Starting phenix.real_space_refine on Fri Sep 11 18:14:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6k7g_9931/09_2026/6k7g_9931.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k7g_9931/09_2026/6k7g_9931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6k7g_9931/09_2026/6k7g_9931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k7g_9931/09_2026/6k7g_9931.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6k7g_9931/09_2026/6k7g_9931.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6k7g_9931/09_2026/6k7g_9931.cif" model { file = "/net/cci-nas-00/data/ceres_data/6k7g_9931/09_2026/6k7g_9931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k7g_9931/09_2026/6k7g_9931.cif" } resolution = 3.3 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= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 6852 2.51 5 N 1747 2.21 5 O 1914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10569 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7852 Classifications: {'peptide': 988} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 957} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2615 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 299} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.55, per 1000 atoms: 0.24 Number of scatterers: 10569 At special positions: 0 Unit cell: (66.4, 111.22, 164.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1914 8.00 N 1747 7.00 C 6852 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.02 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 ALPHA1-4 " NAG B 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 401 " - " ASN C 294 " " NAG C 402 " - " ASN C 107 " Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 382.3 milliseconds 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 10 sheets defined 47.3% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 101 through 132 removed outlier: 4.257A pdb=" N LYS A 122 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 176 through 178 No H-bonds generated for 'chain 'A' and resid 176 through 178' Processing helix chain 'A' and resid 208 through 215 Processing helix chain 'A' and resid 288 through 323 Processing helix chain 'A' and resid 339 through 352 Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 358 through 377 Processing helix chain 'A' and resid 393 through 397 removed outlier: 4.016A pdb=" N LEU A 396 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A 397 " --> pdb=" O SER A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 397' Processing helix chain 'A' and resid 398 through 401 Processing helix chain 'A' and resid 446 through 456 removed outlier: 3.681A pdb=" N HIS A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 removed outlier: 4.935A pdb=" N GLU A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 503 Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 573 through 588 Processing helix chain 'A' and resid 600 through 614 Processing helix chain 'A' and resid 619 through 633 removed outlier: 4.505A pdb=" N LEU A 623 " --> pdb=" O GLN A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 662 Processing helix chain 'A' and resid 673 through 684 Processing helix chain 'A' and resid 731 through 737 Processing helix chain 'A' and resid 742 through 751 Processing helix chain 'A' and resid 762 through 777 Processing helix chain 'A' and resid 787 through 797 removed outlier: 4.390A pdb=" N SER A 792 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N MET A 793 " --> pdb=" O ASN A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 815 Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'A' and resid 824 through 831 Processing helix chain 'A' and resid 833 through 856 Processing helix chain 'A' and resid 856 through 861 removed outlier: 3.746A pdb=" N TRP A 860 " --> pdb=" O ILE A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 866 Processing helix chain 'A' and resid 875 through 880 Processing helix chain 'A' and resid 887 through 896 removed outlier: 4.155A pdb=" N LEU A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 908 Processing helix chain 'A' and resid 910 through 918 removed outlier: 3.717A pdb=" N GLN A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A 917 " --> pdb=" O LYS A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 948 Proline residue: A 944 - end of helix Processing helix chain 'A' and resid 961 through 985 removed outlier: 4.086A pdb=" N LEU A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1013 removed outlier: 3.611A pdb=" N HIS A 993 " --> pdb=" O THR A 989 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL A1004 " --> pdb=" O ILE A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1033 Processing helix chain 'A' and resid 1034 through 1061 removed outlier: 3.747A pdb=" N MET A1038 " --> pdb=" O GLY A1034 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A1041 " --> pdb=" O TRP A1037 " (cutoff:3.500A) Proline residue: A1044 - end of helix removed outlier: 4.992A pdb=" N LEU A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASP A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 74 Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.605A pdb=" N ARG C 161 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.511A pdb=" N