011 0.000 ARG A 850 Details of bonding type rmsd link_NAG-ASN : bond 0.00991 ( 3) link_NAG-ASN : angle 3.35097 ( 9) hydrogen bonds : bond 0.03620 ( 511) hydrogen bonds : angle 3.98226 ( 1497) SS BOND : bond 0.00198 ( 3) SS BOND : angle 0.47492 ( 6) covalent geometry : bond 0.00212 (10343) covalent geometry : angle 0.48429 (14017) *********************** 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 137 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 143 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8331 (tp) REVERT: A 192 ASP cc_start: 0.7564 (m-30) cc_final: 0.6856 (p0) REVERT: A 216 GLN cc_start: 0.7968 (mt0) cc_final: 0.7712 (tt0) REVERT: A 453 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7380 (ttmm) REVERT: A 572 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.6926 (mppt) REVERT: A 844 ARG cc_start: 0.8175 (mmp80) cc_final: 0.7728 (mmm160) REVERT: A 946 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.7844 (mpt90) REVERT: B 29 MET cc_start: 0.7642 (ttt) cc_final: 0.7348 (ttp) REVERT: B 135 LYS cc_start: 0.7277 (tptp) cc_final: 0.7023 (tttm) outliers start: 19 outliers final: 10 residues processed: 131 average time/residue: 2.1020 time to fit residues: 291.4518 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 : 1.113 ------------------------------------------------------------------------------- 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 73 SER Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 196 VAL 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 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 946 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 A 495 ASN A 705 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.153153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107448 restraints weight = 9160.238| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.34 r_work: 0.2986 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10349 Z= 0.176 Angle : 0.586 7.428 14032 Z= 0.302 Chirality : 0.046 0.256 1566 Planarity : 0.005 0.052 1779 Dihedral : 12.673 172.729 1709 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.07 % Allowed : 18.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.23), residues: 1244 helix: 1.74 (0.21), residues: 587 sheet: 0.17 (0.39), residues: 155 loop : 0.24 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 427 HIS 0.005 0.001 HIS B 275 PHE 0.018 0.002 PHE A 300 TYR 0.016 0.002 TYR A 802 ARG 0.011 0.001 ARG A 850 Details of bonding type rmsd link_NAG-ASN : bond 0.00797 ( 3) link_NAG-ASN : angle 3.44765 ( 9) hydrogen bonds : bond 0.04983 ( 511) hydrogen bonds : angle 4.27230 ( 1497) SS BOND : bond 0.00513 ( 3) SS BOND : angle 0.76424 ( 6) covalent geometry : bond 0.00402 (10343) covalent geometry : angle 0.57973 (14017) *********************** 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 130 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 1.165 Fit side-chains REVERT: A 143 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8322 (tp) REVERT: A 453 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7484 (ttmm) REVERT: A 572 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.6943 (mppt) REVERT: A 946 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8041 (mpt90) REVERT: B 29 MET cc_start: 0.7652 (ttt) cc_final: 0.7348 (ttp) REVERT: B 135 LYS cc_start: 0.7582 (tptp) cc_final: 0.7253 (tttm) outliers start: 22 outliers final: 12 residues processed: 123 average time/residue: 1.7843 time to fit residues: 231.8876 Evaluate side-chains 123 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 73 SER 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 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 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 85 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.153122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.107499 restraints weight = 9305.349| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.37 r_work: 0.2985 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10349 Z= 0.167 Angle : 0.583 6.904 14032 Z= 0.301 Chirality : 0.046 0.267 1566 Planarity : 0.005 0.053 1779 Dihedral : 12.700 173.241 1705 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.79 % Allowed : 18.