Starting phenix.real_space_refine on Wed Sep 17 19:40:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k7g_9931/09_2025/6k7g_9931.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k7g_9931/09_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_9931/09_2025/6k7g_9931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k7g_9931/09_2025/6k7g_9931.map" model { file = "/net/cci-nas-00/data/ceres_data/6k7g_9931/09_2025/6k7g_9931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k7g_9931/09_2025/6k7g_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-2.0-5805/lib/python3.9/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 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: 3.13, per 1000 atoms: 0.30 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: 1.37 Conformation dependent library (CDL) restraints added in 671.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.43 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: 2.15 Time building geometry restraints manager: 1.72 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: 1.570 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.900 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.720 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 covalent geometry : bond 0.01242 (10818) covalent geometry : angle 1.18294 (14689) SS BOND : bond 0.00635 ( 3) SS BOND : angle 1.36695 ( 6) hydrogen bonds : bond 0.11610 ( 466) hydrogen bonds : angle 6.81702 ( 1350) 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) link_NAG-ASN : bond 0.00687 ( 3) link_NAG-ASN : angle 4.18616 ( 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 : 0.422 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: 0.1675 time to fit residues: 27.9009 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 : 0.414 ------------------------------------------------------------------------------- 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... 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 = 0.3987 r_free = 0.3987 target = 0.184827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.130042 restraints weight = 11222.450| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 4.15 r_work: 0.2892 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1333 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= 0.132 Angle : 0.652 11.092 14710 Z= 0.334 Chirality : 0.044 0.199 1683 Planarity : 0.005 0.060 1836 Dihedral : 6.941 58.607 1596 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.29 % Favored : 93.63 % Rotamer: Outliers : 1.39 % Allowed : 11.48 % Favored : 87.13 % 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 aren not related in a simple way. whole: -2.38 (0.21), residues: 1303 helix: -0.78 (0.20), residues: 572 sheet: -1.15 (0.36), residues: 179 loop : -2.56 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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 0.004 0.001 HIS A 936 Details of bonding type rmsd covalent geometry : bond 0.00286 (10818) covalent geometry : angle 0.64561 (14689) SS BOND : bond 0.00078 ( 3) SS BOND : angle 0.89141 ( 6) hydrogen bonds : bond 0.04519 ( 466) hydrogen bonds : angle 5.45020 ( 1350) link_ALPHA1-4 : bond 0.01987 ( 1) link_ALPHA1-4 : angle 5.27702 ( 3) link_BETA1-4 : bond 0.00307 ( 1) link_BETA1-4 : angle 2.02678 ( 3) link_NAG-ASN : bond 0.00516 ( 3) link_NAG-ASN : angle 1.73230 ( 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 129 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLN cc_start: 0.4821 (OUTLIER) cc_final: 0.3960 (tm-30) REVERT: A 155 ASP cc_start: 0.7550 (t70) cc_final: 0.7069 (t70) REVERT: A 256 GLN cc_start: 0.7054 (tt0) cc_final: 0.6202 (tp40) REVERT: A 261 GLN cc_start: 0.5718 (tt0) cc_final: 0.5499 (tm-30) REVERT: A 262 TRP cc_start: 0.7247 (p-90) cc_final: 0.6610 (p-90) REVERT: A 264 HIS cc_start: 0.8040 (m170) cc_final: 0.7492 (m90) REVERT: A 468 MET cc_start: 0.8624 (tmm) cc_final: 0.7659 (tpp) REVERT: A 650 ASP cc_start: 0.7877 (m-30) cc_final: 0.7480 (m-30) REVERT: A 651 GLN cc_start: 0.7894 (mt0) cc_final: 0.7609 (mt0) REVERT: A 754 LYS cc_start: 0.8175 (tptt) cc_final: 0.7724 (tttt) REVERT: A 984 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7692 (mt-10) REVERT: A 1058 LYS cc_start: 0.7320 (mmmt) cc_final: 0.7019 (ttpt) REVERT: C 136 LYS cc_start: 0.9068 (ptmt) cc_final: 0.8802 (ptmm) REVERT: C 238 LYS cc_start: 0.8925 (pttt) cc_final: 0.8648 (mtmm) outliers start: 16 outliers final: 9 residues processed: 126 average time/residue: 0.1139 time to fit residues: 20.0670 Evaluate side-chains 105 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 25 optimal weight: 3.9990 chunk 58 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 117 optimal weight: 0.3980 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.182397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.142961 restraints weight = 11213.078| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.29 r_work: 0.3147 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10826 Z= 0.207 Angle : 0.696 11.379 14710 Z= 0.352 Chirality : 0.046 0.186 1683 Planarity : 0.005 0.057 1836 Dihedral : 6.602 59.966 1591 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.83 % Favored : 92.10 % Rotamer: Outliers : 1.74 % Allowed : 13.74 % Favored : 84.52 % 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 aren not related in a simple way. whole: -1.80 (0.22), residues: 1303 helix: -0.23 (0.21), residues: 579 sheet: -0.61 (0.40), residues: 163 loop : -2.42 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 37 TYR 0.023 0.002 TYR C 122 PHE 0.023 0.002 PHE C 304 TRP 0.018 0.001 TRP A 927 HIS 0.012 0.002 HIS A 473 Details of bonding type rmsd covalent geometry : bond 0.00497 (10818) covalent geometry : angle 0.68927 (14689) SS BOND : bond 0.00157 ( 3) SS BOND : angle 0.86047 ( 6) hydrogen bonds : bond 0.04940 ( 466) hydrogen bonds : angle 5.33169 ( 1350) link_ALPHA1-4 : bond 0.01756 ( 1) link_ALPHA1-4 : angle 5.50609 ( 3) link_BETA1-4 : bond 0.00251 ( 1) link_BETA1-4 : angle 1.92023 ( 3) link_NAG-ASN : bond 0.00170 ( 3) link_NAG-ASN : angle 1.88349 ( 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 124 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7584 (t70) cc_final: 0.7110 (t70) REVERT: A 262 TRP cc_start: 0.7504 (p-90) cc_final: 0.6815 (p-90) REVERT: A 264 HIS cc_start: 0.7971 (m-70) cc_final: 0.7624 (m90) REVERT: A 468 MET cc_start: 0.8526 (tmm) cc_final: 0.7628 (tpp) REVERT: A 650 ASP cc_start: 0.7819 (m-30) cc_final: 0.7502 (m-30) REVERT: A 754 LYS cc_start: 0.8364 (tptt) cc_final: 0.7978 (tttt) REVERT: A 817 TYR cc_start: 0.8788 (m-80) cc_final: 0.8532 (m-80) REVERT: A 984 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7846 (mt-10) REVERT: C 136 LYS cc_start: 0.9062 (ptmt) cc_final: 0.8828 (ptmm) REVERT: C 147 SER cc_start: 0.8686 (m) cc_final: 0.8466 (t) REVERT: C 238 LYS cc_start: 0.8907 (pttt) cc_final: 0.8671 (mtmm) outliers start: 20 outliers final: 14 residues processed: 118 average time/residue: 0.1180 time to fit residues: 19.6480 Evaluate side-chains 106 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 97 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 89 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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** C 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.183381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.137601 restraints weight = 11255.419| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.47 r_work: 0.3076 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10826 Z= 0.152 Angle : 0.631 11.875 14710 Z= 0.320 Chirality : 0.044 0.183 1683 Planarity : 0.004 0.056 1836 Dihedral : 6.388 59.128 1591 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 1.65 % Allowed : 15.