Starting phenix.real_space_refine on Tue Jul 29 00:33:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k7g_9931/07_2025/6k7g_9931.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k7g_9931/07_2025/6k7g_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_9931/07_2025/6k7g_9931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k7g_9931/07_2025/6k7g_9931.map" model { file = "/net/cci-nas-00/data/ceres_data/6k7g_9931/07_2025/6k7g_9931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k7g_9931/07_2025/6k7g_9931.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.28, per 1000 atoms: 0.59 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: 2.66 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.24 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: 3.50 Time building geometry restraints manager: 3.14 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: 5757 17.70 - 35.40: 628 35.40 - 53.10: 127 53.10 - 70.80: 25 70.80 - 88.50: 12 Dihedral angle restraints: 6549 sinusoidal: 2717 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 6546 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: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.710 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 15.478 88.497 4068 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (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 TRP 0.022 0.003 TRP A 927 HIS 0.020 0.003 HIS A 936 PHE 0.037 0.003 PHE C 304 TYR 0.036 0.004 TYR C 122 ARG 0.008 0.001 ARG A 392 Details of bonding type rmsd link_NAG-ASN : bond 0.00687 ( 3) link_NAG-ASN : angle 4.18616 ( 9) link_ALPHA1-4 : bond 0.02354 ( 1) link_ALPHA1-4 : angle 7.22725 ( 3) link_BETA1-4 : bond 0.00446 ( 1) link_BETA1-4 : angle 3.04670 ( 3) hydrogen bonds : bond 0.11610 ( 466) hydrogen bonds : angle 6.81702 ( 1350) SS BOND : bond 0.00635 ( 3) SS BOND : angle 1.36695 ( 6) covalent geometry : bond 0.01242 (10818) covalent geometry : angle 1.18294 (14689) *********************** 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 : 1.088 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: 0.3227 time to fit residues: 54.0481 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 : 1.221 ------------------------------------------------------------------------------- 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 109 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 101 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 147 HIS A 187 ASN ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.183948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.134004 restraints weight = 11128.266| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.55 r_work: 0.2910 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1237 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= 0.137 Angle : 0.668 11.217 14710 Z= 0.342 Chirality : 0.044 0.201 1683 Planarity : 0.005 0.060 1836 Dihedral : 7.032 58.820 1596 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.68 % Favored : 93.25 % Rotamer: Outliers : 1.39 % Allowed : 11.39 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.21), residues: 1303 helix: -0.85 (0.20), residues: 578 sheet: -1.15 (0.36), residues: 179 loop : -2.59 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 927 HIS 0.003 0.001 HIS A 323 PHE 0.020 0.001 PHE A 465 TYR 0.016 0.001 TYR C 82 ARG 0.005 0.000 ARG C 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 3) link_NAG-ASN : angle 1.97751 ( 9) link_ALPHA1-4 : bond 0.01689 ( 1) link_ALPHA1-4 : angle 5.46218 ( 3) link_BETA1-4 : bond 0.00480 ( 1) link_BETA1-4 : angle 2.12730 ( 3) hydrogen bonds : bond 0.04724 ( 466) hydrogen bonds : angle 5.52290 ( 1350) SS BOND : bond 0.00064 ( 3) SS BOND : angle 0.89819 ( 6) covalent geometry : bond 0.00298 (10818) covalent geometry : angle 0.66122 (14689) *********************** 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 126 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLN cc_start: 0.5005 (OUTLIER) cc_final: 0.4142 (tm-30) REVERT: A 155 ASP cc_start: 0.7586 (t70) cc_final: 0.7144 (t70) REVERT: A 262 TRP cc_start: 0.7442 (p-90) cc_final: 0.6860 (p-90) REVERT: A 264 HIS cc_start: 0.8193 (m170) cc_final: 0.7653 (m90) REVERT: A 468 MET cc_start: 0.8661 (tmm) cc_final: 0.7740 (tpp) REVERT: A 650 ASP