Starting phenix.real_space_refine on Mon Jun 9 20:23:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k7l_9939/06_2025/6k7l_9939.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k7l_9939/06_2025/6k7l_9939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6k7l_9939/06_2025/6k7l_9939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k7l_9939/06_2025/6k7l_9939.map" model { file = "/net/cci-nas-00/data/ceres_data/6k7l_9939/06_2025/6k7l_9939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k7l_9939/06_2025/6k7l_9939.cif" } resolution = 2.83 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= 0.005 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: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 54 5.16 5 Be 1 3.05 5 C 6881 2.51 5 N 1756 2.21 5 O 1919 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10615 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7893 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 961} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2615 Classifications: {'peptide': 325} Link IDs: {'PCIS': 2, 'PTRANS': 23, '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: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' MG': 1, 'BEF': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.85, per 1000 atoms: 0.65 Number of scatterers: 10615 At special positions: 0 Unit cell: (73.04, 107.07, 166.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 54 16.00 Mg 1 11.99 F 3 9.00 O 1919 8.00 N 1756 7.00 C 6881 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.04 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.04 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=1, 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 404 " - " ASN C 294 " " NAG C 405 " - " ASN C 107 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.5 seconds 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2476 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 11 sheets defined 49.5% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 60 through 74 removed outlier: 4.137A pdb=" N LEU A 65 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Proline residue: A 66 - end of helix Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 101 through 132 removed outlier: 4.932A pdb=" N ALA A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) 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 185 through 190 Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 208 through 215 removed outlier: 4.437A pdb=" N ILE A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 323 Processing helix chain 'A' and resid 339 through 351 Processing helix chain 'A' and resid 352 through 355 removed outlier: 3.568A pdb=" N ILE A 355 " --> pdb=" O ASN A 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 358 through 377 Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.996A pdb=" N LEU A 396 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 3.571A 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 448 through 455 Processing helix chain 'A' and resid 458 through 472 removed outlier: 3.925A pdb=" N ILE A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 503 Processing helix chain 'A' and resid 559 through 564 removed outlier: 3.722A pdb=" N TYR A 564 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 588 Processing helix chain 'A' and resid 600 through 617 removed outlier: 3.892A pdb=" N THR A 616 " --> pdb=" O GLN A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 632 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 739 Processing helix chain 'A' and resid 742 through 753 Processing helix chain 'A' and resid 762 through 775 Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 790 through 797 Processing helix chain 'A' and resid 809 through 815 Processing helix chain 'A' and resid 823 through 831 removed outlier: 4.320A pdb=" N ASN A 827 " --> pdb=" O LYS A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 856 removed outlier: 3.730A pdb=" N LEU A 854 " --> pdb=" O LYS A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 866 removed outlier: 3.897A pdb=" N PHE A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL A 864 " --> pdb=" O TRP A 860 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 881 Processing helix chain 'A' and resid 887 through 896 removed outlier: 3.914A 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 919 removed outlier: 3.574A pdb=" N THR A 914 " --> pdb=" O GLU A 910 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 918 " --> pdb=" O THR A 914 " (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: 3.835A pdb=" N LEU A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1011 Processing helix chain 'A' and resid 1020 through 1024 removed outlier: 3.547A pdb=" N MET A1023 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A1024 " --> pdb=" O PRO A1021 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1020 through 1024' Processing helix chain 'A' and resid 1025 through 1032 Processing helix chain 'A' and resid 1033 through 1062 removed outlier: 4.055A pdb=" N LEU A1041 " --> pdb=" O TRP A1037 " (cutoff:3.500A) Proline residue: A1044 - end of