Starting phenix.real_space_refine on Tue May 13 14:15:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ijm_35489/05_2025/8ijm_35489.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ijm_35489/05_2025/8ijm_35489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ijm_35489/05_2025/8ijm_35489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ijm_35489/05_2025/8ijm_35489.map" model { file = "/net/cci-nas-00/data/ceres_data/8ijm_35489/05_2025/8ijm_35489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ijm_35489/05_2025/8ijm_35489.cif" } resolution = 3.13 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= -0.001 sd= 0.037 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 S 49 5.16 5 Na 2 4.78 5 C 6435 2.51 5 N 1638 2.21 5 O 1853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9982 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7592 Classifications: {'peptide': 976} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 34, 'TRANS': 941} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2215 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 252} Chain breaks: 1 Chain: "A" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 161 Unusual residues: {' NA': 2, 'ACP': 1, 'CLR': 1, 'PCW': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.06, per 1000 atoms: 0.61 Number of scatterers: 9982 At special positions: 0 Unit cell: (72.21, 98.355, 179.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 49 16.00 P 5 15.00 Na 2 11.00 O 1853 8.00 N 1638 7.00 C 6435 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 277 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied NAG-ASN " NAG B 401 " - " ASN B 158 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.3 seconds 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2322 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 11 sheets defined 46.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 60 through 69 removed outlier: 3.620A pdb=" N GLN A 66 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 89 removed outlier: 4.048A pdb=" N GLU A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 112 through 134 removed outlier: 4.623A pdb=" N LEU A 116 " --> pdb=" O GLY A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 162 removed outlier: 3.625A pdb=" N TYR A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 173 removed outlier: 3.777A pdb=" N PHE A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 273 through 277 Processing helix chain 'A' and resid 294 through 325 removed outlier: 4.234A pdb=" N CYS A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 343 removed outlier: 3.601A pdb=" N ALA A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 366 Processing helix chain 'A' and resid 372 through 380 removed outlier: 3.732A pdb=" N VAL A 376 " --> pdb=" O ASN A 372 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 441 removed outlier: 3.723A pdb=" N SER A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 476 Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 522 through 529 Processing helix chain 'A' and resid 543 through 560 removed outlier: 3.758A pdb=" N SER A 549 " --> pdb=" O SER A 545 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 621 Processing helix chain 'A' and resid 634 through 644 removed outlier: 3.527A pdb=" N SER A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 661 Processing helix chain 'A' and resid 668 through 672 Processing helix chain 'A' and resid 678 through 684 Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 709 through 718 Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 730 through 732 No H-bonds generated for 'chain 'A' and resid 730 through 732' Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 751 through 758 Processing helix chain 'A' and resid 768 through 794 removed outlier: 3.592A pdb=" N VAL A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU A 776 " --> pdb=" O THR A 772 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 780 " --> pdb=" O GLU A 776 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE A 781 " --> pdb=" O GLY A 777 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 789 " --> pdb=" O LYS A 785 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 790 " --> pdb=" O LYS A 786 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 791 " --> pdb=" O THR A 787 