LEU C 243 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 removed outlier: 4.076A pdb=" N ASN C 250 " --> pdb=" O PRO C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 261 Processing helix chain 'C' and resid 323 through 350 removed outlier: 3.884A pdb=" N HIS C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 137 removed outlier: 3.709A pdb=" N VAL A 146 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 155 through 160 removed outlier: 3.971A pdb=" N ASP A 155 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TRP A 262 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER A 174 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N HIS A 264 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 195 through 198 Processing sheet with id=AA5, first strand: chain 'A' and resid 390 through 391 removed outlier: 6.633A pdb=" N THR A 781 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL A 801 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA A 783 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE A 803 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLY A 785 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N VAL A 403 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU A 782 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR A 405 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE A 784 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE A 407 " --> pdb=" O ILE A 784 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS A 404 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N TRP A 667 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ILE A 406 " --> pdb=" O TRP A 667 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU A 669 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N SER A 408 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE A 666 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N CYS A 758 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE A 668 " --> pdb=" O CYS A 758 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU A 727 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE A 694 " --> pdb=" O ILE A 728 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 415 through 425 removed outlier: 6.499A pdb=" N VAL A 418 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LYS A 647 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA A 643 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N CYS A 424 " --> pdb=" O ALA A 641 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA A 641 " --> pdb=" O CYS A 424 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 592 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 553 " --> pdb=" O VAL A 545 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 506 through 508 removed outlier: 3.510A pdb=" N VAL A 515 " --> pdb=" O THR A 508 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 81 removed outlier: 3.764A pdb=" N MET C 120 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG C 274 " --> pdb=" O MET C 120 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU C 124 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ARG C 270 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 102 through 103 removed outlier: 4.205A pdb=" N CYS C 102 " --> pdb=" O TYR C 297 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 108 through 110 removed outlier: 3.568A pdb=" N GLY C 289 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE C 186 " --> pdb=" O SER C 292 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1350 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.18 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1899 1.32 - 1.45: 2821 1.45 - 1.57: 6013 1.57 - 1.70: 0 1.70 - 1.82: 85 Bond restraints: 10818 Sorted by residual: bond pdb=" C SER A 223 " pdb=" N PRO A 224 " ideal model delta sigma weight residual 1.330 1.370 -0.040 1.19e-02 7.06e+03 1.13e+01 bond pdb=" C VAL C 99 " pdb=" N THR C 100 " ideal model delta sigma weight residual 1.331 1.269 0.062 2.07e-02 2.33e+03 9.10e+00 bond pdb=" C1 MAN B 3 " pdb=" O5 MAN B 3 " ideal model delta sigma weight residual 1.399 1.453 -0.054 2.00e-02 2.50e+03 7.23e+00 bond pdb=" CG GLN A 870 " pdb=" CD GLN A 870 " ideal model delta sigma weight residual 1.516 1.450 0.066 2.50e-02 1.60e+03 7.04e+00 bond pdb=" CB VAL A 853 " pdb=" CG2 VAL A 853 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.61e+00 ... (remaining 10813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 14158 2.78 - 5.56: 447 5.56 - 8.34: 66 8.34 - 11.13: 14 11.13 - 13.91: 4 Bond angle restraints: 14689 Sorted by residual: angle pdb=" C HIS A 227 " pdb=" N LEU A 228 " pdb=" CA LEU A 228 " ideal model delta sigma weight residual 121.54 130.37 -8.83 1.91e+00 2.74e-01 2.14e+01 angle pdb=" C GLU A 633 " pdb=" N LYS A 634 " pdb=" CA LYS A 634 " ideal model delta sigma weight residual 121.54 130.04 -8.50 1.91e+00 2.74e-01 1.98e+01 angle pdb=" C ILE A 803 " pdb=" N SER A 804 " pdb=" CA SER A 804 " ideal model delta sigma weight residual 121.19 128.16 -6.97 1.59e+00 3.96e-01 1.92e+01 angle pdb=" N GLU C 158 " pdb=" CA GLU C 158 " pdb=" C GLU C 158 " ideal model delta sigma weight residual 109.81 119.38 -9.57 2.21e+00 2.05e-01 1.88e+01 angle pdb=" C THR A 511 " pdb=" N PRO A 512 " pdb=" CA PRO A 512 " ideal model delta sigma weight residual 127.00 137.15 -10.15 2.40e+00 1.74e-01 1.79e+01 ... (remaining 14684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 5607 17.70 - 35.40: 621 35.40 - 53.10: 126 53.10 - 70.80: 22 70.80 - 88.50: 12 Dihedral angle restraints: 6388 sinusoidal: 2556 harmonic: 3832 Sorted by residual: dihedral pdb=" CB CYS C 91 " pdb=" SG CYS C 91 " pdb=" SG CYS C 104 " pdb=" CB CYS C 104 " ideal model delta sinusoidal sigma weight residual 93.00 155.87 -62.87 1 1.00e+01 1.00e-02 5.22e+01 dihedral pdb=" CA ALA C 169 " pdb=" C ALA C 169 " pdb=" N PRO C 170 " pdb=" CA PRO C 170 " ideal model delta harmonic sigma weight residual 180.00 150.36 29.64 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA GLU C 111 " pdb=" C GLU C 111 " pdb=" N LYS C 112 " pdb=" CA LYS C 112 " ideal model delta harmonic sigma weight residual -180.00 -151.67 -28.33 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 6385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1272 0.074 - 0.147: 361 0.147 - 0.221: 40 0.221 - 0.295: 8 0.295 - 0.369: 2 Chirality restraints: 1683 Sorted by residual: chirality pdb=" CB VAL A 103 " pdb=" CA VAL A 103 " pdb=" CG1 VAL A 103 " pdb=" CG2 VAL A 103 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CB ILE A 784 " pdb=" CA ILE A 784 " pdb=" CG1 ILE A 784 " pdb=" CG2 ILE A 784 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CB ILE A 145 " pdb=" CA ILE A 145 " pdb=" CG1 ILE A 145 " pdb=" CG2 ILE A 145 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 1680 not shown) Planarity restraints: 1839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.323 2.00e-02 2.50e+03 2.81e-01 9.89e+02 pdb=" C7 NAG B 1 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.065 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.499 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " 0.052 2.00e-02 2.50e+03 4.27e-02 2.28e+01 pdb=" C7 NAG C 401 " -0.014 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " 0.040 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " -0.067 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 255 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C GLU C 255 " -0.066 2.00e-02 2.50e+03 pdb=" O GLU C 255 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP C 256 " 0.023 2.00e-02 2.50e+03 ... (remaining 1836 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2616 2.79 - 3.32: 9540 3.32 - 3.84: 17816 3.84 - 4.37: 20955 4.37 - 4.90: 36245 Nonbonded interactions: 87172 Sorted by model distance: nonbonded pdb=" OH TYR C 134 " pdb=" OG SER C 177 " model vdw 2.262 3.040 nonbonded pdb=" OG SER A 94 " pdb=" O GLY A 97 " model vdw 2.275 3.040 nonbonded pdb=" O MET A1038 " pdb=" OH TYR C 329 " model vdw 2.313 3.040 nonbonded pdb=" NE2 GLN A 795 " pdb=" OG SER A 814 " model vdw 2.314 3.120 nonbonded pdb=" OH TYR A 611 " pdb=" OE1 GLU A 626 " model vdw 2.329 3.040 ... (remaining 87167 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: 0.010 Normalize map: mean=0, sd=1: 1.790 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.120 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 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 : 0.012 0.108 10826 Z= 0.504 Angle : 1.192 13.907 14710 Z= 0.625 Chirality : 0.068 0.369 1683 Planarity : 0.011 0.281 1836 Dihedral : 15.602 88.497 3907 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.13 % Favored : 90.71 % Rotamer: Outliers : 0.43 % Allowed : 9.39 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -4.12 (0.18), residues: 1303 helix: -2.64 (0.15), residues: 589 sheet: -1.36 (0.37), residues: 171 loop : -3.20 (0.22), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 392 TYR 0.036 0.004 TYR C 122 PHE 0.037 0.003 PHE C 304 TRP 0.022 0.003 TRP A 927 HIS 0.020 0.003 HIS A 936 Details of bonding type rmsd/Z covalent geometry : bond 0.01242 / 0.50 (10818) covalent geometry : angle 1.18294 / 0.62 (14689) SS BOND : bond 0.00635 / 0.32 ( 3) SS BOND : angle 1.36695 / 0.64 ( 6) hydrogen bonds : bond 0.11610 / 7.73 ( 466) hydrogen bonds : angle 6.81702 / 4.93 ( 1350) link_ALPHA1-4 : bond 0.02354 / 1.24 ( 1) link_ALPHA1-4 : angle 7.22725 / 3.81 ( 3) link_BETA1-4 : bond 0.00446 / 0.23 ( 1) link_BETA1-4 : angle 3.04670 / 1.60 ( 3) link_NAG-ASN : bond 0.00687 / 0.34 ( 3) link_NAG-ASN : angle 4.18616 / 2.06 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 125 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.5292 (mpt90) cc_final: 0.4583 (mtm110) REVERT: A 155 ASP cc_start: 0.7595 (t70) cc_final: 0.7125 (t70) REVERT: A 262 TRP cc_start: 0.7037 (p-90) cc_final: 0.6424 (p-90) REVERT: A 264 HIS cc_start: 0.7839 (m170) cc_final: 0.7557 (m-70) REVERT: A 468 MET cc_start: 0.8586 (tmm) cc_final: 0.7989 (tpp) REVERT: A 496 LEU cc_start: 0.7718 (tp) cc_final: 0.7366 (tp) REVERT: A 650 ASP cc_start: 0.7811 (m-30) cc_final: 0.7326 (m-30) REVERT: A 754 LYS cc_start: 0.8032 (tptt) cc_final: 0.7541 (tttt) REVERT: A 870 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8626 (tp-100) REVERT: A 917 ASN cc_start: 0.7164 (m-40) cc_final: 0.6805 (m-40) REVERT: A 984 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7308 (mt-10) REVERT: A 997 TRP cc_start: 0.8222 (m-10) cc_final: 0.7920 (m100) REVERT: A 1058 LYS cc_start: 