Starting phenix.real_space_refine on Thu Jul 2 22:19:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ijm_35489/07_2026/8ijm_35489.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ijm_35489/07_2026/8ijm_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ijm_35489/07_2026/8ijm_35489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ijm_35489/07_2026/8ijm_35489.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ijm_35489/07_2026/8ijm_35489.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ijm_35489/07_2026/8ijm_35489.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ijm_35489/07_2026/8ijm_35489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ijm_35489/07_2026/8ijm_35489.map" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 chiralities: 1 Time building chain proxies: 1.87, per 1000 atoms: 0.19 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: 0.97 Conformation dependent library (CDL) restraints added in 347.0 milliseconds 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: 0.28 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: 1.16 Time building geometry restraints manager: 1.26 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: 5820 28.29 - 56.59: 259 56.59 - 84.88: 19 84.88 - 113.18: 6 113.18 - 141.47: 1 Dihedral angle restraints: 6105 sinusoidal: 2492 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 6102 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.040 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 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 : 15.447 141.471 3774 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.33 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (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 ARG 0.004 0.000 ARG A 563 TYR 0.014 0.001 TYR A 881 PHE 0.023 0.001 PHE A 105 TRP 0.008 0.001 TRP A 902 HIS 0.009 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.23 (10181) covalent geometry : angle 0.78048 / 0.38 (13793) SS BOND : bond 0.00231 / 0.13 ( 3) SS BOND : angle 0.51060 / 0.29 ( 6) hydrogen bonds : bond 0.21422 / 14.58 ( 402) hydrogen bonds : angle 7.39192 / 5.36 ( 1155) Misc. bond : bond 0.00089 / 0.05 ( 2) link_NAG-ASN : bond 0.00271 / 0.17 ( 1) link_NAG-ASN : angle 2.01091 / 0.92 ( 3) *********************** 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 : 0.238 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 72 average time/residue: 0.0828 time to fit residues: 8.6542 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 : 0.293 ------------------------------------------------------------------------------- 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 108 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 40.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 GLN A 941 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.232269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.210105 restraints weight = 10575.228| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 0.99 r_work: 0.4109 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10187 Z= 0.175 Angle : 0.628 13.351 13802 Z= 0.322 Chirality : 0.045 0.181 1575 Planarity : 0.005 0.083 1733 Dihedral : 8.345 116.091 1436 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.24 % Allowed : 12.67 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.24), residues: 1240 helix: -0.15 (0.23), residues: 528 sheet: -0.21 (0.44), residues: 128 loop : -0.78 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 563 TYR 0.019 0.002 TYR A 881 PHE 0.014 0.002 PHE B 186 TRP 0.011 0.001 TRP A 902 HIS 0.005 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 (10181) covalent geometry : angle 0.62761 / 0.32 (13793) SS BOND : bond 0.00442 / 0.24 ( 3) SS BOND : angle 0.88127 / 0.51 ( 6) hydrogen bonds : bond 0.04604 / 3.13 ( 402) hydrogen bonds : angle 5.39915 / 3.91 ( 1155) Misc. bond : bond 0.00056 / 0.03 ( 2) link_NAG-ASN : bond 0.00041 / 0.03 ( 1) link_NAG-ASN : angle 1.79461 / 0.68 ( 3) *********************** 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 101 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: B 96 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8091 (mttp) REVERT: B 99 GLU cc_start: 0.7491 (tp30) cc_final: 0.7276 (tp30) outliers start: 24 outliers final: 15 residues processed: 94 average time/residue: 0.0776 time to fit residues: 10.6877 Evaluate side-chains 89 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 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 519 MET Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain B residue 80 ILE 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 107 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 22 optimal weight: 0.0070 chunk 69 optimal weight: 2.9990 chunk 51 optimal weight: 30.0000 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.238537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.193566 restraints weight = 11068.946| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 1.80 r_work: 0.3679 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10187 Z= 0.146 Angle : 0.589 13.142 13802 Z= 0.301 Chirality : 0.044 0.174 1575 Planarity : 0.005 0.084 1733 Dihedral : 7.878 114.905 1429 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.89 % Allowed : 13.79 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.24), residues: 1240 helix: 0.08 (0.23), residues: 527 sheet: -0.38 (0.44), residues: 129 loop : -0.79 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 563 TYR 0.017 0.001 TYR A 881 PHE 0.014 0.001 PHE A 105 TRP 0.010 0.001 TRP A 902 HIS 0.008 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (10181) covalent geometry : angle 0.58834 / 0.30 (13793) SS BOND : bond 0.00354 / 0.19 ( 3) SS BOND : angle 0.63765 / 0.38 ( 6) hydrogen bonds : bond 0.03905 / 2.64 ( 402) hydrogen bonds : angle 5.09433 / 3.68 ( 1155) Misc. bond : bond 0.00045 / 0.03 ( 2) link_NAG-ASN : bond 0.00163 / 0.10 ( 1) link_NAG-ASN : angle 1.78908 / 0.69 ( 3) *********************** 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 110 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 665 GLU cc_start: 0.7143 (mp0) cc_final: 0.6870 (mp0) REVERT: A 