cc_start: 0.7846 (m-30) cc_final: 0.7479 (m-30) REVERT: A 651 GLN cc_start: 0.7909 (mt0) cc_final: 0.7647 (mt0) REVERT: A 754 LYS cc_start: 0.8280 (tptt) cc_final: 0.7874 (tttt) REVERT: A 984 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7758 (mt-10) REVERT: A 1058 LYS cc_start: 0.7494 (mmmt) cc_final: 0.7154 (ttpt) REVERT: C 136 LYS cc_start: 0.9087 (ptmt) cc_final: 0.8885 (ptmm) REVERT: C 238 LYS cc_start: 0.8957 (pttt) cc_final: 0.8669 (mtmm) REVERT: C 349 LYS cc_start: 0.6347 (tttm) cc_final: 0.5878 (tttt) outliers start: 16 outliers final: 9 residues processed: 123 average time/residue: 0.2920 time to fit residues: 50.3789 Evaluate side-chains 107 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 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 84 optimal weight: 0.9980 chunk 59 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 HIS ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 ASN A 993 HIS C 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.182302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.135434 restraints weight = 11310.198| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.39 r_work: 0.3074 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10826 Z= 0.168 Angle : 0.669 11.508 14710 Z= 0.339 Chirality : 0.045 0.173 1683 Planarity : 0.004 0.058 1836 Dihedral : 6.554 59.857 1591 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.83 % Favored : 92.10 % Rotamer: Outliers : 1.65 % Allowed : 13.65 % 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 (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: -1.74 (0.22), residues: 1303 helix: -0.16 (0.21), residues: 578 sheet: -0.64 (0.40), residues: 163 loop : -2.39 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 927 HIS 0.006 0.001 HIS A 323 PHE 0.019 0.002 PHE C 304 TYR 0.018 0.002 TYR C 122 ARG 0.006 0.000 ARG C 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00177 ( 3) link_NAG-ASN : angle 1.81177 ( 9) link_ALPHA1-4 : bond 0.01678 ( 1) link_ALPHA1-4 : angle 5.46275 ( 3) link_BETA1-4 : bond 0.00364 ( 1) link_BETA1-4 : angle 1.80832 ( 3) hydrogen bonds : bond 0.04626 ( 466) hydrogen bonds : angle 5.27111 ( 1350) SS BOND : bond 0.00116 ( 3) SS BOND : angle 0.77236 ( 6) covalent geometry : bond 0.00394 (10818) covalent geometry : angle 0.66301 (14689) *********************** 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 126 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7574 (t70) cc_final: 0.7104 (t70) REVERT: A 262 TRP cc_start: 0.7391 (p-90) cc_final: 0.6680 (p-90) REVERT: A 264 HIS cc_start: 0.7898 (m-70) cc_final: 0.7512 (m90) REVERT: A 468 MET cc_start: 0.8532 (tmm) cc_final: 0.7604 (tpp) REVERT: A 650 ASP cc_start: 0.7806 (m-30) cc_final: 0.7473 (m-30) REVERT: A 651 GLN cc_start: 0.7958 (mt0) cc_final: 0.7740 (mt0) REVERT: A 754 LYS cc_start: 0.8281 (tptt) cc_final: 0.7923 (tttt) REVERT: A 772 MET cc_start: 0.8533 (ttp) cc_final: 0.7841 (mmt) REVERT: A 817 TYR cc_start: 0.8729 (m-80) cc_final: 0.8442 (m-80) REVERT: A 870 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8694 (tp40) REVERT: A 984 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7800 (mt-10) REVERT: C 136 LYS cc_start: 0.9088 (ptmt) cc_final: 0.8867 (ptmm) REVERT: C 147 SER cc_start: 0.8648 (m) cc_final: 0.8410 (t) REVERT: C 238 LYS cc_start: 0.8904 (pttt) cc_final: 0.8642 (mtmm) outliers start: 19 outliers final: 14 residues processed: 121 average time/residue: 0.3590 time to fit residues: 62.1934 Evaluate side-chains 112 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL 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 742 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 870 GLN 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 110 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 0.0470 chunk 106 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.183153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.137186 restraints weight = 11145.270| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.35 r_work: 0.3107 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10826 Z= 0.164 Angle : 0.639 11.988 14710 Z= 0.324 Chirality : 0.045 0.186 1683 Planarity : 0.004 0.055 1836 Dihedral : 6.405 59.468 1591 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 1.91 % Allowed : 15.04 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.45 (0.23), residues: 1303 helix: 0.10 (0.21), residues: 577 sheet: -0.48 (0.41), residues: 161 loop : -2.26 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 927 HIS 0.011 0.001 HIS A 473 PHE 0.017 0.001 PHE C 304 TYR 0.018 0.002 TYR C 122 ARG 0.006 0.000 ARG C 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00174 ( 3) link_NAG-ASN : angle 1.70434 ( 9) link_ALPHA1-4 : bond 0.01901 ( 1) link_ALPHA1-4 : angle 5.28292 ( 3) link_BETA1-4 : bond 0.00302 ( 1) link_BETA1-4 : angle 1.80157 ( 3) hydrogen bonds : bond 0.04481 ( 466) hydrogen bonds : angle 5.16147 ( 1350) SS BOND : bond 0.00153 ( 3) SS BOND : angle 0.71620 ( 6) covalent geometry : bond 0.00386 (10818) covalent geometry : angle 0.63281 (14689) *********************** 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 123 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7667 (t70) cc_final: 0.7109 (t70) REVERT: A 468 MET cc_start: 0.8566 (tmm) cc_final: 0.7801 (tpp) REVERT: A 469 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7183 (mpp) REVERT: A 650 ASP cc_start: 0.7780 (m-30) cc_final: 0.7433 (m-30) REVERT: A 754 LYS cc_start: 0.8325 (tptt) cc_final: 0.7931 (tttt) REVERT: A 772 MET cc_start: 0.8514 (ttp) cc_final: 0.7846 (mmt) REVERT: A 817 TYR cc_start: 0.8762 (m-80) cc_final: 0.8466 (m-80) REVERT: A 870 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8659 (tp40) REVERT: A 968 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.7997 (m-80) REVERT: A 984 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7815 (mt-10) REVERT: C 147 SER cc_start: 0.8684 (m) cc_final: 0.8450 (t) REVERT: C 238 LYS cc_start: 0.8904 (pttt) cc_final: 0.8636 (mtmm) outliers start: 22 outliers final: 15 residues processed: 115 average time/residue: 0.3712 time to fit residues: 60.6010 Evaluate side-chains 111 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL 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 469 MET 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 803 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 870 GLN 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 124 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 51 optimal weight: 0.2980 chunk 110 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.186075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.140235 restraints weight = 11153.402| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.35 r_work: 0.3114 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10826 Z= 0.116 Angle : 0.589 12.279 14710 Z= 0.298 Chirality : 0.043 0.165 1683 Planarity : 0.004 0.054 1836 Dihedral : 6.120 59.945 1591 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.91 % Allowed : 15.13 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.13 (0.23), residues: 1303 helix: 0.40 (0.22), residues: 582 sheet: -0.43 (0.41), residues: 165 loop : -2.13 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.006 0.001 HIS A 264 PHE 0.016 0.001 PHE A 465 TYR 0.011 0.001 TYR C 82 ARG 0.007 0.000 ARG C 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 3) link_NAG-ASN : angle 1.61661 ( 9) link_ALPHA1-4 : bond 0.02085 ( 1) link_ALPHA1-4 : angle 4.84585 ( 3) link_BETA1-4 : bond 0.00258 ( 1) link_BETA1-4 : angle 1.41415 ( 3) hydrogen bonds : bond 0.03876 ( 466) hydrogen bonds : angle 4.89731 ( 1350) SS BOND : bond 0.00117 ( 3) SS BOND : angle 0.60972 ( 6) covalent geometry : bond 0.00253 (10818) covalent geometry : angle 0.58373 (14689) *********************** 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 125 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7770 (t70) cc_final: 0.7110 (t70) REVERT: A 468 MET cc_start: 0.8568 (tmm) cc_final: 0.7990 (tpp) REVERT: A 469 MET cc_start: 0.7943 (tpp) cc_final: 0.7013 (mpp) REVERT: A 492 ASP cc_start: 0.7962 (p0) cc_final: 0.7366 (t70) REVERT: A 554 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6471 (tp) REVERT: A 650 ASP cc_start: 0.7684 (m-30) cc_final: 0.7349 (m-30) REVERT: A 754 LYS cc_start: 0.8305 (tptt) cc_final: 0.7908 (mttt) REVERT: A 817 TYR cc_start: 0.8726 (m-80) cc_final: 0.8427 (m-80) REVERT: A 968 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: A 984 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7785 (mt-10) REVERT: C 86 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6574 (tp30) REVERT: C 147 SER cc_start: 0.8655 (m) cc_final: 0.8423 (t) REVERT: C 238 LYS cc_start: 0.8856 (pttt) cc_final: 0.8597 (mtmm) outliers start: 22 outliers final: 14 residues processed: 119 average time/residue: 0.3135 time to fit residues: 53.1753 Evaluate side-chains 113 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL 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 511 THR Chi-restraints excluded: chain A residue 554 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 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 318 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 1 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 121 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.179739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.133907 restraints weight = 11299.836| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.37 r_work: 0.3048 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 10826 Z= 0.266 Angle : 0.711 12.276 14710 Z= 0.360 Chirality : 0.047 0.216 1683 Planarity : 0.005 0.055 1836 Dihedral : 6.426 59.038 1591 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.90 % Favored : 92.02 % Rotamer: Outliers : 2.35 % Allowed : 15.91 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.34 (0.23), residues: 1303 helix: 0.19 (0.21), residues: 580 sheet: -0.45 (0.42), residues: 163 loop : -2.21 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1014 HIS 0.009 0.002 HIS A 323 PHE 0.025 0.002 PHE C 304 TYR 0.027 0.002 TYR C 122 ARG 0.006 0.001 ARG C 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 3) link_NAG-ASN : angle 1.83433 ( 9) link_ALPHA1-4 : bond 0.01900 ( 1) link_ALPHA1-4 : angle 5.09988 ( 3) link_BETA1-4 : bond 0.00120 ( 1) link_BETA1-4 : angle 2.14095 ( 3) hydrogen bonds : bond 0.05189 ( 466) hydrogen bonds : angle 5.17987 ( 1350) SS BOND : bond 0.00247 ( 3) SS BOND : angle 0.87629 ( 6) covalent geometry : bond 0.00655 (10818) covalent geometry : angle 0.70559 (14689) *********************** 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 119 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 1.731 Fit side-chains revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7740 (t70) cc_final: 0.7179 (t70) REVERT: A 262 TRP cc_start: 0.7353 (p-90) cc_final: 0.7021 (p-90) REVERT: A 264 HIS cc_start: 0.8011 (m90) cc_final: 0.7609 (m90) REVERT: A 468 MET cc_start: 0.8576 (tmm) cc_final: 0.7946 (tpp) REVERT: A 469 MET cc_start: 0.8003 (tpp) cc_final: 0.7248 (mpp) REVERT: A 492 ASP cc_start: 0.8089 (p0) cc_final: 0.7576 (t70) REVERT: A 554 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6493 (tp) REVERT: A 650 ASP cc_start: 0.7755 (m-30) cc_final: 0.7392 (m-30) REVERT: A 754 LYS cc_start: 0.8341 (tptt) cc_final: 0.7882 (mttt) REVERT: A 817 TYR cc_start: 0.8851 (m-80) cc_final: 0.8567 (m-80) REVERT: A 870 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8829 (tp40) REVERT: A 984 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7872 (mt-10) REVERT: C 86 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6708 (tp30) REVERT: C 147 SER cc_start: 0.8756 (m) cc_final: 0.8528 (t) REVERT: C 238 LYS cc_start: 0.8867 (pttt) cc_final: 0.8637 (mtmm) outliers start: 27 outliers final: 19 residues processed: 112 average time/residue: 0.2953 time to fit residues: 47.8246 Evaluate side-chains 109 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 108 ILE 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 260 THR Chi-restraints excluded: chain A residue 348 ILE 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 803 ILE Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 168 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 87 optimal weight: 0.8980 chunk 72 optimal weight: 0.0770 chunk 61 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 66 optimal weight: 0.0970 chunk 42 optimal weight: 0.0030 chunk 36 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.3346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN C 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.185773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.139764 restraints weight = 11312.484| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.35 r_work: 