helix removed outlier: 5.102A pdb=" N LEU A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASP A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 74 Proline residue: C 52 - end of helix Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 91 through 95 removed outlier: 3.562A pdb=" N CYS C 94 " --> pdb=" O CYS C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 146 through 152 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: 3.515A pdb=" N LEU C 243 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 253 removed outlier: 3.865A pdb=" N ASN C 250 " --> pdb=" O PRO C 247 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N GLY C 251 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE C 252 " --> pdb=" O ASN C 249 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE C 253 " --> pdb=" O ASN C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 323 through 350 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 160 removed outlier: 6.556A pdb=" N TRP A 262 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N SER A 174 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N HIS A 264 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ASP A 168 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 194 through 198 removed outlier: 3.645A pdb=" N TYR A 182 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 381 through 382 Processing sheet with id=AA5, first strand: chain 'A' and resid 390 through 391 removed outlier: 6.697A pdb=" N THR A 781 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL A 801 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA A 783 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE A 803 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLY A 785 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL A 403 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU A 782 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR A 405 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE A 784 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N PHE A 407 " --> pdb=" O ILE A 784 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE A 666 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N CYS A 758 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE A 668 " --> pdb=" O CYS A 758 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 727 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N CYS A 759 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 729 " --> pdb=" O CYS A 759 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE A 694 " --> pdb=" O ILE A 728 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASP A 730 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE A 696 " --> pdb=" O ASP A 730 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 429 through 431 removed outlier: 3.638A pdb=" N VAL A 429 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS A 424 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL A 418 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA A 643 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 514 through 517 Processing sheet with id=AA8, first strand: chain 'A' and resid 531 through 532 removed outlier: 3.970A pdb=" N THR A 547 " --> pdb=" O LYS A 551 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 551 " --> pdb=" O THR A 547 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 79 removed outlier: 7.056A pdb=" N VAL C 118 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LEU C 275 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N MET C 120 " --> pdb=" O TYR C 273 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 110 removed outlier: 4.749A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 162 through 163 497 hydrogen bonds defined for protein. 1437 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: 3.69 Time building geometry restraints manager: 3.27 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: 1815 1.32 - 1.44: 2878 1.44 - 1.57: 6083 1.57 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 10861 Sorted by residual: bond pdb=" F2 BEF A1801 " pdb="BE BEF A1801 " ideal model delta sigma weight residual 1.476 1.760 -0.284 2.00e-02 2.50e+03 2.02e+02 bond pdb=" F1 BEF A1801 " pdb="BE BEF A1801 " ideal model delta sigma weight residual 1.476 1.758 -0.282 2.00e-02 2.50e+03 1.99e+02 bond pdb=" F3 BEF A1801 " pdb="BE BEF A1801 " ideal model delta sigma weight residual 1.476 1.756 -0.280 2.00e-02 2.50e+03 1.96e+02 bond pdb=" C ARG C 215 " pdb=" N ASN C 216 " ideal model delta sigma weight residual 1.329 1.218 0.111 1.86e-02 2.89e+03 3.53e+01 bond pdb=" CB VAL A 853 " pdb=" CG1 VAL A 853 " ideal model delta sigma weight residual 1.521 1.423 0.098 3.30e-02 9.18e+02 8.79e+00 ... (remaining 10856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 13956 2.31 - 4.62: 673 4.62 - 6.93: 73 6.93 - 9.25: 23 9.25 - 11.56: 14 Bond angle restraints: 14739 Sorted by residual: angle pdb=" C LEU A 330 " pdb=" N ASN A 331 " pdb=" CA ASN A 331 " ideal model delta sigma weight residual 121.54 133.10 -11.56 1.91e+00 2.74e-01 3.66e+01 angle pdb=" N SER A 223 " pdb=" CA SER A 223 " pdb=" C SER A 223 " ideal