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.23), residues: 1303 helix: 0.09 (0.21), residues: 577 sheet: -0.61 (0.40), residues: 167 loop : -2.19 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 37 TYR 0.017 0.001 TYR C 122 PHE 0.020 0.001 PHE A 594 TRP 0.016 0.001 TRP A 927 HIS 0.005 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00354 (10818) covalent geometry : angle 0.62498 (14689) SS BOND : bond 0.00140 ( 3) SS BOND : angle 0.72408 ( 6) hydrogen bonds : bond 0.04417 ( 466) hydrogen bonds : angle 5.13005 ( 1350) link_ALPHA1-4 : bond 0.01956 ( 1) link_ALPHA1-4 : angle 5.23086 ( 3) link_BETA1-4 : bond 0.00252 ( 1) link_BETA1-4 : angle 1.75682 ( 3) link_NAG-ASN : bond 0.00187 ( 3) link_NAG-ASN : angle 1.68271 ( 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 120 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7677 (t70) cc_final: 0.7088 (t70) REVERT: A 261 GLN cc_start: 0.5835 (tt0) cc_final: 0.5626 (tm-30) REVERT: A 468 MET cc_start: 0.8535 (tmm) cc_final: 0.7782 (tpp) REVERT: A 469 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7195 (mpp) REVERT: A 650 ASP cc_start: 0.7816 (m-30) cc_final: 0.7458 (m-30) REVERT: A 754 LYS cc_start: 0.8313 (tptt) cc_final: 0.7909 (mttt) REVERT: A 817 TYR cc_start: 0.8800 (m-80) cc_final: 0.8525 (m-80) REVERT: A 984 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7839 (mt-10) REVERT: C 147 SER cc_start: 0.8702 (m) cc_final: 0.8466 (t) REVERT: C 238 LYS cc_start: 0.8910 (pttt) cc_final: 0.8644 (mtmm) outliers start: 19 outliers final: 13 residues processed: 114 average time/residue: 0.1169 time to fit residues: 18.7009 Evaluate side-chains 108 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 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 803 ILE Chi-restraints excluded: chain A residue 844 ILE 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: 3.9990 chunk 40 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 22 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 453 GLN ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.185877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.132631 restraints weight = 11218.854| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.32 r_work: 0.2901 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10826 Z= 0.183 Angle : 0.644 11.977 14710 Z= 0.326 Chirality : 0.045 0.191 1683 Planarity : 0.004 0.056 1836 Dihedral : 6.332 58.990 1591 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.67 % Favored : 92.25 % Rotamer: Outliers : 1.91 % Allowed : 15.83 % Favored : 82.26 % 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 aren not related in a simple way. whole: -1.35 (0.23), residues: 1303 helix: 0.20 (0.21), residues: 582 sheet: -0.52 (0.41), residues: 167 loop : -2.23 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 37 TYR 0.019 0.002 TYR C 122 PHE 0.019 0.002 PHE C 304 TRP 0.016 0.001 TRP A 927 HIS 0.007 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00441 (10818) covalent geometry : angle 0.63825 (14689) SS BOND : bond 0.00184 ( 3) SS BOND : angle 0.73657 ( 6) hydrogen bonds : bond 0.04565 ( 466) hydrogen bonds : angle 5.08769 ( 1350) link_ALPHA1-4 : bond 0.01955 ( 1) link_ALPHA1-4 : angle 5.10641 ( 3) link_BETA1-4 : bond 0.00273 ( 1) link_BETA1-4 : angle 1.82534 ( 3) link_NAG-ASN : bond 0.00175 ( 3) link_NAG-ASN : angle 1.73783 ( 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 118 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7678 (t70) cc_final: 0.7108 (t70) REVERT: A 262 TRP cc_start: 0.7060 (p-90) cc_final: 0.6747 (p-90) REVERT: A 264 HIS cc_start: 0.7868 (m90) cc_final: 0.7594 (m90) REVERT: A 468 MET cc_start: 0.8619 (tmm) cc_final: 0.7925 (tpp) REVERT: A 469 MET cc_start: 0.7898 (tpp) cc_final: 0.7041 (mpp) REVERT: A 492 ASP cc_start: 0.8162 (p0) cc_final: 0.7454 (t70) REVERT: A 554 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6580 (tp) REVERT: A 650 ASP cc_start: 0.7878 (m-30) cc_final: 0.7452 (m-30) REVERT: A 754 LYS cc_start: 0.8235 (tptt) cc_final: 0.7673 (mttt) REVERT: A 817 TYR cc_start: 0.8790 (m-80) cc_final: 0.8511 (m-80) REVERT: A 984 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7873 (mt-10) REVERT: C 86 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6505 (tp30) REVERT: C 147 SER cc_start: 0.8812 (m) cc_final: 0.8508 (t) REVERT: C 238 LYS cc_start: 0.8872 (pttt) cc_final: 0.8573 (mtmm) outliers start: 22 outliers final: 17 residues processed: 113 average time/residue: 0.1176 time to fit residues: 18.6897 Evaluate side-chains 110 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 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 844 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 40 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.183701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.137516 restraints weight = 11310.940| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.36 r_work: 0.3083 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10826 Z= 0.130 Angle : 0.594 12.480 14710 Z= 0.300 Chirality : 0.043 0.176 1683 Planarity : 0.004 0.054 1836 Dihedral : 6.143 58.857 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 : 2.00 % Allowed : 16.00 % Favored : 82.00 % 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 aren not related in a simple way. whole: -1.10 (0.23), residues: 1303 helix: 0.44 (0.22), residues: 585 sheet: -0.37 (0.41), residues: 166 loop : -2.17 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 37 TYR 0.014 0.001 TYR C 122 PHE 0.016 0.001 PHE A 465 TRP 0.016 0.001 TRP A 927 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00296 (10818) covalent geometry : angle 0.58844 (14689) SS BOND : bond 0.00149 ( 3) SS BOND : angle 0.66107 ( 6) hydrogen bonds : bond 0.03998 ( 466) hydrogen bonds : angle 4.90891 ( 1350) link_ALPHA1-4 : bond 0.01998 ( 1) link_ALPHA1-4 : angle 4.82217 ( 3) link_BETA1-4 : bond 0.00310 ( 1) link_BETA1-4 : angle 1.51554 ( 3) link_NAG-ASN : bond 0.00192 ( 3) link_NAG-ASN : angle 1.63812 ( 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 124 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7715 (t70) cc_final: 0.7161 (t70) REVERT: A 262 TRP cc_start: 0.7105 (p-90) cc_final: 0.6785 (p-90) REVERT: A 264 HIS cc_start: 0.7999 (m90) cc_final: 0.7795 (m-70) REVERT: A 468 MET cc_start: 0.8563 (tmm) cc_final: 0.7973 (tpp) REVERT: A 492 ASP cc_start: 0.8023 (p0) cc_final: 0.7373 (t70) REVERT: A 554 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6582 (tp) REVERT: A 650 ASP cc_start: 0.7706 (m-30) cc_final: 0.7334 (m-30) REVERT: A 754 LYS cc_start: 0.8305 (tptt) cc_final: 0.7872 (mttt) REVERT: A 817 TYR cc_start: 0.8764 (m-80) cc_final: 0.8536 (m-80) REVERT: A 984 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7774 (mt-10) REVERT: C 86 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6514 (tp30) REVERT: C 147 SER cc_start: 0.8687 (m) cc_final: 0.8459 (t) REVERT: C 238 LYS cc_start: 0.8853 (pttt) cc_final: 0.8608 (mtmm) outliers start: 23 outliers final: 18 residues processed: 119 average time/residue: 0.1184 time to fit residues: 19.8179 Evaluate side-chains 116 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 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 799 VAL Chi-restraints excluded: chain A residue 803 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 118 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.182478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.136162 restraints weight = 11341.433| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.34 r_work: 0.3072 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10826 Z= 0.174 Angle : 0.626 12.768 14710 Z= 0.316 Chirality : 0.044 0.192 1683 Planarity : 0.004 0.053 1836 Dihedral : 6.149 58.950 1591 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.35 % Allowed : 16.00 % 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 aren not related in a simple way. whole: -1.09 (0.23), residues: 1303 helix: 