0.3114 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10826 Z= 0.106 Angle : 0.585 12.951 14710 Z= 0.296 Chirality : 0.042 0.157 1683 Planarity : 0.004 0.054 1836 Dihedral : 6.043 59.544 1591 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.74 % Allowed : 16.70 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -0.96 (0.23), residues: 1303 helix: 0.56 (0.22), residues: 583 sheet: -0.29 (0.42), residues: 165 loop : -2.08 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 262 HIS 0.002 0.001 HIS A 323 PHE 0.024 0.001 PHE A 465 TYR 0.013 0.001 TYR A 70 ARG 0.005 0.000 ARG C 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 3) link_NAG-ASN : angle 1.53708 ( 9) link_ALPHA1-4 : bond 0.02049 ( 1) link_ALPHA1-4 : angle 4.66470 ( 3) link_BETA1-4 : bond 0.00299 ( 1) link_BETA1-4 : angle 1.26744 ( 3) hydrogen bonds : bond 0.03733 ( 466) hydrogen bonds : angle 4.82066 ( 1350) SS BOND : bond 0.00103 ( 3) SS BOND : angle 0.62823 ( 6) covalent geometry : bond 0.00219 (10818) covalent geometry : angle 0.57995 (14689) *********************** 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 121 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 2.509 Fit side-chains revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7698 (t70) cc_final: 0.7117 (t70) REVERT: A 262 TRP cc_start: 0.7280 (p-90) cc_final: 0.6988 (p-90) REVERT: A 264 HIS cc_start: 0.8051 (m90) cc_final: 0.7671 (m90) REVERT: A 468 MET cc_start: 0.8542 (tmm) cc_final: 0.7912 (tpp) REVERT: A 492 ASP cc_start: 0.7997 (p0) cc_final: 0.7404 (t70) REVERT: A 650 ASP cc_start: 0.7686 (m-30) cc_final: 0.7325 (m-30) REVERT: A 747 LEU cc_start: 0.8689 (mt) cc_final: 0.8431 (mt) REVERT: A 754 LYS cc_start: 0.8278 (tptt) cc_final: 0.7820 (mttt) REVERT: A 772 MET cc_start: 0.8454 (ttp) cc_final: 0.7793 (mmt) REVERT: A 817 TYR cc_start: 0.8741 (m-80) cc_final: 0.8526 (m-80) REVERT: A 984 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7802 (mt-10) REVERT: C 147 SER cc_start: 0.8694 (m) cc_final: 0.8456 (t) REVERT: C 238 LYS cc_start: 0.8807 (pttt) cc_final: 0.8577 (mtmm) outliers start: 20 outliers final: 14 residues processed: 116 average time/residue: 0.4789 time to fit residues: 79.6009 Evaluate side-chains 107 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL 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 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 799 VAL Chi-restraints excluded: chain A residue 989 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 108 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 HIS ** 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 = 0.180051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.134442 restraints weight = 11305.990| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.42 r_work: 0.3013 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 10826 Z= 0.274 Angle : 0.706 12.867 14710 Z= 0.357 Chirality : 0.048 0.214 1683 Planarity : 0.005 0.057 1836 Dihedral : 6.360 58.945 1591 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.21 % Favored : 91.71 % Rotamer: Outliers : 2.09 % Allowed : 17.04 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.19 (0.23), residues: 1303 helix: 0.27 (0.21), residues: 582 sheet: -0.32 (0.42), residues: 162 loop : -2.10 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 262 HIS 0.008 0.001 HIS A 323 PHE 0.022 0.002 PHE C 304 TYR 0.027 0.002 TYR C 122 ARG 0.008 0.001 ARG A 525 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 3) link_NAG-ASN : angle 1.82486 ( 9) link_ALPHA1-4 : bond 0.01849 ( 1) link_ALPHA1-4 : angle 4.89475 ( 3) link_BETA1-4 : bond 0.00394 ( 1) link_BETA1-4 : angle 2.09418 ( 3) hydrogen bonds : bond 0.05087 ( 466) hydrogen bonds : angle 5.11209 ( 1350) SS BOND : bond 0.00260 ( 3) SS BOND : angle 0.88294 ( 6) covalent geometry : bond 0.00674 (10818) covalent geometry : angle 0.70118 (14689) *********************** 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 112 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 4.321 Fit side-chains revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7733 (t70) cc_final: 0.7188 (t70) REVERT: A 262 TRP cc_start: 0.7432 (p-90) cc_final: 0.7137 (p-90) REVERT: A 264 HIS cc_start: 0.8110 (m90) cc_final: 0.7777 (m90) REVERT: A 468 MET cc_start: 