0.7125 (mmmt) cc_final: 0.6781 (ttpt) REVERT: C 136 LYS cc_start: 0.8923 (ptmt) cc_final: 0.8533 (ptmm) REVERT: C 184 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8048 (mt-10) REVERT: C 238 LYS cc_start: 0.8710 (pttt) cc_final: 0.8384 (mtmm) REVERT: C 349 LYS cc_start: 0.6218 (tttm) cc_final: 0.5807 (tttt) outliers start: 5 outliers final: 3 residues processed: 129 average time/residue: 0.1396 time to fit residues: 23.5452 Evaluate side-chains 92 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain C residue 240 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 chunk 129 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 GLN A 147 HIS A 187 ASN A 264 HIS ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN A 456 HIS A 530 ASN A 679 ASN A 682 HIS C 92 ASN C 131 HIS C 254 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.185539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.131132 restraints weight = 11215.353| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 4.31 r_work: 0.2881 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10826 Z= 0.134 Angle : 0.663 11.091 14710 Z= 0.339 Chirality : 0.044 0.232 1683 Planarity : 0.005 0.061 1836 Dihedral : 6.412 52.814 1435 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.52 % Favored : 93.40 % Rotamer: Outliers : 1.39 % Allowed : 11.30 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -2.44 (0.21), residues: 1303 helix: -0.86 (0.20), residues: 578 sheet: -1.16 (0.36), residues: 179 loop : -2.58 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 37 TYR 0.015 0.001 TYR C 82 PHE 0.020 0.001 PHE A 465 TRP 0.018 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (10818) covalent geometry : angle 0.65707 / 0.34 (14689) SS BOND : bond 0.00075 / 0.04 ( 3) SS BOND : angle 0.90920 / 0.46 ( 6) hydrogen bonds : bond 0.04681 / 3.06 ( 466) hydrogen bonds : angle 5.50259 / 4.01 ( 1350) link_ALPHA1-4 : bond 0.01816 / 0.96 ( 1) link_ALPHA1-4 : angle 4.87362 / 2.56 ( 3) link_BETA1-4 : bond 0.01180 / 0.62 ( 1) link_BETA1-4 : angle 1.51134 / 0.82 ( 3) link_NAG-ASN : bond 0.00698 / 0.34 ( 3) link_NAG-ASN : angle 1.93428 / 1.02 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLN cc_start: 0.4758 (OUTLIER) cc_final: 0.3889 (tm-30) REVERT: A 155 ASP cc_start: 0.7521 (t70) cc_final: 0.7036 (t70) REVERT: A 261 GLN cc_start: 0.5687 (tt0) cc_final: 0.5467 (tm-30) REVERT: A 262 TRP cc_start: 0.7185 (p-90) cc_final: 0.6562 (p-90) REVERT: A 264 HIS cc_start: 0.7726 (m-70) cc_final: 0.7437 (m90) REVERT: A 468 MET cc_start: 0.8588 (tmm) cc_final: 0.7717 (tpp) REVERT: A 473 HIS cc_start: 0.6616 (m90) cc_final: 0.5853 (m90) REVERT: A 650 ASP cc_start: 0.7892 (m-30) cc_final: 0.7475 (m-30) REVERT: A 651 GLN cc_start: 0.7900 (mt0) cc_final: 0.7619 (mt0) REVERT: A 754 LYS cc_start: 0.8165 (tptt) cc_final: 0.7703 (tttt) REVERT: A 984 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7688 (mt-10) REVERT: A 1058 LYS cc_start: 0.7331 (mmmt) cc_final: 0.6922 (ttpt) REVERT: C 136 LYS cc_start: 0.9077 (ptmt) cc_final: 0.8814 (ptmm) REVERT: C 238 LYS cc_start: 0.8927 (pttt) cc_final: 0.8647 (mtmm) outliers start: 16 outliers final: 10 residues processed: 124 average time/residue: 0.1019 time to fit residues: 17.8050 Evaluate side-chains 105 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain C residue 240 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 117 optimal weight: 0.0970 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 ASN A 993 HIS C 144 ASN C 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.184388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.138165 restraints weight = 11194.453| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.37 r_work: 0.3095 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10826 Z= 0.134 Angle : 0.638 11.520 14710 Z= 0.322 Chirality : 0.044 0.176 1683 Planarity : 0.004 0.055 1836 Dihedral : 5.737 46.112 1430 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.68 % Favored : 93.25 % Rotamer: Outliers : 1.57 % Allowed : 13.74 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.69 (0.22), residues: 1303 helix: -0.11 (0.21), residues: 580 sheet: -0.93 (0.37), residues: 186 loop : -2.30 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 37 TYR 0.015 0.001 TYR C 122 PHE 0.020 0.001 PHE A 465 TRP 0.017 0.001 TRP A 927 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (10818) covalent geometry : angle 0.63278 / 0.32 (14689) SS BOND : bond 0.00092 / 0.04 ( 3) SS BOND : angle 0.70393 / 0.36 ( 6) hydrogen bonds : bond 0.04334 / 2.85 ( 466) hydrogen bonds : angle 5.17161 / 3.74 ( 1350) link_ALPHA1-4 : bond 0.02048 / 1.08 ( 1) link_ALPHA1-4 : angle 4.77029 / 2.49 ( 3) link_BETA1-4 : bond 0.00171 / 0.09 ( 1) link_BETA1-4 : angle 1.39207 / 0.73 ( 3) link_NAG-ASN : bond 0.00228 / 0.11 ( 3) link_NAG-ASN : angle 1.72616 / 0.85 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7602 (t70) cc_final: 0.7134 (t70) REVERT: A 468 MET cc_start: 0.8638 (tmm) cc_final: 0.7627 (tpp) REVERT: A 650 ASP cc_start: 0.7802 (m-30) cc_final: 0.7474 (m-30) REVERT: A 651 GLN cc_start: 0.7957 (mt0) cc_final: 0.7748 (mt0) REVERT: A 754 LYS cc_start: 0.8256 (tptt) cc_final: 0.7916 (tttt) REVERT: A 772 MET cc_start: 0.8523 (ttp) cc_final: 0.7855 (mmt) REVERT: A 817 TYR cc_start: 0.8710 (m-80) cc_final: 0.8410 (m-80) REVERT: A 870 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8665 (tp40) REVERT: A 968 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7991 (m-80) REVERT: A 984 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7808 (mt-10) REVERT: A 1023 MET cc_start: 0.8656 (mtp) cc_final: 0.8430 (ttt) REVERT: C 147 SER cc_start: 0.8617 (m) cc_final: 0.8394 (t) REVERT: C 238 LYS cc_start: 0.8905 (pttt) cc_final: 0.8693 (mtmm) outliers start: 18 outliers final: 10 residues processed: 121 average time/residue: 0.1043 time to fit residues: 17.8814 Evaluate side-chains 109 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 968 PHE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 318 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 86 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 60 optimal weight: 0.0020 chunk 102 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 110 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.185793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.139673 restraints weight = 11215.845| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.37 r_work: 0.3115 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10826 Z= 0.114 Angle : 0.598 12.006 14710 Z= 0.302 Chirality : 0.043 0.170 1683 Planarity : 0.004 0.054 1836 Dihedral : 5.503 41.772 1430 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.65 % Allowed : 14.70 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.30 (0.23), residues: 1303 helix: 0.31 (0.22), residues: 575 sheet: -0.59 (0.40), residues: 169 loop : -2.23 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 37 TYR 0.012 0.001 TYR C 122 PHE 0.014 0.001 PHE A 465 TRP 0.014 0.001 TRP A 927 HIS 0.008 0.001 HIS A 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (10818) covalent geometry : angle 0.59339 / 0.30 (14689) SS BOND : bond 0.00105 / 0.05 ( 3) SS BOND : angle 0.60164 / 0.30 ( 6) hydrogen bonds : bond 0.03981 / 2.62 ( 466) hydrogen bonds : angle 4.99123 / 3.60 ( 1350) link_ALPHA1-4 : bond 0.02033 / 1.07 ( 1) link_ALPHA1-4 : angle 4.38273 / 2.29 ( 3) link_BETA1-4 : bond 0.00197 / 0.10 ( 1) link_BETA1-4 : angle 1.21660 / 0.64 ( 3) link_NAG-ASN : bond 0.00240 / 0.12 ( 3) link_NAG-ASN : angle 1.60749 / 0.80 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7667 (t70) cc_final: 0.7093 (t70) REVERT: A 262 TRP cc_start: 0.7331 (p-90) cc_final: 0.6994 (p-90) REVERT: A 468 MET cc_start: 0.8555 (tmm) cc_final: 0.7822 (tpp) REVERT: A 469 MET cc_start: 0.8074 (tpp) cc_final: 0.7090 (mpp) REVERT: A 650 ASP cc_start: 0.7741 (m-30) cc_final: 0.7377 (m-30) REVERT: A 754 LYS cc_start: 0.8270 (tptt) cc_final: 0.7922 (tttt) REVERT: A 772 MET cc_start: 0.8459 (ttp) cc_final: 0.7826 (mmt) REVERT: A 817 TYR cc_start: 0.8689 (m-80) cc_final: 0.8367 (m-80) REVERT: A 968 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: A 984 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7755 (mt-10) REVERT: C 147 SER cc_start: 0.8641 (m) cc_final: 0.8413 (t) REVERT: C 238 LYS cc_start: 0.8887 (pttt) cc_final: 0.8621 (mtmm) outliers start: 19 outliers final: 13 residues processed: 115 average time/residue: 0.0992 time to fit residues: 16.4714 Evaluate side-chains 113 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 968 PHE Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 318 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 64 optimal weight: 0.3980 chunk 40 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 96 optimal weight: 0.0470 chunk 22 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 99 optimal weight: 0.0020 chunk 102 optimal weight: 0.4980 overall best weight: 0.3486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 GLN A 453 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.188985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.145155 restraints weight = 11203.388| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.53 r_work: 0.3149 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10826 Z= 0.100 Angle : 0.562 10.542 14710 Z= 0.283 Chirality : 0.042 0.161 1683 Planarity : 0.004 0.056 1836 Dihedral : 5.131 42.107 1430 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.57 % Allowed : 15.04 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -0.94 (0.23), residues: 1303 helix: 0.60 (0.22), residues: 585 sheet: -0.32 (0.41), residues: 165 loop : -2.11 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 37 TYR 0.021 0.001 TYR A 70 PHE 0.015 0.001 PHE A 465 TRP 0.014 0.001 TRP A 927 HIS 0.008 0.001 HIS A 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 (10818) covalent geometry : angle 0.55790 / 0.28 (14689) SS BOND : bond 0.00087 / 0.04 ( 3) SS BOND : angle 0.58424 / 0.30 ( 6) hydrogen bonds : bond 0.03525 / 2.31 ( 466) hydrogen bonds : angle 4.72722 / 3.40 ( 1350) link_ALPHA1-4 : bond 0.02127 / 1.12 ( 1) link_ALPHA1-4 : angle 3.95606 / 2.07 ( 3) link_BETA1-4 : bond 0.00232 / 0.12 ( 1) link_BETA1-4 : angle 0.97803 / 0.51 ( 3) link_NAG-ASN : bond 0.00300 / 0.15 ( 3) link_NAG-ASN : angle 1.54635 / 0.77 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ILE cc_start: 0.5870 (mp) cc_final: 0.5652 (mm) REVERT: A 155 ASP cc_start: 0.7691 (t70) cc_final: 0.7055 (t70) REVERT: A 468 MET cc_start: 0.8566 (tmm) cc_final: 0.7938 (tpp) REVERT: A 469 MET cc_start: 0.8105 (tpp) cc_final: 0.7886 (mmp) REVERT: A 492 ASP cc_start: 0.8014 (p0) cc_final: 0.7346 (t70) REVERT: A 553 ARG cc_start: 0.4254 (mmt-90) cc_final: 0.3909 (tpp-160) REVERT: A 650 ASP cc_start: 0.7679 (m-30) cc_final: 0.7318 (m-30) REVERT: A 754 LYS cc_start: 0.8250 (tptt) cc_final: 0.7828 (mttt) REVERT: A 817 TYR cc_start: 0.8724 (m-80) cc_final: 0.8484 (m-80) REVERT: A 984 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7656 (mt-10) REVERT: C 86 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6550 (tp30) REVERT: C 147 SER cc_start: 0.8636 (m) cc_final: 0.8412 (t) REVERT: C 238 LYS cc_start: 0.8849 (pttt) cc_final: 0.8572 (mtmm) outliers start: 18 outliers final: 11 residues processed: 126 average time/residue: 0.1099 time to fit residues: 19.5403 Evaluate side-chains 113 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 318 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 40 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 108 optimal weight: 0.5980 chunk 63 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 103 optimal weight: 0.0980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.187022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.142084 restraints weight = 11266.991| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.54 r_work: 0.3114 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10826 Z= 0.117 Angle : 0.571 9.486 14710 Z= 0.289 Chirality : 0.043 0.164 1683 Planarity : 0.004 0.053 1836 Dihedral : 5.071 43.840 1430 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.48 % Allowed : 16.35 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -0.88 (0.23), residues: 1303 helix: 0.63 (0.22), residues: 589 sheet: -0.19 (0.42), residues: 165 loop : -2.09 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 525 TYR 0.014 0.001 TYR C 122 PHE 0.016 0.001 PHE A 465 TRP 0.017 0.001 TRP A 262 HIS 0.004 0.001 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (10818) covalent geometry : angle 0.56658 / 0.29 (14689) SS BOND : bond 0.00119 / 0.06 ( 3) SS BOND : angle 0.56941 / 0.28 ( 6) hydrogen bonds : bond 0.03730 / 2.47 ( 466) hydrogen bonds : angle 4.71948 / 3.39 ( 1350) link_ALPHA1-4 : bond 0.02054 / 1.08 ( 1) link_ALPHA1-4 : angle 3.99997 / 2.09 ( 3) link_BETA1-4 : bond 0.00250 / 0.13 ( 1) link_BETA1-4 : angle 1.11290 / 0.59 ( 3) link_NAG-ASN : bond 0.00206 / 0.10 ( 3) link_NAG-ASN : angle 1.59006 / 0.78 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ILE cc_start: 0.5867 (mp) cc_final: 0.5661 (mm) REVERT: A 155 ASP cc_start: 0.7671 (t70) cc_final: 0.7093 (t70) REVERT: A 372 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.8422 (m-10) REVERT: A 468 MET cc_start: 0.8579 (tmm) cc_final: 0.8012 (tpp) REVERT: A 492 ASP cc_start: 0.8024 (p0) cc_final: 0.7326 (t70) REVERT: A 650 ASP cc_start: 0.7691 (m-30) cc_final: 0.7322 (m-30) REVERT: A 747 LEU cc_start: 0.8769 (mt) cc_final: 0.8485 (mt) REVERT: A 754 LYS cc_start: 0.8266 (tptt) cc_final: 0.7788 (mttt) REVERT: A 772 MET cc_start: 0.8498 (ttp) cc_final: 0.7867 (mmt) REVERT: A 817 TYR cc_start: 0.8740 (m-80) cc_final: 0.8478 (m-80) REVERT: A 984 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7721 (mt-10) REVERT: C 86 GLU cc_start: 0.6926 (mm-30) cc_final: 0.6526 (tp30) REVERT: C 147 SER cc_start: 0.8645 (m) cc_final: 0.8441 (t) REVERT: C 238 LYS cc_start: 0.8866 (pttt) cc_final: 0.8600 (mtmm) outliers start: 17 outliers final: 11 residues processed: 116 average time/residue: 0.0927 time to fit residues: 15.7096 Evaluate side-chains 108 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 318 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 118 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 47 optimal weight: 0.0010 chunk 43 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.182923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.137074 restraints weight = 11322.510| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.38 r_work: 0.3095 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10826 Z= 0.178 Angle : 0.622 8.859 14710 Z= 0.314 Chirality : 0.044 0.187 1683 Planarity : 0.004 0.052 1836 Dihedral : 5.146 36.619 1429 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.65 % Allowed : 16.70 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -0.91 (0.23), residues: 1303 helix: 0.54 (0.21), residues: 585 sheet: -0.11 (0.42), residues: 165 loop : -2.05 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 525 TYR 0.022 0.002 TYR C 122 PHE 0.021 0.002 PHE C 304 TRP 0.015 0.001 TRP A1014 HIS 0.007 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (10818) covalent geometry : angle 0.61748 / 0.31 (14689) SS BOND : bond 0.00192 / 0.09 ( 3) SS BOND : angle 0.70598 / 0.34 ( 6) hydrogen bonds : bond 0.04352 / 2.90 ( 466) hydrogen bonds : angle 4.84321 / 3.50 ( 1350) link_ALPHA1-4 : bond 0.02166 / 1.14 ( 1) link_ALPHA1-4 : angle 4.24504 / 2.22 ( 3) link_BETA1-4 : bond 0.00016 / 0.01 ( 1) link_BETA1-4 : angle 1.50522 / 0.79 ( 3) link_NAG-ASN : bond 0.00187 / 0.09 ( 3) link_NAG-ASN : angle 1.71990 / 0.84 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7736 (t70) cc_final: 0.7147 (t70) REVERT: A 372 