0.39 (0.21), residues: 585 sheet: -0.30 (0.41), residues: 166 loop : -2.10 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 37 TYR 0.019 0.002 TYR C 122 PHE 0.019 0.002 PHE A 465 TRP 0.015 0.001 TRP A 927 HIS 0.006 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00417 (10818) covalent geometry : angle 0.62034 (14689) SS BOND : bond 0.00176 ( 3) SS BOND : angle 0.70760 ( 6) hydrogen bonds : bond 0.04348 ( 466) hydrogen bonds : angle 4.94817 ( 1350) link_ALPHA1-4 : bond 0.02020 ( 1) link_ALPHA1-4 : angle 4.82571 ( 3) link_BETA1-4 : bond 0.00283 ( 1) link_BETA1-4 : angle 1.71261 ( 3) link_NAG-ASN : bond 0.00177 ( 3) link_NAG-ASN : angle 1.67093 ( 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 122 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7710 (t70) cc_final: 0.7135 (t70) REVERT: A 262 TRP cc_start: 0.7134 (p-90) cc_final: 0.6845 (p-90) REVERT: A 468 MET cc_start: 0.8594 (tmm) cc_final: 0.7929 (tpp) REVERT: A 492 ASP cc_start: 0.8092 (p0) cc_final: 0.7424 (t70) REVERT: A 554 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6605 (tp) REVERT: A 650 ASP cc_start: 0.7696 (m-30) cc_final: 0.7323 (m-30) REVERT: A 754 LYS cc_start: 0.8307 (tptt) cc_final: 0.7887 (mttt) REVERT: A 817 TYR cc_start: 0.8795 (m-80) cc_final: 0.8502 (m-80) REVERT: A 984 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7808 (mt-10) REVERT: C 86 GLU cc_start: 0.6897 (mm-30) cc_final: 0.6469 (tp30) REVERT: C 147 SER cc_start: 0.8711 (m) cc_final: 0.8484 (t) REVERT: C 238 LYS cc_start: 0.8843 (pttt) cc_final: 0.8603 (mtmm) outliers start: 27 outliers final: 23 residues processed: 117 average time/residue: 0.1216 time to fit residues: 19.9255 Evaluate side-chains 116 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 451 ASN 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 742 VAL Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 973 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 92 ASN Chi-restraints excluded: chain C residue 174 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 109 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3930 r_free = 0.3930 target = 0.179623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.133712 restraints weight = 11303.386| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.36 r_work: 0.3021 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10826 Z= 0.249 Angle : 0.686 13.192 14710 Z= 0.346 Chirality : 0.047 0.210 1683 Planarity : 0.005 0.055 1836 Dihedral : 6.326 58.294 1591 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.06 % Favored : 91.86 % Rotamer: Outliers : 2.43 % Allowed : 16.43 % Favored : 81.13 % 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 aren not related in a simple way. whole: -1.24 (0.23), residues: 1303 helix: 0.23 (0.21), residues: 587 sheet: -0.29 (0.42), residues: 162 loop : -2.16 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 37 TYR 0.025 0.002 TYR C 122 PHE 0.022 0.002 PHE C 304 TRP 0.017 0.002 TRP A1014 HIS 0.008 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00611 (10818) covalent geometry : angle 0.68027 (14689) SS BOND : bond 0.00231 ( 3) SS BOND : angle 0.82014 ( 6) hydrogen bonds : bond 0.04926 ( 466) hydrogen bonds : angle 5.09672 ( 1350) link_ALPHA1-4 : bond 0.01961 ( 1) link_ALPHA1-4 : angle 4.92459 ( 3) link_BETA1-4 : bond 0.00282 ( 1) link_BETA1-4 : angle 2.05527 ( 3) link_NAG-ASN : bond 0.00210 ( 3) link_NAG-ASN : angle 1.78818 ( 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 126 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7818 (t70) cc_final: 0.7462 (t70) REVERT: A 264 HIS cc_start: 0.8043 (m90) cc_final: 0.7299 (m90) REVERT: A 468 MET cc_start: 0.8603 (tmm) cc_final: 0.7975 (tpp) REVERT: A 492 ASP cc_start: 0.8180 (p0) cc_final: 0.7519 (t70) REVERT: A 554 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6515 (tp) REVERT: A 650 ASP cc_start: 0.7767 (m-30) cc_final: 0.7373 (m-30) REVERT: A 754 LYS