model delta sigma weight residual 109.81 120.43 -10.62 2.21e+00 2.05e-01 2.31e+01 angle pdb=" N SER A1024 " pdb=" CA SER A1024 " pdb=" C SER A1024 " ideal model delta sigma weight residual 112.38 117.89 -5.51 1.22e+00 6.72e-01 2.04e+01 angle pdb=" C ILE A 235 " pdb=" N ARG A 236 " pdb=" CA ARG A 236 " ideal model delta sigma weight residual 121.70 129.52 -7.82 1.80e+00 3.09e-01 1.89e+01 angle pdb=" N THR A 135 " pdb=" CA THR A 135 " pdb=" C THR A 135 " ideal model delta sigma weight residual 114.75 109.56 5.19 1.26e+00 6.30e-01 1.70e+01 ... (remaining 14734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.07: 6046 22.07 - 44.13: 436 44.13 - 66.20: 64 66.20 - 88.26: 18 88.26 - 110.33: 4 Dihedral angle restraints: 6568 sinusoidal: 2729 harmonic: 3839 Sorted by residual: dihedral pdb=" CA ILE A 485 " pdb=" C ILE A 485 " pdb=" N TYR A 486 " pdb=" CA TYR A 486 " ideal model delta harmonic sigma weight residual -180.00 -130.47 -49.53 0 5.00e+00 4.00e-02 9.81e+01 dihedral pdb=" CA THR A 535 " pdb=" C THR A 535 " pdb=" N SER A 536 " pdb=" CA SER A 536 " ideal model delta harmonic sigma weight residual 180.00 -134.93 -45.07 0 5.00e+00 4.00e-02 8.12e+01 dihedral pdb=" CA GLY A 336 " pdb=" C GLY A 336 " pdb=" N ALA A 337 " pdb=" CA ALA A 337 " ideal model delta harmonic sigma weight residual -180.00 -147.63 -32.37 0 5.00e+00 4.00e-02 4.19e+01 ... (remaining 6565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1259 0.071 - 0.142: 379 0.142 - 0.213: 38 0.213 - 0.284: 5 0.284 - 0.355: 3 Chirality restraints: 1684 Sorted by residual: chirality pdb=" C1 NAG C 404 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 404 " pdb=" O5 NAG C 404 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CB ILE A 485 " pdb=" CA ILE A 485 " pdb=" CG1 ILE A 485 " pdb=" CG2 ILE A 485 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CG LEU A 529 " pdb=" CB LEU A 529 " pdb=" CD1 LEU A 529 " pdb=" CD2 LEU A 529 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1681 not shown) Planarity restraints: 1844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 405 " -0.262 2.00e-02 2.50e+03 2.20e-01 6.06e+02 pdb=" C7 NAG C 405 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG C 405 " -0.175 2.00e-02 2.50e+03 pdb=" N2 NAG C 405 " 0.372 2.00e-02 2.50e+03 pdb=" O7 NAG C 405 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.132 2.00e-02 2.50e+03 1.14e-01 1.64e+02 pdb=" C7 NAG B 1 " -0.027 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.021 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.189 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.067 2.00e-02 2.50e+03 5.53e-02 3.82e+01 pdb=" C7 NAG B 2 " -0.020 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.051 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.088 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.011 2.00e-02 2.50e+03 ... (remaining 1841 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 70 2.56 - 3.15: 7857 3.15 - 3.73: 16812 3.73 - 4.32: 24631 4.32 - 4.90: 40210 Nonbonded interactions: 89580 Sorted by model distance: nonbonded pdb=" F3 BEF A1801 " pdb="MG MG A1802 " model vdw 1.976 2.120 nonbonded pdb=" OD1 ASP A 786 " pdb="MG MG A1802 " model vdw 2.077 2.170 nonbonded pdb=" OD2 ASP A 409 " pdb="MG MG A1802 " model vdw 2.096 2.170 nonbonded pdb=" O THR A 411 " pdb="MG MG A1802 " model vdw 2.132 2.170 nonbonded pdb=" OD2 ASP A 409 " pdb=" F3 BEF A1801 " model vdw 2.187 2.990 ... (remaining 89575 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: 1.190 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.770 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 : 0.015 0.900 10870 Z= 1.004 Angle : 1.167 16.286 14760 Z= 0.616 Chirality : 0.065 0.355 1684 Planarity : 0.011 0.220 1841 Dihedral : 15.834 110.326 4083 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.46 % Favored : 92.31 % Rotamer: Outliers : 0.17 % Allowed : 7.21 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.27 (0.19), residues: 1301 helix: -2.16 (0.16), residues: 612 sheet: -0.76 (0.39), residues: 181 loop : -2.54 (0.23), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP A 607 HIS 0.012 0.002 HIS A 147 PHE 0.027 0.004 PHE C 179 TYR 0.030 0.004 TYR C 297 ARG 0.014 0.001 ARG C 37 Details of bonding type rmsd link_NAG-ASN : bond 0.01499 ( 3) link_NAG-ASN : angle 6.60432 ( 9) link_ALPHA1-4 : bond 0.01855 ( 1) link_ALPHA1-4 : angle 6.06332 ( 3) link_BETA1-4 : bond 0.00123 ( 1) link_BETA1-4 : angle 1.71954 ( 3) hydrogen bonds : bond 0.11942 ( 497) hydrogen bonds : angle 6.63560 ( 1437) SS BOND : bond 0.00831 ( 3) SS BOND : angle 3.73710 ( 6) covalent geometry : bond 0.01209 (10861) covalent geometry : angle 1.15075 (14739) Misc. bond : bond 0.90047 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 1.118 Fit side-chains REVERT: A 116 GLU cc_start: 0.6650 (mt-10) cc_final: 0.6187 (tt0) REVERT: A 184 GLU cc_start: 0.8204 (tp30) cc_final: 0.7898 (tp30) REVERT: A 187 ASN cc_start: 0.8318 (t0) cc_final: 0.8070 (t0) REVERT: A 191 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7154 (mm-30) REVERT: A 253 ARG cc_start: 0.7054 (ttt-90) cc_final: 0.6776 (ttt-90) REVERT: A 256 GLN cc_start: 