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 792 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA A 794 " --> pdb=" O TYR A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 808 Processing helix chain 'A' and resid 817 through 826 removed outlier: 3.721A pdb=" N ASP A 823 " --> pdb=" O ILE A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 834 Processing helix chain 'A' and resid 858 through 867 Processing helix chain 'A' and resid 871 through 887 removed outlier: 3.711A pdb=" N LEU A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 876 " --> pdb=" O MET A 872 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 877 " --> pdb=" O GLN A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 895 removed outlier: 3.516A pdb=" N LEU A 895 " --> pdb=" O PRO A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 903 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 943 through 948 removed outlier: 3.795A pdb=" N ILE A 948 " --> pdb=" O ALA A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 960 Processing helix chain 'A' and resid 965 through 984 removed outlier: 3.719A pdb=" N VAL A 969 " --> pdb=" O LYS A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1003 removed outlier: 4.465A pdb=" N PHE A1002 " --> pdb=" O VAL A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1025 removed outlier: 3.555A pdb=" N ILE A1011 " --> pdb=" O HIS A1007 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP A1012 " --> pdb=" O ALA A1008 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL A1013 " --> pdb=" O ILE A1009 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE A1021 " --> pdb=" O MET A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1034 Processing helix chain 'B' and resid 37 through 58 removed outlier: 3.508A pdb=" N TYR B 43 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL B 56 " --> pdb=" O GLY B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 98 through 110 removed outlier: 3.540A pdb=" N ILE B 105 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 117 removed outlier: 6.456A pdb=" N ASP B 114 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N SER B 115 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 117 " --> pdb=" O ASP B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 218 through 226 removed outlier: 3.830A pdb=" N LYS B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY B 226 " --> pdb=" O LYS B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 removed outlier: 3.527A pdb=" N GLY B 235 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing sheet with id=AA1, first strand: chain 'A' and resid 182 through 185 removed outlier: 4.285A pdb=" N VAL A 183 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 192 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS A 190 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 206 removed outlier: 6.239A pdb=" N ILE A 269 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU A 217 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 210 removed outlier: 3.590A pdb=" N ASP A 209 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LYS A 224 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS A 223 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 368 through 370 removed outlier: 6.924A pdb=" N ILE A 384 " --> pdb=" O ALA A 725 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N THR A 727 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N CYS A 386 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE A 385 " --> pdb=" O ILE A 626 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 408 through 411 removed outlier: 7.202A pdb=" N SER A 602 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LEU A 403 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU A 600 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 521 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET A 519 " --> pdb=" O CYS A 568 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 518 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA A 490 " --> pdb=" O ILE A 504 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 532 through 535 Processing sheet with id=AA7, first strand: chain 'A' and resid 674 through 677 removed outlier: 6.650A pdb=" N ALA A 675 " --> pdb=" O VAL A 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 910 through 911 Processing sheet with id=AA9, first strand: chain 'B' and resid 77 through 79 removed outlier: 6.621A pdb=" N ASN B 227 " --> pdb=" O THR B 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 87 through 90 Processing sheet with id=AB2, first strand: chain 'B' and resid 123 through 124 402 hydrogen bonds defined for protein. 