0.8630 (tmm) cc_final: 0.8003 (tpp) REVERT: A 492 ASP cc_start: 0.8000 (p0) cc_final: 0.7493 (t70) REVERT: A 554 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6569 (tp) REVERT: A 650 ASP cc_start: 0.7789 (m-30) cc_final: 0.7401 (m-30) REVERT: A 754 LYS cc_start: 0.8359 (tptt) cc_final: 0.7930 (mttt) REVERT: A 817 TYR cc_start: 0.8844 (m-80) cc_final: 0.8542 (m-80) REVERT: A 984 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7915 (mt-10) REVERT: C 147 SER cc_start: 0.8767 (m) cc_final: 0.8550 (t) REVERT: C 238 LYS cc_start: 0.8867 (pttt) cc_final: 0.8645 (mtmm) outliers start: 24 outliers final: 18 residues processed: 108 average time/residue: 0.5841 time to fit residues: 92.5877 Evaluate side-chains 107 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 121 ILE 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 511 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 168 ILE 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 95 optimal weight: 0.8980 chunk 82 optimal weight: 0.2980 chunk 10 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 108 optimal weight: 0.5980 chunk 56 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 116 optimal weight: 0.0060 chunk 112 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3978 r_free = 0.3978 target = 0.184887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.138870 restraints weight = 11337.809| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.43 r_work: 0.3098 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 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 : 0.002 0.029 10826 Z= 0.113 Angle : 0.590 13.662 14710 Z= 0.299 Chirality : 0.043 0.161 1683 Planarity : 0.004 0.053 1836 Dihedral : 6.065 59.545 1591 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.48 % Allowed : 17.22 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.90 (0.23), residues: 1303 helix: 0.60 (0.22), residues: 583 sheet: -0.24 (0.41), residues: 165 loop : -2.06 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 262 HIS 0.002 0.001 HIS A 323 PHE 0.024 0.001 PHE A 465 TYR 0.013 0.001 TYR A 70 ARG 0.006 0.000 ARG C 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 3) link_NAG-ASN : angle 1.55469 ( 9) link_ALPHA1-4 : bond 0.02235 ( 1) link_ALPHA1-4 : angle 4.50267 ( 3) link_BETA1-4 : bond 0.00257 ( 1) link_BETA1-4 : angle 1.29778 ( 3) hydrogen bonds : bond 0.03767 ( 466) hydrogen bonds : angle 4.79445 ( 1350) SS BOND : bond 0.00134 ( 3) SS BOND : angle 0.61564 ( 6) covalent geometry : bond 0.00245 (10818) covalent geometry : angle 0.58491 (14689) *********************** 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 114 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 1.277 Fit side-chains revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7852 (t70) cc_final: 0.7280 (t70) REVERT: A 264 HIS cc_start: 0.7992 (m90) cc_final: 0.7587 (m90) REVERT: A 390 MET cc_start: 0.9053 (tpp) cc_final: 0.8780 (tpt) REVERT: A 468 MET cc_start: 0.8527 (tmm) cc_final: 0.7909 (tpp) REVERT: A 492 ASP cc_start: 0.8073 (p0) cc_final: 0.7568 (t70) REVERT: A 650 ASP cc_start: 0.7635 (m-30) cc_final: 0.7244 (m-30) REVERT: A 747 LEU cc_start: 0.8651 (mt) cc_final: 0.8415 (mt) REVERT: A 754 LYS cc_start: 0.8307 (tptt) cc_final: 0.7821 (mttt) REVERT: A 772 MET cc_start: 0.8417 (ttp) cc_final: 0.7783 (mmt) REVERT: A 817 TYR cc_start: 0.8773 (m-80) cc_final: 0.8556 (m-80) REVERT: A 984 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7839 (mt-10) REVERT: C 147 SER cc_start: 0.8767 (m) cc_final: 0.8501 (t) REVERT: C 238 LYS cc_start: 0.8798 (pttt) cc_final: 0.8574 (mtmm) outliers start: 17 outliers final: 16 residues processed: 111 average time/residue: 0.2612 time to fit residues: 43.3147 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 : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL 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 511 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 799 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 174 ILE 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 113 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 49 optimal weight: 40.0000 chunk 118 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 43 optimal weight: 0.0370 chunk 88 