0.7424 (tt0) cc_final: 0.7217 (tt0) REVERT: A 390 MET cc_start: 0.7829 (ttt) cc_final: 0.7298 (tpp) REVERT: A 469 MET cc_start: 0.6715 (mtp) cc_final: 0.6320 (mtp) REVERT: A 560 ASP cc_start: 0.7189 (p0) cc_final: 0.6709 (t70) REVERT: A 582 GLU cc_start: 0.5960 (pp20) cc_final: 0.5725 (mt-10) REVERT: A 1041 LEU cc_start: 0.8504 (tp) cc_final: 0.8245 (tt) REVERT: A 1059 ARG cc_start: 0.6662 (mtp85) cc_final: 0.6430 (tpt170) REVERT: C 59 LEU cc_start: 0.8534 (mt) cc_final: 0.8218 (mp) REVERT: C 112 LYS cc_start: 0.7711 (mtmt) cc_final: 0.7434 (mtmt) REVERT: C 136 LYS cc_start: 0.8655 (ptmt) cc_final: 0.8072 (pttp) REVERT: C 242 MET cc_start: 0.8171 (mmm) cc_final: 0.7842 (mmt) outliers start: 2 outliers final: 0 residues processed: 135 average time/residue: 1.3389 time to fit residues: 194.1586 Evaluate side-chains 101 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 147 HIS A 187 ASN A 249 GLN A 323 HIS A 352 ASN A 433 GLN A 765 GLN ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 ASN A1127 ASN C 36 GLN C 176 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.189193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.152656 restraints weight = 10037.170| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.27 r_work: 0.3176 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10870 Z= 0.161 Angle : 0.694 12.273 14760 Z= 0.356 Chirality : 0.046 0.388 1684 Planarity : 0.006 0.079 1841 Dihedral : 9.867 110.637 1595 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.61 % Favored : 94.24 % Rotamer: Outliers : 1.91 % Allowed : 10.34 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.77 (0.22), residues: 1301 helix: -0.58 (0.20), residues: 612 sheet: -0.37 (0.39), residues: 184 loop : -2.16 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 927 HIS 0.004 0.001 HIS A 147 PHE 0.021 0.002 PHE A 968 TYR 0.015 0.001 TYR C 297 ARG 0.003 0.000 ARG A 898 Details of bonding type rmsd link_NAG-ASN : bond 0.00992 ( 3) link_NAG-ASN : angle 4.92029 ( 9) link_ALPHA1-4 : bond 0.01780 ( 1) link_ALPHA1-4 : angle 4.24335 ( 3) link_BETA1-4 : bond 0.00185 ( 1) link_BETA1-4 : angle 1.32115 ( 3) hydrogen bonds : bond 0.05352 ( 497) hydrogen bonds : angle 5.42782 ( 1437) SS BOND : bond 0.00343 ( 3) SS BOND : angle 2.17611 ( 6) covalent geometry : bond 0.00372 (10861) covalent geometry : angle 0.67923 (14739) Misc. bond : bond 0.00121 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 1.107 Fit side-chains REVERT: A 116 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6880 (tt0) REVERT: A 180 MET cc_start: 0.6116 (OUTLIER) cc_final: 0.5506 (mpm) REVERT: A 322 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7596 (ttp-170) REVERT: A 390 MET cc_start: 0.8833 (ttt) cc_final: 0.8582 (tpp) REVERT: A 469 MET cc_start: 0.6862 (mtp) cc_final: 0.6620 (mtp) REVERT: A 764 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7316 (pt) REVERT: A 772 MET cc_start: 0.8673 (tmm) cc_final: 0.8459 (ttp) REVERT: C 136 LYS cc_start: 0.9027 (ptmt) cc_final: 0.8727 (pttp) REVERT: C 242 MET cc_start: 0.8783 (mmm) cc_final: 0.8538 (mmt) outliers start: 22 outliers final: 6 residues processed: 130 average time/residue: 1.1790 time to fit residues: 166.6855 Evaluate side-chains 116 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 875 ARG Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 215 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 27 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 ASN A 776 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.191420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.156123 restraints weight = 10091.606| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.24 r_work: 0.3100 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10870 Z= 0.145 Angle : 0.649 11.685 14760 Z= 0.331 Chirality : 0.045 0.406 1684 Planarity : 0.005 0.077 1841 Dihedral : 9.346 108.474 1595 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.00 % Favored : 93.93 % Rotamer: Outliers : 1.82 % Allowed : 13.21 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.00 (0.23), residues: 1301 helix: 0.23 (0.21), residues: 607 sheet: -0.18 (0.40), residues: 184 loop : -1.92 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 927 HIS 0.003 0.001 HIS A 456 PHE 0.020 0.002 PHE A 968 TYR 0.015 0.001 TYR C 297 ARG 0.004 0.000 ARG A1059 Details of bonding type rmsd link_NAG-ASN : bond 0.00888 ( 3) link_NAG-ASN : angle 4.73512 ( 9) link_ALPHA1-4 : bond 0.01792 ( 1) link_ALPHA1-4 : angle 4.19103 ( 3) link_BETA1-4 : bond 0.00308 ( 1) link_BETA1-4 : angle 1.05156 ( 3) hydrogen bonds : bond 0.04941 ( 497) hydrogen bonds : angle 5.11526 ( 1437) SS BOND : bond 0.00347 ( 3) SS BOND : angle 1.77216 ( 6) covalent geometry : bond 0.00330 (10861) covalent geometry : angle 0.63477 (14739) Misc. bond : bond 0.00108 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 1.132 Fit side-chains REVERT: A 116 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6986 (tt0) REVERT: A 180 MET cc_start: 0.6167 (OUTLIER) cc_final: 0.5282 (mpm) REVERT: A 187 ASN cc_start: 0.8658 (t0) cc_final: 0.8332 (t0) REVERT: A 390 MET cc_start: 0.9127 (ttt) cc_final: 0.8765 (tpp) REVERT: A 469 MET cc_start: 0.6672 (mtp) cc_final: 0.6159 (mtt) REVERT: A 560 ASP cc_start: 0.7406 (p0) cc_final: 0.6973 (t70) REVERT: A 680 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7492 (mp) REVERT: A 776 GLN cc_start: 0.7060 (tt0) cc_final: 0.6737 (mt0) REVERT: A 1059 ARG cc_start: 0.7596 (tpt-90) cc_final: 0.7384 (ttm110) REVERT: C 136 LYS cc_start: 0.9124 (ptmt) cc_final: 0.8854 (ptmm) REVERT: C 155 LYS cc_start: 0.8711 (pttp) cc_final: 0.8428 (ttmt) REVERT: C 242 MET cc_start: 0.8920 (mmm) cc_final: 0.8574 (mmt) outliers start: 21 outliers final: 7 residues processed: 131 average time/residue: 1.1864 time to fit residues: 168.8274 Evaluate side-chains 116 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 215 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 114 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 HIS A1118 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.190449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.151096 restraints weight = 10014.655| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.29 r_work: 0.3070 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10870 Z= 0.160 Angle : 0.648 11.303 14760 Z= 0.330 Chirality : 0.046 0.406 1684 Planarity : 0.005 0.075 1841 Dihedral : 9.204 110.204 1595 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.61 % Favored : 94.31 % Rotamer: Outliers : 2.52 % Allowed : 14.77 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.77 (0.23), residues: 1301 helix: 0.47 (0.21), residues: 610 sheet: -0.13 (0.39), residues: 184 loop : -1.85 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 927 HIS 0.005 0.001 HIS A1118 PHE 0.020 0.002 PHE A 968 TYR 0.014 0.001 TYR C 297 ARG 0.004 0.000 ARG A 898 Details of bonding type rmsd link_NAG-ASN : bond 0.00873 ( 3) link_NAG-ASN : angle 4.64456 ( 9) link_ALPHA1-4 : bond 0.01824 ( 1) link_ALPHA1-4 : angle 4.09836 ( 3) link_BETA1-4 : bond 0.00158 ( 1) link_BETA1-4 : angle 1.01753 ( 3) hydrogen bonds : bond 0.04976 ( 497) hydrogen bonds : angle 5.03953 ( 1437) SS BOND : bond 0.00335 ( 3) SS BOND : angle 1.95543 ( 6) covalent geometry : bond 0.00372 (10861) covalent geometry : angle 0.63440 (14739) Misc. bond : bond 0.00118 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 1.111 Fit side-chains REVERT: A 116 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7017 (tt0) REVERT: A 180 MET cc_start: 0.6313 (OUTLIER) cc_final: 0.5424 (mpm) REVERT: A 187 ASN cc_start: 0.8692 (t0) cc_final: 0.8312 (t0) REVERT: A 322 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.8001 (ttp-170) REVERT: A 390 MET cc_start: 0.9144 (ttt) cc_final: 0.8791 (tpp) REVERT: A 469 MET cc_start: 0.6721 (mtp) cc_final: 0.6372 (mtp) REVERT: A 582 GLU cc_start: 0.5644 (OUTLIER) cc_final: 0.5439 (mm-30) REVERT: A 734 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7213 (tm) REVERT: A 764 LEU cc_start: 0.7755 (pt) cc_final: 0.7480 (tp) REVERT: A 772 MET cc_start: 0.8924 (ttp) cc_final: 0.8703 (ttt) REVERT: A 776 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6815 (mt0) REVERT: C 155 LYS cc_start: 0.8762 (pttp) cc_final: 0.8455 (ttmt) REVERT: C 242 MET cc_start: 0.9000 (mmm) cc_final: 0.8571 (mmm) outliers start: 29 outliers final: 8 residues processed: 132 average time/residue: 1.0851 time to fit residues: 156.5233 Evaluate side-chains 120 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 215 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 21 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** 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 = 0.4045 r_free = 0.4045 target = 0.192058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.149600 restraints weight = 9897.963| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.26 r_work: 0.3068 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10870 Z= 0.137 Angle : 0.621 10.438 14760 Z= 0.317 Chirality : 0.044 0.391 1684 Planarity : 0.004 0.073 1841 Dihedral : 8.853 108.213 1595 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.87 % Allowed : 15.38 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.56 (0.24), residues: 1301 helix: 0.63 (0.21), residues: 614 sheet: -0.00 (0.40), residues: 184 loop : -1.76 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 927 HIS 0.006 0.001 HIS A 456 PHE 0.019 0.002 PHE A 968 TYR 0.013 0.001 TYR C 122 ARG 0.003 0.000 ARG A 898 Details of bonding type rmsd link_NAG-ASN : bond 0.00809 ( 3) link_NAG-ASN : angle 4.40350 ( 9) link_ALPHA1-4 : bond 0.01686 ( 1) link_ALPHA1-4 : angle 3.92473 ( 3) link_BETA1-4 : bond 0.00213 ( 1) link_BETA1-4 : angle 0.96830 ( 3) hydrogen bonds : bond 0.04703 ( 497) hydrogen bonds : angle 4.94570 ( 1437) SS BOND : bond 0.00332 ( 3) SS BOND : angle 1.71418 ( 6) covalent geometry : bond 0.00312 (10861) covalent geometry : angle 0.60863 (14739) Misc. bond : bond 0.00089 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7062 (tt0) REVERT: A 180 MET cc_start: 0.6358 (OUTLIER) cc_final: 0.5398 (mpm) REVERT: A 187 ASN cc_start: 0.8702 (t0) cc_final: 0.8326 (t0) REVERT: A 322 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.8062 (ttp-170) REVERT: A 390 MET cc_start: 0.9131 (ttt) cc_final: 0.8793 (tpp) REVERT: A 469 MET cc_start: 0.6740 (mtp) cc_final: 0.6178 (mtt) REVERT: A 582 GLU cc_start: 0.5746 (OUTLIER) cc_final: 0.5539 (mm-30) REVERT: A 638 LEU cc_start: 0.5222 (OUTLIER) cc_final: 0.4998 (mm) REVERT: A 691 MET cc_start: 0.5664 (OUTLIER) cc_final: 0.4353 (mtm) REVERT: A 727 LEU cc_start: 0.7803 (mt) cc_final: 0.7491 (tt) REVERT: A 734 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7292 (tm) REVERT: A 764 LEU cc_start: 0.7652 (pt) cc_final: 0.7416 (tp) REVERT: A 772 MET cc_start: 0.8898 (ttp) cc_final: 0.8686 (ttt) REVERT: A 776 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6772 (mt0) REVERT: C 136 LYS cc_start: 0.9139 (ptmt) cc_final: 0.8850 (ptmm) REVERT: C 155 LYS cc_start: 0.8773 (pttp) cc_final: 0.8402 (ttmt) REVERT: C 158 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: C 242 MET cc_start: 0.8989 (mmm) cc_final: 0.8566 (mmm) REVERT: C 278 ARG cc_start: 0.8399 (ptm160) cc_final: 0.8185 (ptm-80) outliers start: 33 outliers final: 11 residues processed: 134 average time/residue: 1.0891 time to fit residues: 159.2986 Evaluate side-chains 127 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 215 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 35 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.187745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.150368 restraints weight = 10085.921| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.30 r_work: 0.3053 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10870 Z= 0.203 Angle : 0.672 10.788 14760 Z= 0.342 Chirality : 0.047 0.393 1684 Planarity : 0.005 0.073 1841 Dihedral : 9.053 111.683 1595 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.69 % Allowed : 16.59 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.62 (0.23), residues: 1301 helix: 0.52 (0.21), residues: 616 sheet: 0.04 (0.40), residues: 184 loop : -1.75 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 260 HIS 0.005 0.001 HIS A 456 PHE 0.022 0.002 PHE A 968 TYR 0.018 0.002 TYR C 297 ARG 0.004 0.000 ARG A 898 Details of bonding type rmsd link_NAG-ASN : bond 0.00839 ( 3) link_NAG-ASN : angle 4.59585 ( 9) link_ALPHA1-4 : bond 0.01714 ( 1) link_ALPHA1-4 : angle 4.22976 ( 3) link_BETA1-4 : bond 0.00067 ( 1) link_BETA1-4 : angle 1.06557 ( 3) hydrogen bonds : bond 0.05356 ( 497) hydrogen bonds : angle 5.03167 ( 1437) SS BOND : bond 0.00428 ( 3) SS BOND : angle 2.07079 ( 6) covalent geometry : bond 0.00490 (10861) covalent geometry : angle 0.65847 (14739) Misc. bond : bond 0.00148 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7085 (tt0) REVERT: A 180 MET cc_start: 0.6349 (OUTLIER) cc_final: 0.5343 (mpm) REVERT: A 187 ASN cc_start: 0.8681 (t0) cc_final: 0.8288 (t0) REVERT: A 322 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7943 (ttp-170) REVERT: A 390 MET cc_start: 0.9129 (ttt) cc_final: 0.8774 (tpp) REVERT: A 452 LEU cc_start: 0.5699 (OUTLIER) cc_final: 0.5457 (pp) REVERT: A 469 MET cc_start: 0.6689 (mtp) cc_final: 0.6279 (mtp) REVERT: A 638 LEU cc_start: 0.5131 (OUTLIER) cc_final: 0.4910 (mm) REVERT: A 691 MET cc_start: 0.5468 (OUTLIER) cc_final: 0.4127 (mtm) REVERT: A 734 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7168 (tm) REVERT: A 764 LEU cc_start: 0.7648 (pt) cc_final: 0.7409 (tp) REVERT: A 776 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.6878 (mt0) REVERT: C 155 LYS cc_start: 0.8685 (pttp) cc_final: 0.8395 (ttmt) REVERT: C 242 MET cc_start: 0.8918 (mmm) cc_final: 0.8503 (mmm) outliers start: 31 outliers final: 9 residues processed: 128 average time/residue: 1.0623 time to fit residues: 148.3614 Evaluate side-chains 116 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 3.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 215 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 77 optimal weight: 0.5980 chunk 114 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 105 optimal weight: 0.0770 chunk 24 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.191654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.152121 restraints weight = 10222.951| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.37 r_work: 0.3085 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10870 Z= 0.115 Angle : 0.600 10.098 14760 Z= 0.305 Chirality : 0.043 0.302 1684 Planarity : 0.004 0.071 1841 Dihedral : 8.112 105.268 1595 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.09 % Allowed : 17.20 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.34 (0.24), residues: 1301 helix: 0.84 (0.21), residues: 614 sheet: 0.13 (0.40), residues: 187 loop : -1.71 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 927 HIS 0.005 0.001 HIS A 456 PHE 0.017 0.001 PHE A 968 TYR 0.011 0.001 TYR C 297 ARG 0.002 0.000 ARG A 898 Details of bonding type rmsd link_NAG-ASN : bond 0.00614 ( 3) link_NAG-ASN : angle 4.07109 ( 9) link_ALPHA1-4 : bond 0.01749 ( 1) link_ALPHA1-4 : angle 3.82866 ( 3) link_BETA1-4 : bond 0.00447 ( 1) link_BETA1-4 : angle 0.86707 ( 3) hydrogen bonds : bond 0.04278 ( 497) hydrogen bonds : angle 4.80601 ( 1437) SS BOND : bond 0.00244 ( 3) SS BOND : angle 1.35866 ( 6) covalent geometry : bond 0.00251 (10861) covalent