1155 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: 3.13 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3154 1.34 - 1.46: 2142 1.46 - 1.58: 4795 1.58 - 1.70: 10 1.70 - 1.82: 80 Bond restraints: 10181 Sorted by residual: bond pdb=" C11 PCW A1103 " pdb=" O3 PCW A1103 " ideal model delta sigma weight residual 1.326 1.455 -0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" C11 PCW A1102 " pdb=" O3 PCW A1102 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" C31 PCW A1103 " pdb=" O2 PCW A1103 " ideal model delta sigma weight residual 1.333 1.458 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C31 PCW A1102 " pdb=" O2 PCW A1102 " ideal model delta sigma weight residual 1.333 1.453 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" O2B ACP A1101 " pdb=" PB ACP A1101 " ideal model delta sigma weight residual 1.507 1.611 -0.104 2.00e-02 2.50e+03 2.70e+01 ... (remaining 10176 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 13631 3.02 - 6.03: 123 6.03 - 9.05: 33 9.05 - 12.06: 5 12.06 - 15.08: 1 Bond angle restraints: 13793 Sorted by residual: angle pdb=" N ILE A 940 " pdb=" CA ILE A 940 " pdb=" C ILE A 940 " ideal model delta sigma weight residual 112.96 107.32 5.64 1.00e+00 1.00e+00 3.19e+01 angle pdb=" CA LEU A 468 " pdb=" CB LEU A 468 " pdb=" CG LEU A 468 " ideal model delta sigma weight residual 116.30 131.38 -15.08 3.50e+00 8.16e-02 1.86e+01 angle pdb=" C3B ACP A1101 " pdb=" PB ACP A1101 " pdb=" O3A ACP A1101 " ideal model delta sigma weight residual 98.05 109.76 -11.71 3.00e+00 1.11e-01 1.52e+01 angle pdb=" N GLY B 248 " pdb=" CA GLY B 248 " pdb=" C GLY B 248 " ideal model delta sigma weight residual 113.18 121.49 -8.31 2.37e+00 1.78e-01 1.23e+01 angle pdb=" CB MET A 680 " pdb=" CG MET A 680 " pdb=" SD MET A 680 " ideal model delta sigma weight residual 112.70 123.00 -10.30 3.00e+00 1.11e-01 1.18e+01 ... (remaining 13788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.29: 5923 28.29 - 56.59: 281 56.59 - 84.88: 19 84.88 - 113.18: 6 113.18 - 141.47: 1 Dihedral angle restraints: 6230 sinusoidal: 2617 harmonic: 3613 Sorted by residual: dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 -178.43 -88.57 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CB CYS B 159 " pdb=" SG CYS B 159 " pdb=" SG CYS B 175 " pdb=" CB CYS B 175 " ideal model delta sinusoidal sigma weight residual 93.00 144.76 -51.76 1 1.00e+01 1.00e-02 3.66e+01 dihedral pdb=" CA PRO A 95 " pdb=" C PRO A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta harmonic sigma weight residual 180.00 -154.86 -25.14 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 6227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1193 0.047 - 0.094: 298 0.094 - 0.141: 78 0.141 - 0.188: 3 0.188 - 0.235: 3 Chirality restraints: 1575 Sorted by residual: chirality pdb=" C2 PCW A1102 " pdb=" C1 PCW A1102 " pdb=" C3 PCW A1102 " pdb=" O2 PCW A1102 " both_signs ideal model delta sigma weight residual False -2.32 -2.56 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ASN B 206 " pdb=" N ASN B 206 " pdb=" C ASN B 206 " pdb=" CB ASN B 206 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C1 NAG B 401 " pdb=" ND2 ASN B 158 " pdb=" C2 NAG B 401 " pdb=" O5 NAG B 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.15e-01 ... (remaining 1572 not shown) Planarity restraints: 1734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 401 " -0.047 2.00e-02 2.50e+03 3.86e-02 1.86e+01 pdb=" C7 NAG B 401 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG B 401 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG B 401 " 0.061 2.00e-02 2.50e+03 pdb=" O7 NAG B 401 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 94 " 0.056 5.00e-02 4.00e+02 8.51e-02 1.16e+01 pdb=" N PRO B 95 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 95 " -0.056 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO A 96 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 96 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 96 " -0.047 5.00e-02 4.00e+02 ... (remaining 1731 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1438 