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.8461 (m-10) REVERT: A 409 ASP cc_start: 0.8054 (p0) cc_final: 0.7846 (p0) REVERT: A 468 MET cc_start: 0.8576 (tmm) cc_final: 0.8030 (tpp) REVERT: A 469 MET cc_start: 0.8140 (tpp) cc_final: 0.7842 (mmp) REVERT: A 492 ASP cc_start: 0.7985 (p0) cc_final: 0.7376 (t70) REVERT: A 650 ASP cc_start: 0.7723 (m-30) cc_final: 0.7346 (m-30) REVERT: A 754 LYS cc_start: 0.8317 (tptt) cc_final: 0.7856 (mttt) REVERT: A 817 TYR cc_start: 0.8803 (m-80) cc_final: 0.8582 (m-80) REVERT: A 984 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7862 (mt-10) REVERT: C 86 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6498 (tp30) REVERT: C 238 LYS cc_start: 0.8877 (pttt) cc_final: 0.8627 (mtmm) outliers start: 19 outliers final: 15 residues processed: 110 average time/residue: 0.0880 time to fit residues: 14.5944 Evaluate side-chains 110 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 318 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 25 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.179931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.133064 restraints weight = 11299.180| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.38 r_work: 0.3032 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10826 Z= 0.233 Angle : 0.670 9.136 14710 Z= 0.341 Chirality : 0.046 0.216 1683 Planarity : 0.004 0.050 1836 Dihedral : 5.500 45.101 1429 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.26 % Allowed : 16.35 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.08 (0.23), residues: 1303 helix: 0.34 (0.21), residues: 585 sheet: -0.16 (0.42), residues: 166 loop : -2.08 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 525 TYR 0.026 0.002 TYR C 122 PHE 0.023 0.002 PHE C 304 TRP 0.016 0.002 TRP A1014 HIS 0.009 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.23 (10818) covalent geometry : angle 0.66556 / 0.34 (14689) SS BOND : bond 0.00242 / 0.12 ( 3) SS BOND : angle 0.82568 / 0.40 ( 6) hydrogen bonds : bond 0.04877 / 3.24 ( 466) hydrogen bonds : angle 4.98845 / 3.61 ( 1350) link_ALPHA1-4 : bond 0.02024 / 1.07 ( 1) link_ALPHA1-4 : angle 4.47815 / 2.34 ( 3) link_BETA1-4 : bond 0.00231 / 0.12 ( 1) link_BETA1-4 : angle 1.77003 / 0.93 ( 3) link_NAG-ASN : bond 0.00191 / 0.09 ( 3) link_NAG-ASN : angle 1.86807 / 0.90 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7752 (t70) cc_final: 0.7190 (t70) REVERT: A 327 ASP cc_start: 0.8928 (OUTLIER) cc_final: 0.8083 (p0) REVERT: A 419 MET cc_start: 0.6573 (tpp) cc_final: 0.6326 (mpp) REVERT: A 468 MET cc_start: 0.8574 (tmm) cc_final: 0.8006 (tpp) REVERT: A 469 MET cc_start: 0.8140 (tpp) cc_final: 0.7899 (mmp) REVERT: A 492 ASP cc_start: 0.8057 (p0) cc_final: 0.7555 (t70) REVERT: A 554 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6555 (tp) REVERT: A 650 ASP cc_start: 0.7763 (m-30) cc_final: 0.7393 (m-30) REVERT: A 754 LYS cc_start: 0.8310 (tptt) cc_final: 0.7873 (mttt) REVERT: A 772 MET cc_start: 0.8512 (ttp) cc_final: 0.7804 (mmt) REVERT: A 817 TYR cc_start: 0.8833 (m-80) cc_final: 0.8525 (m-80) REVERT: A 984 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7857 (mt-10) REVERT: C 86 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6352 (tp30) REVERT: C 238 LYS cc_start: 0.8871 (pttt) cc_final: 0.8644 (mtmm) outliers start: 26 outliers final: 20 residues processed: 111 average time/residue: 0.0902 time to fit residues: 14.7247 Evaluate side-chains 110 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 318 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 13 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 102 optimal weight: 0.0470 chunk 108 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 48 optimal weight: 0.0570 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS A 451 ASN C 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.185734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.139998 restraints weight = 11168.221| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.39 r_work: 0.3113 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10826 Z= 0.112 Angle : 0.593 13.182 14710 Z= 0.297 Chirality : 0.043 0.175 1683 Planarity : 0.004 0.052 1836 Dihedral : 5.129 42.652 1429 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.48 % Allowed : 17.13 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -0.77 (0.23), residues: 1303 helix: 0.68 (0.22), residues: 586 sheet: -0.08 (0.42), residues: 165 loop : -2.00 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 510 TYR 0.012 0.001 TYR A 970 PHE 0.018 0.001 PHE A 465 TRP 0.016 0.001 TRP A 927 HIS 0.018 0.001 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (10818) covalent geometry : angle 0.58897 / 0.30 (14689) SS BOND : bond 0.00135 / 0.07 ( 3) SS BOND : angle 0.58196 / 0.28 ( 6) hydrogen bonds : bond 0.03697 / 2.44 ( 466) hydrogen bonds : angle 4.71940 / 3.40 ( 1350) link_ALPHA1-4 : bond 0.02127 / 1.12 ( 1) link_ALPHA1-4 : angle 3.91305 / 2.05 ( 3) link_BETA1-4 : bond 0.00206 / 0.11 ( 1) link_BETA1-4 : angle 1.10331 / 0.58 ( 3) link_NAG-ASN : bond 0.00275 / 0.14 ( 3) link_NAG-ASN : angle 1.64308 / 0.81 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7857 (t70) cc_final: 0.7295 (t70) REVERT: A 468 MET cc_start: 0.8509 (tmm) cc_final: 0.7987 (tpp) REVERT: A 469 MET cc_start: 0.8064 (tpp) cc_final: 0.7833 (mmp) REVERT: A 492 ASP cc_start: 0.7989 (p0) cc_final: 0.7458 (t70) REVERT: A 650 ASP cc_start: 0.7713 (m-30) cc_final: 0.7296 (m-30) REVERT: A 747 LEU cc_start: 0.8664 (mt) cc_final: 0.8406 (mt) REVERT: A 754 LYS cc_start: 0.8257 (tptt) cc_final: 0.7756 (mttt) REVERT: A 772 MET cc_start: 0.8432 (ttp) cc_final: 0.7789 (mmt) REVERT: A 817 TYR cc_start: 0.8763 (m-80) cc_final: 0.8561 (m-80) REVERT: A 984 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7773 (mt-10) REVERT: C 146 ASP cc_start: 0.8233 (m-30) cc_final: 0.8016 (m-30) REVERT: C 238 LYS cc_start: 0.8807 (pttt) cc_final: 0.8591 (mtmm) outliers start: 17 outliers final: 15 residues processed: 115 average time/residue: 0.0875 time to fit residues: 15.0820 Evaluate side-chains 111 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 318 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 38 optimal weight: 20.0000 chunk 56 optimal weight: 0.0770 chunk 107 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 72 optimal weight: 0.0010 chunk 33 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 overall best weight: 1.5348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.183727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.137533 restraints weight = 11137.627| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.36 r_work: 0.3078 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10826 Z= 0.158 Angle : 0.619 13.354 14710 Z= 0.309 Chirality : 0.044 0.184 1683 Planarity : 0.004 0.051 1836 Dihedral : 5.146 42.439 1429 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.48 % Allowed : 17.30 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -0.83 (0.23), residues: 1303 helix: 0.64 (0.21), residues: 589 sheet: -0.07 (0.42), residues: 165 loop : -2.07 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 37 TYR 0.019 0.001 TYR C 122 PHE 0.017 0.001 PHE C 304 TRP 0.013 0.001 TRP A 927 HIS 0.015 0.001 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (10818) covalent geometry : angle 0.61430 / 0.31 (14689) SS BOND : bond 0.00167 / 0.08 ( 3) SS BOND : angle 0.66519 / 0.32 ( 6) hydrogen bonds : bond 0.04085 / 2.72 ( 466) hydrogen bonds : angle 4.75629 / 3.43 ( 1350) link_ALPHA1-4 : bond 0.02045 / 1.08 ( 1) link_ALPHA1-4 : angle 4.12794 / 2.16 ( 3) link_BETA1-4 : bond 0.00204 / 0.11 ( 1) link_BETA1-4 : angle 1.42481 / 0.75 ( 3) link_NAG-ASN : bond 0.00183 / 0.09 ( 3) link_NAG-ASN : angle 1.73007 / 0.84 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7816 (t70) cc_final: 0.7292 (t70) REVERT: A 264 HIS cc_start: 0.7993 (m-70) cc_final: 0.7713 (m-70) REVERT: A 419 MET cc_start: 0.6518 (tpp) cc_final: 0.6301 (mpp) REVERT: A 468 MET cc_start: 0.8524 (tmm) cc_final: 0.7993 (tpp) REVERT: A 469 MET cc_start: 0.8066 (tpp) cc_final: 0.7832 (mmp) REVERT: A 492 ASP cc_start: 0.7989 (p0) cc_final: 0.7553 (t70) REVERT: A 650 ASP cc_start: 0.7712 (m-30) cc_final: 0.7324 (m-30) REVERT: A 747 LEU cc_start: 0.8718 (mt) cc_final: 0.8444 (mt) REVERT: A 754 LYS cc_start: 0.8291 (tptt) cc_final: 0.7836 (mttt) REVERT: A 772 MET cc_start: 0.8524 (ttp) cc_final: 0.7855 (mmt) REVERT: A 984 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7869 (mt-10) REVERT: C 146 ASP cc_start: 0.8225 (m-30) cc_final: 0.8007 (m-30) REVERT: C 238 LYS cc_start: 0.8820 (pttt) cc_final: 0.8597 (mtmm) outliers start: 17 outliers final: 17 residues processed: 106 average time/residue: 0.0880 time to fit residues: 14.0041 Evaluate side-chains 110 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 318 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 127 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 46 optimal weight: 30.0000 chunk 43 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.183179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.137068 restraints weight = 11332.837| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.41 r_work: 0.3073 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.146 10826 Z= 0.217 Angle : 0.878 59.200 14710 Z= 0.500 Chirality : 0.047 0.569 1683 Planarity : 0.004 0.051 1836 Dihedral : 5.175 42.516 1429 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.74 % Allowed : 16.96 % Favored : 81.30 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.45 % 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: -0.84 (0.23), residues: 1303 helix: 0.61 (0.21), residues: 586 sheet: -0.07 (0.42), residues: 165 loop : -2.04 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 37 TYR 0.020 0.002 TYR C 122 PHE 0.017 0.002 PHE C 304 TRP 0.014 0.001 TRP A 262 HIS 0.015 0.001 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 (10818) covalent geometry : angle 0.87479 / 0.50 (14689) SS BOND : bond 0.00188 / 0.09 ( 3) SS BOND : angle 0.68518 / 0.32 ( 6) hydrogen bonds : bond 0.04202 / 2.80 ( 466) hydrogen bonds : angle 4.76523 / 3.44 ( 1350) link_ALPHA1-4 : bond 0.01817 / 0.96 ( 1) link_ALPHA1-4 : angle 4.16537 / 2.18 ( 3) link_BETA1-4 : bond 0.00039 / 0.02 ( 1) link_BETA1-4 : angle 1.51922 / 0.80 ( 3) link_NAG-ASN : bond 0.00205 / 0.10 ( 3) link_NAG-ASN : angle 1.73999 / 0.85 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2552.85 seconds wall clock time: 44 minutes 27.07 seconds (2667.07 seconds total)