geometry : angle 0.58823 (14739) Misc. bond : bond 0.00054 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6949 (tt0) REVERT: A 180 MET cc_start: 0.6296 (OUTLIER) cc_final: 0.5304 (mpm) REVERT: A 187 ASN cc_start: 0.8662 (t0) cc_final: 0.8296 (t0) REVERT: A 322 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7929 (ttp-170) REVERT: A 390 MET cc_start: 0.9127 (ttt) cc_final: 0.8751 (tpp) REVERT: A 469 MET cc_start: 0.6563 (mtp) cc_final: 0.6195 (mtp) REVERT: A 582 GLU cc_start: 0.6251 (mm-30) cc_final: 0.5865 (mp0) REVERT: A 691 MET cc_start: 0.5115 (OUTLIER) cc_final: 0.3700 (mtm) REVERT: A 727 LEU cc_start: 0.7801 (mt) cc_final: 0.7587 (tt) REVERT: A 875 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7283 (ptt180) REVERT: C 155 LYS cc_start: 0.8635 (pttp) cc_final: 0.8325 (ttmt) REVERT: C 158 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: C 215 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7766 (mmp-170) REVERT: C 242 MET cc_start: 0.8967 (mmm) cc_final: 0.8546 (mmm) outliers start: 24 outliers final: 8 residues processed: 127 average time/residue: 1.1185 time to fit residues: 154.9261 Evaluate side-chains 121 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 334 TYR Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 875 ARG Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 215 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 125 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 73 optimal weight: 0.0970 chunk 121 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 48 optimal weight: 9.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** 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 = 0.4041 r_free = 0.4041 target = 0.191962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.155307 restraints weight = 10058.070| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.26 r_work: 0.3121 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10870 Z= 0.116 Angle : 0.597 9.717 14760 Z= 0.304 Chirality : 0.043 0.182 1684 Planarity : 0.004 0.070 1841 Dihedral : 7.606 105.755 1595 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.74 % Allowed : 18.16 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.19 (0.24), residues: 1301 helix: 0.96 (0.22), residues: 615 sheet: 0.21 (0.40), residues: 187 loop : -1.66 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.005 0.001 HIS A 456 PHE 0.017 0.001 PHE A 968 TYR 0.012 0.001 TYR C 297 ARG 0.003 0.000 ARG A 898 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 3) link_NAG-ASN : angle 4.01607 ( 9) link_ALPHA1-4 : bond 0.01624 ( 1) link_ALPHA1-4 : angle 3.64881 ( 3) link_BETA1-4 : bond 0.00396 ( 1) link_BETA1-4 : angle 0.75714 ( 3) hydrogen bonds : bond 0.04190 ( 497) hydrogen bonds : angle 4.72651 ( 1437) SS BOND : bond 0.00277 ( 3) SS BOND : angle 1.38722 ( 6) covalent geometry : bond 0.00256 (10861) covalent geometry : angle 0.58653 (14739) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6917 (tt0) REVERT: A 180 MET cc_start: 0.6389 (OUTLIER) cc_final: 0.5386 (mpm) REVERT: A 187 ASN cc_start: 0.8669 (t0) cc_final: 0.8267 (t0) REVERT: A 390 MET cc_start: 0.9021 (ttt) cc_final: 0.8646 (tpp) REVERT: A 452 LEU cc_start: 0.5566 (OUTLIER) cc_final: 0.5335 (pp) REVERT: A 469 MET cc_start: 0.6564 (mtp) cc_final: 0.6199 (mtp) REVERT: A 582 GLU cc_start: 0.6321 (mm-30) cc_final: 0.5889 (mp0) REVERT: A 727 LEU cc_start: 0.7778 (mt) cc_final: 0.7555 (tt) REVERT: A 875 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7178 (ptt180) REVERT: C 136 LYS cc_start: 0.9050 (ptmt) cc_final: 0.8647 (pttp) REVERT: C 215 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7742 (mmp-170) REVERT: C 242 MET cc_start: 0.8888 (mmm) cc_final: 0.8498 (mmm) outliers start: 20 outliers final: 8 residues processed: 132 average time/residue: 1.2336 time to fit residues: 176.6411 Evaluate side-chains 118 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 334 TYR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 875 ARG Chi-restraints excluded: chain C residue 215 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.191936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.155189 restraints weight = 10081.323| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.29 r_work: 0.3229 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10870 Z= 0.162 Angle : 0.637 9.854 14760 Z= 0.325 Chirality : 0.045 0.153 1684 Planarity : 0.004 0.071 1841 Dihedral : 7.762 108.366 1595 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.39 % Allowed : 18.77 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.25 (0.24), residues: 1301 helix: 0.89 (0.21), residues: 614 sheet: 0.25 (0.41), residues: 184 loop : -1.67 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 927 HIS 0.005 0.001 HIS A 456 PHE 0.019 0.002 PHE A 968 TYR 0.016 0.001 TYR C 297 ARG 0.004 0.000 ARG A 898 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 3) link_NAG-ASN : angle 3.98637 ( 9) link_ALPHA1-4 : bond 0.01565 ( 1) link_ALPHA1-4 : angle 3.86810 ( 3) link_BETA1-4 : bond 0.00116 ( 1) link_BETA1-4 : angle 0.89001 ( 3) hydrogen bonds : bond 0.04802 ( 497) hydrogen bonds : angle 4.83508 ( 1437) SS BOND : bond 0.00393 ( 3) SS BOND : angle 1.80892 ( 6) covalent geometry : bond 0.00383 (10861) covalent geometry : angle 0.62609 (14739) Misc. bond : bond 0.00109 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 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: 16 poor density : 107 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.6466 (OUTLIER) cc_final: 0.5758 (mpm) REVERT: A 187 ASN cc_start: 0.8762 (t0) cc_final: 0.8271 (t0) REVERT: A 390 MET cc_start: 0.8989 (ttt) cc_final: 0.8755 (tpp) REVERT: A 452 LEU cc_start: 0.5565 (OUTLIER) cc_final: 0.5271 (pp) REVERT: A 469 MET cc_start: 0.7098 (mtp) cc_final: 0.6891 (mtp) REVERT: A 582 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6608 (mp0) REVERT: A 875 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7360 (ptt180) REVERT: C 242 MET cc_start: 0.8873 (mmm) cc_final: 0.8572 (mmm) outliers start: 16 outliers final: 10 residues processed: 118 average time/residue: 1.0796 time to fit residues: 139.4261 Evaluate side-chains 118 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 334 TYR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 875 ARG Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 215 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 128 optimal weight: 0.3980 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 87 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.191278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.153070 restraints weight = 10092.221| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.29 r_work: 0.3098 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10870 Z= 0.119 Angle : 0.599 7.991 14760 Z= 0.306 Chirality : 0.043 0.151 1684 Planarity : 0.004 0.070 1841 Dihedral : 7.341 105.155 1595 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.13 % Allowed : 19.29 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.16 (0.24), residues: 1301 helix: 1.02 (0.22), residues: 615 sheet: 0.26 (0.40), residues: 187 loop : -1.70 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 927 HIS 0.005 0.001 HIS A 456 PHE 0.017 0.001 PHE A 968 TYR 0.012 0.001 TYR C 122 ARG 0.002 0.000 ARG A 898 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 3) link_NAG-ASN : angle 3.19800 ( 9) link_ALPHA1-4 : bond 0.01703 ( 1) link_ALPHA1-4 : angle 3.72391 ( 3) link_BETA1-4 : bond 0.00434 ( 1) link_BETA1-4 : angle 0.79673 ( 3) hydrogen bonds : bond 0.04221 ( 497) hydrogen bonds : angle 4.71272 ( 1437) SS BOND : bond 0.00282 ( 3) SS BOND : angle 1.38497 ( 6) covalent geometry : bond 0.00263 (10861) covalent geometry : angle 0.59088 (14739) Misc. bond : bond 0.00065 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 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: 13 poor density : 107 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.6419 (OUTLIER) cc_final: 0.5386 (mpm) REVERT: A 187 ASN cc_start: 0.8713 (t0) cc_final: 0.8300 (t0) REVERT: A 390 MET cc_start: 0.9007 (ttt) cc_final: 0.8642 (tpp) REVERT: A 452 LEU cc_start: 0.5566 (OUTLIER) cc_final: 0.5335 (pp) REVERT: A 469 MET cc_start: 0.6659 (mtp) cc_final: 0.6321 (mtp) REVERT: A 875 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7234 (ptt180) REVERT: C 215 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7755 (mmp-170) REVERT: C 242 MET cc_start: 0.8891 (mmm) cc_final: 0.8507 (mmm) outliers start: 13 outliers final: 9 residues processed: 117 average time/residue: 1.0847 time to fit residues: 138.7666 Evaluate side-chains 116 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 334 TYR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 875 ARG Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 215 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 89 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.191136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.153713 restraints weight = 10083.065| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.34 r_work: 0.3093 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10870 Z= 0.124 Angle : 0.603 7.628 14760 Z= 0.307 Chirality : 0.043 0.154 1684 Planarity : 0.004 0.070 1841 Dihedral : 7.315 105.533 1595 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.22 % Allowed : 19.20 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.12 (0.24), residues: 1301 helix: 1.05 (0.21), residues: 615 sheet: 0.28 (0.40), residues: 187 loop : -1.69 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 927 HIS 0.005 0.001 HIS A 456 PHE 0.018 0.001 PHE A 968 TYR 0.013 0.001 TYR C 297 ARG 0.003 0.000 ARG A 898 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 3) link_NAG-ASN : angle 3.05058 ( 9) link_ALPHA1-4 : bond 0.01676 ( 1) link_ALPHA1-4 : angle 3.73799 ( 3) link_BETA1-4 : bond 0.00380 ( 1) link_BETA1-4 : angle 0.80877 ( 3) hydrogen bonds : bond 0.04287 ( 497) hydrogen bonds : angle 4.70216 ( 1437) SS BOND : bond 0.00296 ( 3) SS BOND : angle 1.44886 ( 6) covalent geometry : bond 0.00277 (10861) covalent geometry : angle 0.59529 (14739) Misc. bond : bond 0.00069 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7703.90 seconds wall clock time: 132 minutes 22.32 seconds (7942.32 seconds total)