2.76 - 3.29: 9605 3.29 - 3.83: 16217 3.83 - 4.36: 19623 4.36 - 4.90: 33554 Nonbonded interactions: 80437 Sorted by model distance: nonbonded pdb=" OG1 THR A 686 " pdb=" OE1 GLN A 689 " model vdw 2.222 3.040 nonbonded pdb=" OG1 THR A 695 " pdb=" OE1 GLN A 720 " model vdw 2.247 3.040 nonbonded pdb=" OG SER A 503 " pdb=" O VAL A 518 " model vdw 2.250 3.040 nonbonded pdb=" NH2 ARG A 619 " pdb=" O GLY A 644 " model vdw 2.256 3.120 nonbonded pdb=" O PHE A 256 " pdb=" OG1 THR A 259 " model vdw 2.267 3.040 ... (remaining 80432 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.360 Find NCS groups from input model: 0.080 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 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 : 0.005 0.129 10187 Z= 0.234 Angle : 0.781 15.080 13802 Z= 0.385 Chirality : 0.044 0.235 1575 Planarity : 0.005 0.085 1733 Dihedral : 15.625 141.471 3899 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.35 % Favored : 95.56 % Rotamer: Outliers : 0.93 % Allowed : 12.95 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.23), residues: 1240 helix: -0.45 (0.23), residues: 517 sheet: -0.34 (0.44), residues: 136 loop : -0.73 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 902 HIS 0.009 0.001 HIS A 632 PHE 0.023 0.001 PHE A 105 TYR 0.014 0.001 TYR A 881 ARG 0.004 0.000 ARG A 563 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 1) link_NAG-ASN : angle 2.01091 ( 3) hydrogen bonds : bond 0.21422 ( 402) hydrogen bonds : angle 7.39192 ( 1155) SS BOND : bond 0.00231 ( 3) SS BOND : angle 0.51060 ( 6) covalent geometry : bond 0.00477 (10181) covalent geometry : angle 0.78048 (13793) Misc. bond : bond 0.00089 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 1.102 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 72 average time/residue: 0.2440 time to fit residues: 25.5891 Evaluate side-chains 69 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 946 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 52 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 112 optimal weight: 0.3980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 941 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.234244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.208390 restraints weight = 10543.733| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 1.38 r_work: 0.4071 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3984 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10187 Z= 0.139 Angle : 0.603 13.102 13802 Z= 0.309 Chirality : 0.044 0.184 1575 Planarity : 0.005 0.084 1733 Dihedral : 9.402 121.225 1561 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.05 % Allowed : 12.21 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.24), residues: 1240 helix: -0.09 (0.23), residues: 528 sheet: -0.13 (0.45), residues: 128 loop : -0.73 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 902 HIS 0.006 0.001 HIS A 632 PHE 0.014 0.001 PHE A 405 TYR 0.018 0.001 TYR A 881 ARG 0.004 0.000 ARG A 563 Details of bonding type rmsd link_NAG-ASN : bond 0.00085 ( 1) link_NAG-ASN : angle 1.69147 ( 3) hydrogen bonds : bond 0.04268 ( 402) hydrogen bonds : angle 5.35019 ( 1155) SS BOND : bond 0.00324 ( 3) SS BOND : angle 0.60521 ( 6) covalent geometry : bond 0.00321 (10181) covalent geometry : angle 0.60220 (13793) Misc. bond : bond 0.00139 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 1.166 Fit side-chains REVERT: B 91 ARG cc_start: 0.7270 (ttt90) cc_final: 0.7061 (ttt180) REVERT: B 96 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8214 (mttp) REVERT: B 99 GLU cc_start: 0.7669 (tp30) cc_final: 0.7444 (tp30) REVERT: B 129 MET cc_start: 0.8007 (mmm) cc_final: 0.7798 (mmm) outliers start: 22 outliers final: 12 residues processed: 94 average time/residue: 0.2286 time to fit residues: 30.7269 Evaluate side-chains 82 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 148 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 16 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN ** B 104 ASN ** 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 = 0.4624 r_free = 0.4624 target = 0.230109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.193582 restraints weight = 10973.645| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 1.52 r_work: 0.3771 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10187 Z= 0.177 