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 102 optimal weight: 0.0870 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 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 = 0.3999 r_free = 0.3999 target = 0.186806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.141147 restraints weight = 11246.670| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.39 r_work: 0.3118 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10826 Z= 0.110 Angle : 0.587 13.551 14710 Z= 0.295 Chirality : 0.042 0.164 1683 Planarity : 0.004 0.053 1836 Dihedral : 5.876 59.701 1591 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.48 % Allowed : 17.57 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -0.79 (0.23), residues: 1303 helix: 0.70 (0.22), residues: 587 sheet: -0.16 (0.42), residues: 163 loop : -2.03 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 927 HIS 0.007 0.001 HIS A 264 PHE 0.022 0.001 PHE A 465 TYR 0.012 0.001 TYR A 229 ARG 0.006 0.000 ARG C 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 3) link_NAG-ASN : angle 1.59862 ( 9) link_ALPHA1-4 : bond 0.02007 ( 1) link_ALPHA1-4 : angle 4.27662 ( 3) link_BETA1-4 : bond 0.00221 ( 1) link_BETA1-4 : angle 1.32250 ( 3) hydrogen bonds : bond 0.03633 ( 466) hydrogen bonds : angle 4.68266 ( 1350) SS BOND : bond 0.00110 ( 3) SS BOND : angle 0.62602 ( 6) covalent geometry : bond 0.00240 (10818) covalent geometry : angle 0.58257 (14689) ********************** 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 113 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7843 (t70) cc_final: 0.7299 (t70) REVERT: A 390 MET cc_start: 0.8978 (tpp) cc_final: 0.8693 (tpt) REVERT: A 468 MET cc_start: 0.8559 (tmm) cc_final: 0.7934 (tpp) REVERT: A 492 ASP cc_start: 0.8069 (p0) cc_final: 0.7799 (t0) REVERT: A 650 ASP cc_start: 0.7623 (m-30) cc_final: 0.7188 (m-30) REVERT: A 693 MET cc_start: 0.3810 (tpt) cc_final: 0.3361 (mmm) REVERT: A 754 LYS cc_start: 0.8280 (tptt) cc_final: 0.7844 (mttt) REVERT: A 817 TYR cc_start: 0.8744 (m-80) cc_final: 0.8470 (m-80) REVERT: A 984 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7810 (mt-10) REVERT: C 146 ASP cc_start: 0.8232 (m-30) cc_final: 0.7987 (m-30) REVERT: C 147 SER cc_start: 0.8678 (m) cc_final: 0.8450 (t) REVERT: C 238 LYS cc_start: 0.8821 (pttt) cc_final: 0.8577 (mtmm) outliers start: 17 outliers final: 16 residues processed: 110 average time/residue: 0.2330 time to fit residues: 36.9999 Evaluate side-chains 109 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL 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 451 ASN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 762 SER 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 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 66 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 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 = 0.3990 r_free = 0.3990 target = 0.185412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.146462 restraints weight = 11218.516| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.25 r_work: 0.3124 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2529 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= 0.135 Angle : 0.604 13.813 14710 Z= 0.303 Chirality : 0.043 0.178 1683 Planarity : 0.004 0.052 1836 Dihedral : 5.900 59.663 1591 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.65 % Allowed : 17.39 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -0.76 (0.23), residues: 1303 helix: 0.71 (0.22), residues: 580 sheet: -0.12 (0.42), residues: 163 loop : -1.97 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 927 HIS 0.017 0.001 HIS A 264 PHE 0.022 0.001 PHE A 465 TYR 0.015 0.001 TYR C 122 ARG 0.006 0.000 ARG C 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 3) link_NAG-ASN : angle 1.61438 ( 9) link_ALPHA1-4 : bond 0.01977 ( 1) link_ALPHA1-4 : angle 4.29102 ( 3) link_BETA1-4 : bond 0.00285 ( 1) link_BETA1-4 : angle 1.37261 ( 3) hydrogen bonds : bond 0.03903 ( 466) hydrogen bonds : angle 4.71453 ( 1350) SS BOND : bond 0.00153 ( 3) SS BOND : angle 0.62573 ( 6) covalent geometry : bond 0.00311 (10818) covalent geometry : angle 0.59966 (14689) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6699.55 seconds wall clock time: 127 minutes 24.61 seconds (7644.61 seconds total)