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.23), residues: 1244 helix: 1.66 (0.21), residues: 586 sheet: 0.02 (0.38), residues: 163 loop : 0.25 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 427 HIS 0.004 0.001 HIS B 275 PHE 0.020 0.002 PHE A 970 TYR 0.015 0.002 TYR A 802 ARG 0.012 0.001 ARG A 850 Details of bonding type rmsd link_NAG-ASN : bond 0.00830 ( 3) link_NAG-ASN : angle 3.47718 ( 9) hydrogen bonds : bond 0.04937 ( 511) hydrogen bonds : angle 4.28558 ( 1497) SS BOND : bond 0.00484 ( 3) SS BOND : angle 0.77422 ( 6) covalent geometry : bond 0.00381 (10343) covalent geometry : angle 0.57664 (14017) *********************** 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 130 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 1.066 Fit side-chains REVERT: A 143 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8325 (tp) REVERT: A 453 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7459 (ttmm) REVERT: A 572 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6897 (mppt) REVERT: A 850 ARG cc_start: 0.7743 (mtm110) cc_final: 0.7223 (ttm170) REVERT: A 946 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8044 (mpt90) REVERT: B 29 MET cc_start: 0.7697 (ttt) cc_final: 0.7339 (ttp) REVERT: B 135 LYS cc_start: 0.7580 (tptp) cc_final: 0.7257 (tttm) outliers start: 19 outliers final: 12 residues processed: 124 average time/residue: 1.8470 time to fit residues: 241.8460 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 : 1.147 ------------------------------------------------------------------------------- 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 494 THR 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 23 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 36 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.154733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.109389 restraints weight = 9263.691| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.37 r_work: 0.3013 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1066 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= 0.124 Angle : 0.536 7.897 14032 Z= 0.275 Chirality : 0.043 0.264 1566 Planarity : 0.005 0.052 1779 Dihedral : 12.415 175.798 1704 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.41 % Allowed : 19.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.24), residues: 1244 helix: 1.79 (0.21), residues: 587 sheet: 0.03 (0.38), residues: 158 loop : 0.31 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.003 0.001 HIS A 502 PHE 0.018 0.002 PHE A 300 TYR 0.013 0.001 TYR A 802 ARG 0.011 0.000 ARG A 850 Details of bonding type rmsd link_NAG-ASN : bond 0.00811 ( 3) link_NAG-ASN : angle 3.20353 ( 9) hydrogen bonds : bond 0.04325 ( 511) hydrogen bonds : angle 4.15276 ( 1497) SS BOND : bond 0.00335 ( 3) SS BOND : angle 0.62774 ( 6) covalent geometry : bond 0.00272 (10343) covalent geometry : angle 0.52967 (14017) ********************** 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 125 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 1.018 Fit side-chains REVERT: A 143 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8323 (tp) REVERT: A 192 ASP cc_start: 0.7543 (m-30) cc_final: 0.6865 (p0) REVERT: A 216 GLN cc_start: 0.7888 (mt0) cc_final: 0.7629 (tt0) REVERT: A 453 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7438 (ttmm) REVERT: A 572 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6867 (mppt) REVERT: A 844 ARG cc_start: 0.8278 (mmp80) cc_final: 0.7828 (mmm160) REVERT: A 850 ARG cc_start: 0.7756 (mtm110) cc_final: 0.7260 (ttm170) REVERT: A 946 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.7984 (mpt90) REVERT: B 29 MET cc_start: 0.7722 (ttt) cc_final: 0.7356 (ttp) REVERT: B 135 LYS cc_start: 0.7490 (tptp) cc_final: 0.7207 (tttm) outliers start: 15 outliers final: 9 residues processed: 121 average time/residue: 2.0254 time to fit residues: 258.3242 Evaluate side-chains 121 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 159 GLN Chi-restraints excluded: chain A residue 196 VAL 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 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 69 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 52 optimal weight: 0.0010 chunk 41 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.155303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110195 restraints weight = 9173.467| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.36 r_work: 0.3025 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1117 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= 0.119 Angle : 0.525 8.367 14032 Z= 0.269 Chirality : 0.043 0.258 1566 Planarity : 0.004 0.051 1779 Dihedral : 12.175 177.619 1703 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.50 % Allowed : 19.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.24), residues: 1244 helix: 1.85 (0.22), residues: 587 sheet: 0.12 (0.39), residues: 155 loop : 0.31 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.003 0.001 HIS A 502 PHE 0.025 0.001 PHE A 970 TYR 0.012 0.001 TYR A 802 ARG 0.010 0.000 ARG A 850 Details of bonding type rmsd link_NAG-ASN : bond 0.00773 ( 3) link_NAG-ASN : angle 3.00028 ( 9) hydrogen bonds : bond 0.04177 ( 511) hydrogen bonds : angle 4.09281 ( 1497) SS BOND : bond 0.00300 ( 3) SS BOND : angle 0.57498 ( 6) covalent geometry : bond 0.00261 (10343) covalent geometry : angle 0.51956 (14017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12895.02 seconds wall clock time: 227 minutes 12.91 seconds (13632.91 seconds total)