Angle : 0.614 13.126 13802 Z= 0.313 Chirality : 0.045 0.171 1575 Planarity : 0.005 0.084 1733 Dihedral : 9.229 130.510 1554 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.80 % Allowed : 13.79 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.24), residues: 1240 helix: 0.03 (0.23), residues: 527 sheet: -0.48 (0.43), residues: 129 loop : -0.80 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 902 HIS 0.009 0.001 HIS A 632 PHE 0.015 0.002 PHE A 105 TYR 0.018 0.002 TYR A 881 ARG 0.004 0.000 ARG B 182 Details of bonding type rmsd link_NAG-ASN : bond 0.00034 ( 1) link_NAG-ASN : angle 1.81835 ( 3) hydrogen bonds : bond 0.04071 ( 402) hydrogen bonds : angle 5.13366 ( 1155) SS BOND : bond 0.00445 ( 3) SS BOND : angle 0.87426 ( 6) covalent geometry : bond 0.00424 (10181) covalent geometry : angle 0.61322 (13793) Misc. bond : bond 0.00148 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.2663 (mmp) cc_final: 0.2325 (mmt) REVERT: A 326 LYS cc_start: 0.6259 (tptt) cc_final: 0.6041 (tptt) REVERT: A 349 LEU cc_start: 0.7708 (mm) cc_final: 0.6971 (tp) REVERT: A 658 LYS cc_start: 0.6429 (OUTLIER) cc_final: 0.6177 (tptt) REVERT: A 665 GLU cc_start: 0.7404 (mp0) cc_final: 0.7059 (mp0) REVERT: A 950 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8324 (mtpt) REVERT: A 999 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8379 (pm20) REVERT: B 91 ARG cc_start: 0.7982 (ttt90) cc_final: 0.7754 (ttt180) REVERT: B 99 GLU cc_start: 0.7997 (tp30) cc_final: 0.7708 (tp30) outliers start: 30 outliers final: 19 residues processed: 95 average time/residue: 0.2327 time to fit residues: 31.2783 Evaluate side-chains 95 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 273 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 87 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 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 = 0.4686 r_free = 0.4686 target = 0.244844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.4183 r_free = 0.4183 target = 0.183391 restraints weight = 11500.392| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 1.63 r_work: 0.3638 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10187 Z= 0.201 Angle : 0.623 13.697 13802 Z= 0.318 Chirality : 0.045 0.172 1575 Planarity : 0.005 0.083 1733 Dihedral : 9.458 143.611 1552 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.82 % Allowed : 13.89 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.24), residues: 1240 helix: 0.12 (0.24), residues: 529 sheet: -0.60 (0.42), residues: 137 loop : -0.88 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 902 HIS 0.006 0.001 HIS A 632 PHE 0.016 0.002 PHE B 186 TYR 0.019 0.002 TYR A 881 ARG 0.004 0.000 ARG B 182 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 1) link_NAG-ASN : angle 2.18292 ( 3) hydrogen bonds : bond 0.03996 ( 402) hydrogen bonds : angle 5.03438 ( 1155) SS BOND : bond 0.00498 ( 3) SS BOND : angle 0.87547 ( 6) covalent geometry : bond 0.00490 (10181) covalent geometry : angle 0.62224 (13793) Misc. bond : bond 0.00142 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 77 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6835 (pttp) REVERT: A 105 PHE cc_start: 0.4981 (m-10) cc_final: 0.4733 (m-10) REVERT: A 349 LEU cc_start: 0.7642 (mm) cc_final: 0.6812 (tp) REVERT: A 658 LYS cc_start: 0.6374 (OUTLIER) cc_final: 0.6156 (tptt) REVERT: A 665 GLU cc_start: 0.7418 (mp0) cc_final: 0.7166 (mp0) REVERT: A 708 GLN cc_start: 0.8336 (tm-30) cc_final: 0.8136 (tm-30) REVERT: A 776 GLU cc_start: 0.7641 (mp0) cc_final: 0.7427 (mp0) REVERT: A 950 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8170 (mtpt) REVERT: A 999 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8459 (pm20) REVERT: B 99 GLU cc_start: 0.7979 (tp30) cc_final: 0.7458 (tt0) outliers start: 41 outliers final: 25 residues processed: 105 average time/residue: 0.2271 time to fit residues: 33.8642 Evaluate side-chains 106 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 233 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 72 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 82 optimal weight: 0.5980 chunk 118 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 102 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.246673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.196448 restraints weight = 11484.735| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 