cc_start: 0.8342 (tptt) cc_final: 0.7890 (mttt) REVERT: A 772 MET cc_start: 0.8519 (ttp) cc_final: 0.7879 (mmt) REVERT: A 817 TYR cc_start: 0.8822 (m-80) cc_final: 0.8521 (m-80) REVERT: A 984 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7876 (mt-10) REVERT: C 147 SER cc_start: 0.8781 (m) cc_final: 0.8545 (t) REVERT: C 238 LYS cc_start: 0.8861 (pttt) cc_final: 0.8638 (mtmm) outliers start: 28 outliers final: 26 residues processed: 121 average time/residue: 0.1269 time to fit residues: 21.2856 Evaluate side-chains 121 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 451 ASN Chi-restraints excluded: chain A residue 501 LYS 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 762 SER Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 973 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 92 ASN Chi-restraints excluded: chain C residue 174 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 13 optimal weight: 8.9990 chunk 117 optimal weight: 0.2980 chunk 2 optimal weight: 7.9990 chunk 73 optimal weight: 0.6980 chunk 64 optimal weight: 0.0000 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 94 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN A 451 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.185666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.140629 restraints weight = 11203.347| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.36 r_work: 0.3132 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10826 Z= 0.109 Angle : 0.586 13.543 14710 Z= 0.296 Chirality : 0.043 0.153 1683 Planarity : 0.004 0.054 1836 Dihedral : 6.049 59.658 1591 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.09 % Allowed : 16.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.24), residues: 1303 helix: 0.60 (0.22), residues: 586 sheet: -0.15 (0.42), residues: 165 loop : -2.04 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 37 TYR 0.013 0.001 TYR C 273 PHE 0.023 0.001 PHE A 465 TRP 0.017 0.001 TRP A 927 HIS 0.002 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00232 (10818) covalent geometry : angle 0.58086 (14689) SS BOND : bond 0.00140 ( 3) SS BOND : angle 0.61015 ( 6) hydrogen bonds : bond 0.03660 ( 466) hydrogen bonds : angle 4.77474 ( 1350) link_ALPHA1-4 : bond 0.02285 ( 1) link_ALPHA1-4 : angle 4.49403 ( 3) link_BETA1-4 : bond 0.00082 ( 1) link_BETA1-4 : angle 1.28724 ( 3) link_NAG-ASN : bond 0.00263 ( 3) link_NAG-ASN : angle 1.53300 ( 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 122 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7861 (t70) cc_final: 0.7287 (t70) REVERT: A 468 MET cc_start: 0.8520 (tmm) cc_final: 0.7919 (tpp) REVERT: A 492 ASP cc_start: 0.8046 (p0) cc_final: 0.7429 (t70) REVERT: A 650 ASP cc_start: 0.7588 (m-30) cc_final: 0.7174 (m-30) REVERT: A 747 LEU cc_start: 0.8657 (mt) cc_final: 0.8344 (mt) REVERT: A 754 LYS cc_start: 0.8260 (tptt) cc_final: 0.7815 (mttt) REVERT: A 772 MET cc_start: 0.8367 (ttp) cc_final: 0.7879 (mmt) REVERT: A 817 TYR cc_start: 0.8744 (m-80) cc_final: 0.8482 (m-80) REVERT: A 984 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7811 (mt-10) REVERT: C 147 SER cc_start: 0.8772 (m) cc_final: 0.8515 (t) REVERT: C 238 LYS cc_start: 0.8802 (pttt) cc_final: 0.8575 (mtmm) outliers start: 24 outliers final: 20 residues processed: 118 average time/residue: 0.1232 time to fit residues: 20.2287 Evaluate side-chains 112 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 260 THR 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 762 SER Chi-restraints excluded: chain A residue 818 SER 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 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 38 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 61 optimal weight: 0.0470 chunk 52 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- 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** ** 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 = 0.3955 r_free = 0.3955 target = 0.182018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.135256 restraints weight = 11170.647| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.38 r_work: 0.3048 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10826 Z= 0.192 Angle : 0.641 13.520 14710 Z= 0.325 Chirality : 0.045 0.197 1683 Planarity : 0.004 0.052 1836 Dihedral : 6.133 59.099 1591 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.65 % Allowed : 17.