950 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.7963 (mtpt) REVERT: A 999 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8277 (pm20) REVERT: B 99 GLU cc_start: 0.7686 (tp30) cc_final: 0.7410 (tp30) outliers start: 31 outliers final: 19 residues processed: 99 average time/residue: 0.0871 time to fit residues: 12.1602 Evaluate side-chains 99 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 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 791 THR 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 999 GLN Chi-restraints excluded: chain B residue 80 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 77 optimal weight: 0.2980 chunk 58 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.248298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.193036 restraints weight = 11604.302| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 1.93 r_work: 0.3625 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10187 Z= 0.134 Angle : 0.565 13.509 13802 Z= 0.289 Chirality : 0.043 0.180 1575 Planarity : 0.005 0.084 1733 Dihedral : 7.528 113.061 1425 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.17 % Allowed : 14.35 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.24), residues: 1240 helix: 0.30 (0.24), residues: 530 sheet: -0.41 (0.42), residues: 139 loop : -0.79 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 182 TYR 0.017 0.001 TYR A 881 PHE 0.012 0.001 PHE B 186 TRP 0.011 0.001 TRP A 902 HIS 0.007 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (10181) covalent geometry : angle 0.56446 / 0.29 (13793) SS BOND : bond 0.00307 / 0.17 ( 3) SS BOND : angle 0.48643 / 0.30 ( 6) hydrogen bonds : bond 0.03447 / 2.34 ( 402) hydrogen bonds : angle 4.86534 / 3.52 ( 1155) Misc. bond : bond 0.00039 / 0.02 ( 2) link_NAG-ASN : bond 0.00206 / 0.13 ( 1) link_NAG-ASN : angle 1.83857 / 0.71 ( 3) *********************** 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 114 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 80 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 665 GLU cc_start: 0.7220 (mp0) cc_final: 0.6973 (mp0) REVERT: A 950 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8079 (mtpt) REVERT: A 999 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8351 (pm20) REVERT: B 96 LYS cc_start: 0.8749 (mttp) cc_final: 0.8469 (mtmm) REVERT: B 99 GLU cc_start: 0.7710 (tp30) cc_final: 0.7431 (tp30) outliers start: 34 outliers final: 24 residues processed: 106 average time/residue: 0.0805 time to fit residues: 12.0547 Evaluate side-chains 101 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 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 776 GLU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 38 optimal weight: 0.9980 chunk 12 optimal weight: 0.0270 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 4 optimal weight: 0.1980 chunk 62 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 92 optimal weight: 0.3980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 887 GLN 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 = 0.237598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.191762 restraints weight = 10875.012| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 3.23 r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10187 Z= 0.119 Angle : 0.551 13.905 13802 Z= 0.282 Chirality : 0.043 0.178 1575 Planarity : 0.004 0.082 1733 Dihedral : 7.381 111.711 1425 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.98 % Allowed : 14.91 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.24), residues: 1240 helix: 0.40 (0.24), residues: 533 sheet: -0.40 (0.42), residues: 138 loop : -0.76 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 91 TYR 0.016 0.001 TYR A 881 PHE 0.018 0.001 PHE A 105 TRP 0.010 0.001 TRP A 902 HIS 0.008 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (10181) covalent geometry : angle 0.55084 / 0.28 (13793) SS BOND : bond 0.00233 / 0.13 ( 3) SS BOND : angle 0.37039 / 0.23 ( 6) hydrogen bonds : bond 0.03143 / 2.14 ( 402) hydrogen bonds : angle 4.75968 / 3.44 ( 1155) Misc. bond : bond 0.00031 / 0.02 ( 2) link_NAG-ASN : bond 0.00242 / 0.15 ( 1) link_NAG-ASN : angle 1.78404 / 0.69 ( 3) *********************** 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 110 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 950 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7837 (mtpt) REVERT: A 999 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8138 (pm20) outliers start: 32 outliers final: 27 residues processed: 99 average time/residue: 0.0827 time to fit residues: 11.7273 Evaluate side-chains 100 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 555 MET 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 999 GLN Chi-restraints excluded: chain B residue 80 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 25 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 99 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.248410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 135)---------------| | r_work = 0.4214 r_free = 0.4214 target = 0.185996 restraints weight = 11615.824| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 1.57 r_work: 0.3691 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10187 Z= 0.135 Angle : 0.567 14.550 13802 Z= 0.289 Chirality : 0.043 0.177 1575 Planarity : 0.004 0.081 1733 Dihedral : 7.436 111.716 1425 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.08 % Allowed : 16.03 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.24), residues: 1240 helix: 0.45 (0.24), residues: 533 sheet: -0.46 (0.44), residues: 128 loop : -0.76 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 91 TYR 0.017 0.001 TYR A 881 PHE 0.015 0.001 PHE A 128 TRP 0.010 0.001 TRP A 902 HIS 0.006 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (10181) covalent geometry : angle 0.56693 / 0.29 (13793) SS BOND : bond 0.00298 / 0.16 ( 3) SS BOND : angle 0.50075 / 0.30 ( 6) hydrogen bonds : bond 0.03249 / 2.21 ( 402) hydrogen bonds : angle 4.71108 / 3.41 ( 1155) Misc. bond : bond 0.00035 / 0.02 ( 2) link_NAG-ASN : bond 0.00144 / 0.09 ( 1) link_NAG-ASN : angle 1.84964 / 0.72 ( 3) *********************** 