1.90 r_work: 0.3596 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10187 Z= 0.138 Angle : 0.574 14.236 13802 Z= 0.293 Chirality : 0.043 0.182 1575 Planarity : 0.005 0.082 1733 Dihedral : 9.283 142.407 1552 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.08 % Allowed : 15.47 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.55 (0.24), residues: 1240 helix: 0.25 (0.24), residues: 534 sheet: -0.50 (0.43), residues: 136 loop : -0.83 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 902 HIS 0.008 0.001 HIS A 632 PHE 0.013 0.001 PHE B 186 TYR 0.016 0.001 TYR A 881 ARG 0.003 0.000 ARG B 182 Details of bonding type rmsd link_NAG-ASN : bond 0.00154 ( 1) link_NAG-ASN : angle 1.95003 ( 3) hydrogen bonds : bond 0.03395 ( 402) hydrogen bonds : angle 4.88036 ( 1155) SS BOND : bond 0.00289 ( 3) SS BOND : angle 0.44207 ( 6) covalent geometry : bond 0.00330 (10181) covalent geometry : angle 0.57387 (13793) Misc. bond : bond 0.00133 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 82 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 LEU cc_start: 0.7586 (mm) cc_final: 0.6815 (tp) REVERT: A 708 GLN cc_start: 0.8214 (tm-30) cc_final: 0.8014 (tm-30) REVERT: A 950 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8086 (mtpt) REVERT: A 999 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8404 (pm20) REVERT: B 96 LYS cc_start: 0.8750 (mttp) cc_final: 0.8455 (mptt) REVERT: B 99 GLU cc_start: 0.7761 (tp30) cc_final: 0.7291 (tt0) outliers start: 33 outliers final: 24 residues processed: 104 average time/residue: 0.2304 time to fit residues: 33.7945 Evaluate side-chains 102 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 273 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 18 optimal weight: 20.0000 chunk 102 optimal weight: 0.0970 chunk 27 optimal weight: 0.5980 chunk 92 optimal weight: 0.4980 chunk 77 optimal weight: 0.2980 chunk 44 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.4643 r_free = 0.4643 target = 0.232197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.191545 restraints weight = 10952.435| |-----------------------------------------------------------------------------| r_work (start): 0.4326 rms_B_bonded: 1.58 r_work: 0.3764 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10187 Z= 0.118 Angle : 0.560 14.445 13802 Z= 0.285 Chirality : 0.043 0.184 1575 Planarity : 0.004 0.081 1733 Dihedral : 9.109 141.512 1552 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.08 % Allowed : 16.68 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.39 (0.24), residues: 1240 helix: 0.42 (0.24), residues: 534 sheet: -0.48 (0.42), residues: 138 loop : -0.77 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 902 HIS 0.006 0.001 HIS A 632 PHE 0.016 0.001 PHE A 128 TYR 0.016 0.001 TYR A 881 ARG 0.003 0.000 ARG A 619 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 1) link_NAG-ASN : angle 1.82447 ( 3) hydrogen bonds : bond 0.03134 ( 402) hydrogen bonds : angle 4.74249 ( 1155) SS BOND : bond 0.00218 ( 3) SS BOND : angle 0.31114 ( 6) covalent geometry : bond 0.00275 (10181) covalent geometry : angle 0.55937 (13793) Misc. bond : bond 0.00126 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 LEU cc_start: 0.7664 (mm) cc_final: 0.6817 (tp) REVERT: A 526 ILE cc_start: 0.4890 (OUTLIER) cc_final: 0.4550 (tt) REVERT: A 844 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8087 (mmp) REVERT: A 950 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8336 (mtpt) REVERT: A 999 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8397 (pm20) REVERT: B 96 LYS cc_start: 0.8763 (mttp) cc_final: 0.8477 (mtmm) REVERT: B 99 GLU cc_start: 0.7837 (tp30) cc_final: 0.7380 (tt0) outliers start: 33 outliers final: 24 residues processed: 104 average time/residue: 0.2262 time to fit residues: 33.6931 Evaluate side-chains 105 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 273 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 98 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 18 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4669 r_free = 0.4669 target = 0.233633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.188979 restraints weight = 11014.613| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 1.79 r_work: 0.3640 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 10187 Z= 0.202 Angle : 0.631 14.853 