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.23), residues: 1303 helix: 0.43 (0.21), residues: 587 sheet: -0.19 (0.42), residues: 166 loop : -2.06 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 37 TYR 0.021 0.002 TYR C 122 PHE 0.019 0.002 PHE A 465 TRP 0.014 0.001 TRP A 927 HIS 0.020 0.002 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00464 (10818) covalent geometry : angle 0.63613 (14689) SS BOND : bond 0.00195 ( 3) SS BOND : angle 0.74465 ( 6) hydrogen bonds : bond 0.04375 ( 466) hydrogen bonds : angle 4.87996 ( 1350) link_ALPHA1-4 : bond 0.02009 ( 1) link_ALPHA1-4 : angle 4.64532 ( 3) link_BETA1-4 : bond 0.00237 ( 1) link_BETA1-4 : angle 1.76195 ( 3) link_NAG-ASN : bond 0.00183 ( 3) link_NAG-ASN : angle 1.66366 ( 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 114 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7904 (t70) cc_final: 0.7339 (t70) REVERT: A 468 MET cc_start: 0.8601 (tmm) cc_final: 0.7968 (tpp) REVERT: A 492 ASP cc_start: 0.8038 (p0) cc_final: 0.7383 (t70) REVERT: A 493 GLU cc_start: 0.7918 (pp20) cc_final: 0.7629 (pp20) REVERT: A 650 ASP cc_start: 0.7707 (m-30) cc_final: 0.7305 (m-30) REVERT: A 754 LYS cc_start: 0.8301 (tptt) cc_final: 0.7872 (mttt) REVERT: A 772 MET cc_start: 0.8453 (ttp) cc_final: 0.7846 (mmt) REVERT: A 817 TYR cc_start: 0.8800 (m-80) cc_final: 0.8581 (m-80) REVERT: A 984 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7818 (mt-10) REVERT: C 147 SER cc_start: 0.8791 (m) cc_final: 0.8534 (t) REVERT: C 238 LYS cc_start: 0.8832 (pttt) cc_final: 0.8609 (mtmm) outliers start: 19 outliers final: 18 residues processed: 110 average time/residue: 0.1260 time to fit residues: 19.2278 Evaluate side-chains 112 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 738 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 818 SER 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 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 127 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 46 optimal weight: 30.0000 chunk 43 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 451 ASN ** 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 = 0.179914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.134820 restraints weight = 11379.750| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.38 r_work: 0.3023 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 10826 Z= 0.236 Angle : 0.687 13.241 14710 Z= 0.348 Chirality : 0.047 0.210 1683 Planarity : 0.004 0.051 1836 Dihedral : 6.316 58.405 1591 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 2.26 % Allowed : 16.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.23), residues: 1303 helix: 0.32 (0.21), residues: 584 sheet: -0.24 (0.43), residues: 162 loop : -2.07 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 262 TYR 0.024 0.002 TYR C 122 PHE 0.021 0.002 PHE C 304 TRP 0.019 0.002 TRP A 262 HIS 0.008 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00576 (10818) covalent geometry : angle 0.68163 (14689) SS BOND : bond 0.00240 ( 3) SS BOND : angle 0.79597 ( 6) hydrogen bonds : bond 0.04844 ( 466) hydrogen bonds : angle 5.05061 ( 1350) link_ALPHA1-4 : bond 0.01927 ( 1) link_ALPHA1-4 : angle 4.70813 ( 3) link_BETA1-4 : bond 0.00330 ( 1) link_BETA1-4 : angle 1.95071 ( 3) link_NAG-ASN : bond 0.00219 ( 3) link_NAG-ASN : angle 1.74669 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2869.91 seconds wall clock time: 49 minutes 58.75 seconds (2998.75 seconds total)