13802 Z= 0.320 Chirality : 0.045 0.182 1575 Planarity : 0.005 0.081 1733 Dihedral : 9.442 151.267 1552 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.08 % Allowed : 16.96 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.57 (0.24), residues: 1240 helix: 0.29 (0.24), residues: 538 sheet: -0.60 (0.42), residues: 136 loop : -0.89 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 902 HIS 0.008 0.001 HIS A 632 PHE 0.017 0.002 PHE A 128 TYR 0.019 0.002 TYR A 881 ARG 0.007 0.000 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 1) link_NAG-ASN : angle 2.18502 ( 3) hydrogen bonds : bond 0.03735 ( 402) hydrogen bonds : angle 4.84869 ( 1155) SS BOND : bond 0.00498 ( 3) SS BOND : angle 0.94681 ( 6) covalent geometry : bond 0.00494 (10181) covalent geometry : angle 0.62998 (13793) Misc. bond : bond 0.00128 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 LEU cc_start: 0.7556 (mm) cc_final: 0.6903 (tp) REVERT: A 708 GLN cc_start: 0.8266 (tm-30) cc_final: 0.8025 (tm-30) REVERT: A 950 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8402 (mtpt) REVERT: A 999 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8374 (pm20) REVERT: B 99 GLU cc_start: 0.7646 (tp30) cc_final: 0.7224 (tt0) outliers start: 33 outliers final: 26 residues processed: 101 average time/residue: 0.2320 time to fit residues: 33.4595 Evaluate side-chains 105 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 233 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 51 optimal weight: 30.0000 chunk 108 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.243652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.192243 restraints weight = 11622.868| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 1.96 r_work: 0.3531 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 10187 Z= 0.237 Angle : 0.663 13.911 13802 Z= 0.337 Chirality : 0.047 0.186 1575 Planarity : 0.005 0.080 1733 Dihedral : 9.903 169.740 1552 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.82 % Allowed : 16.31 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.24), residues: 1240 helix: 0.20 (0.23), residues: 538 sheet: -0.72 (0.42), residues: 137 loop : -0.96 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 902 HIS 0.006 0.001 HIS A 632 PHE 0.021 0.002 PHE A 105 TYR 0.019 0.002 TYR A 881 ARG 0.007 0.001 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 1) link_NAG-ASN : angle 2.57068 ( 3) hydrogen bonds : bond 0.04000 ( 402) hydrogen bonds : angle 4.95825 ( 1155) SS BOND : bond 0.00561 ( 3) SS BOND : angle 1.07996 ( 6) covalent geometry : bond 0.00586 (10181) covalent geometry : angle 0.66154 (13793) Misc. bond : bond 0.00119 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 78 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 708 GLN cc_start: 0.8400 (tm-30) cc_final: 0.8174 (tm-30) REVERT: A 950 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8487 (mtpt) REVERT: A 999 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8467 (pm20) REVERT: B 99 GLU cc_start: 0.7887 (tp30) cc_final: 0.7445 (tt0) outliers start: 41 outliers final: 32 residues processed: 107 average time/residue: 0.2317 time to fit residues: 35.4249 Evaluate side-chains 109 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 295 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 63 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 83 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 850 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.246900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.185626 restraints weight = 11553.708| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 1.76 r_work: 0.3664 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10187 Z= 0.135 Angle : 0.592 14.899 13802 Z= 0.300 Chirality : 0.043 0.192 1575 Planarity : 0.005 0.081 1733 Dihedral : 9.596 171.255 1552 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.98 % Allowed : 16.87 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.45 (0.24), residues: 1240 helix: 0.44 (0.24), residues: 533 sheet: -0.83 (0.42), residues: 144 loop : -0.78 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 902 HIS 0.008 0.001 HIS A 632 PHE 0.016 0.001 PHE A 128 TYR 0.015 0.001 TYR A 881 ARG 0.006 0.000 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 1) link_NAG-ASN : angle 2.26703 ( 3) hydrogen bonds : bond 0.03244 ( 402) hydrogen bonds : angle 4.77206 ( 1155) SS BOND : bond 0.00242 ( 3) SS BOND : angle 0.34648 ( 6) covalent geometry : bond 0.00323 (10181) covalent geometry : angle 0.59101 (13793) Misc. bond : bond 0.00097 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: -0.0267 (OUTLIER) cc_final: -0.0598 (tpt) REVERT: A 349 LEU cc_start: 0.7626 (mm) cc_final: 0.6794 (tp) REVERT: A 824 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7864 (mt) REVERT: A 950 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8217 (mtpt) REVERT: A 999 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8445 (pm20) REVERT: B 99 GLU cc_start: 0.7892 (tp30) cc_final: 0.7433 (tt0) outliers start: 32 outliers final: 26 residues processed: 99 average time/residue: 0.2486 time to fit residues: 35.5139 Evaluate side-chains 107 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 950 LYS Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 273 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 30.0000 chunk 62 optimal weight: 0.0010 chunk 8 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 77 optimal weight: 0.0970 chunk 58 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.230899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.193366 restraints weight = 10995.847| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 1.64 r_work: 0.3769 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10187 Z= 0.138 Angle : 0.608 15.573 13802 Z= 0.306 Chirality : 0.044 0.191 1575 Planarity : 0.005 0.081 1733 Dihedral : 9.506 178.385 1552 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.36 % Allowed : 16.68 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.39 (0.24), residues: 1240 helix: 0.50 (0.24), residues: 533 sheet: -0.80 (0.42), residues: 144 loop : -0.75 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 902 HIS 0.007 0.001 HIS A 632 PHE 0.023 0.001 PHE A 105 TYR 0.016 0.001 TYR A 881 ARG 0.014 0.000 ARG A 397 Details of bonding type rmsd link_NAG-ASN : bond 0.00177 ( 1) link_NAG-ASN : angle 2.14753 ( 3) hydrogen bonds : bond 0.03249 ( 402) hydrogen bonds : angle 4.72499 ( 1155) SS BOND : bond 0.00280 ( 3) SS BOND : angle 0.47530 ( 6) covalent geometry : bond 0.00332 (10181) covalent geometry : angle 0.60696 (13793) Misc. bond : bond 0.00094 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 78 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.1047 (OUTLIER) cc_final: 0.0494 (tpt) REVERT: A 349 LEU cc_start: 0.7547 (mm) cc_final: 0.6944 (tp) REVERT: A 670 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7677 (tpm170) REVERT: A 824 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7855 (mt) REVERT: A 999 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8317 (pm20) outliers start: 36 outliers final: 27 residues processed: 101 average time/residue: 0.2577 time to fit residues: 35.9616 Evaluate side-chains 107 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 295 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 14 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 56 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4698 r_free = 0.4698 target = 0.246206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.186646 restraints weight = 11499.535| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 1.66 r_work: 0.3646 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10187 Z= 0.155 Angle : 0.618 15.476 13802 Z= 0.311 Chirality : 0.044 0.198 1575 Planarity : 0.005 0.081 1733 Dihedral : 9.377 172.458 1552 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.80 % Allowed : 17.43 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.39 (0.24), residues: 1240 helix: 0.50 (0.24), residues: 533 sheet: -0.77 (0.43), residues: 142 loop : -0.78 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 902 HIS 0.006 0.001 HIS A 632 PHE 0.017 0.001 PHE A 128 TYR 0.017 0.001 TYR A 881 ARG 0.005 0.000 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00119 ( 1) link_NAG-ASN : angle 2.34649 ( 3) hydrogen bonds : bond 0.03398 ( 402) hydrogen bonds : angle 4.74434 ( 1155) SS BOND : bond 0.00345 ( 3) SS BOND : angle 0.61183 ( 6) covalent geometry : bond 0.00377 (10181) covalent geometry : angle 0.61699 (13793) Misc. bond : bond 0.00092 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5455.05 seconds wall clock time: 95 minutes 7.43 seconds (5707.43 seconds total)