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 107 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 74 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 LYS cc_start: 0.6329 (tptt) cc_final: 0.6003 (tptt) REVERT: A 950 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8139 (mtpt) REVERT: A 999 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8411 (pm20) outliers start: 33 outliers final: 28 residues processed: 97 average time/residue: 0.0888 time to fit residues: 12.2526 Evaluate side-chains 104 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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 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 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 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 80 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 107 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 19 optimal weight: 20.0000 chunk 66 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 114 optimal weight: 0.3980 chunk 101 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.248153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 134)---------------| | r_work = 0.4210 r_free = 0.4210 target = 0.185733 restraints weight = 11539.630| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 1.66 r_work: 0.3685 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10187 Z= 0.134 Angle : 0.566 14.913 13802 Z= 0.287 Chirality : 0.043 0.178 1575 Planarity : 0.004 0.081 1733 Dihedral : 7.440 111.799 1425 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.26 % Allowed : 16.12 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.24), residues: 1240 helix: 0.50 (0.24), residues: 534 sheet: -0.69 (0.42), residues: 148 loop : -0.68 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 91 TYR 0.016 0.001 TYR A 881 PHE 0.016 0.001 PHE A 128 TRP 0.010 0.001 TRP A 902 HIS 0.005 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (10181) covalent geometry : angle 0.56591 / 0.29 (13793) SS BOND : bond 0.00274 / 0.15 ( 3) SS BOND : angle 0.44828 / 0.26 ( 6) hydrogen bonds : bond 0.03180 / 2.17 ( 402) hydrogen bonds : angle 4.69665 / 3.40 ( 1155) Misc. bond : bond 0.00032 / 0.02 ( 2) link_NAG-ASN : bond 0.00165 / 0.10 ( 1) link_NAG-ASN : angle 1.87672 / 0.73 ( 3) *********************** 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 111 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 LYS cc_start: 0.6417 (tptt) cc_final: 0.6123 (tptt) REVERT: A 950 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8356 (mtpt) REVERT: A 999 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8416 (pm20) outliers start: 35 outliers final: 27 residues processed: 100 average time/residue: 0.0768 time to fit residues: 11.1993 Evaluate side-chains 102 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 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 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 80 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 28 optimal weight: 0.5980 chunk 50 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.247544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.195908 restraints weight = 11646.143| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 2.04 r_work: 0.3573 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10187 Z= 0.159 Angle : 0.592 13.786 13802 Z= 0.300 Chirality : 0.044 0.177 1575 Planarity : 0.004 0.080 1733 Dihedral : 7.596 113.589 1425 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.08 % Allowed : 16.59 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.24), residues: 1240 helix: 0.47 (0.24), residues: 534 sheet: -0.84 (0.43), residues: 138 loop : -0.69 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 91 TYR 0.017 0.002 TYR A 881 PHE 0.020 0.002 PHE A 105 TRP 0.011 0.001 TRP A 902 HIS 0.009 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (10181) covalent geometry : angle 0.59159 / 0.30 (13793) SS BOND : bond 0.00367 / 0.20 ( 3) SS BOND : angle 0.63830 / 0.37 ( 6) hydrogen bonds : bond 0.03385 / 2.29 ( 402) hydrogen bonds : angle 4.73724 / 3.43 ( 1155) Misc. bond : bond 0.00027 / 0.02 ( 2) link_NAG-ASN : bond 0.00067 / 0.04 ( 1) link_NAG-ASN : angle 1.99096 / 0.79 ( 3) *********************** 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 107 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 74 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 950 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8434 (mtpt) REVERT: A 999 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8444 (pm20) outliers start: 33 outliers final: 30 residues processed: 96 average time/residue: 0.0864 time to fit residues: 12.0125 Evaluate side-chains 104 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 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 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 564 VAL 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 80 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 75 optimal weight: 0.4980 chunk 67 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 118 optimal weight: 0.1980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.239477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.196323 restraints weight = 11094.536| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 1.83 r_work: 0.3678 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10187 Z= 0.135 Angle : 0.589 14.777 13802 Z= 0.296 Chirality : 0.043 0.180 1575 Planarity : 0.004 0.081 1733 Dihedral : 7.557 113.088 1425 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.89 % Allowed : 16.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.24), residues: 1240 helix: 0.54 (0.24), residues: 534 sheet: -0.82 (0.44), residues: 136 loop : -0.67 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 91 TYR 0.016 0.001 TYR A 881 PHE 0.026 0.001 PHE A 500 TRP 0.010 0.001 TRP A 902 HIS 0.008 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 (10181) covalent geometry : angle 0.58849 / 0.30 (13793) SS BOND : bond 0.00246 / 0.13 ( 3) SS BOND : angle 0.41586 / 0.25 ( 6) hydrogen bonds : bond 0.03210 / 2.19 ( 402) hydrogen bonds : angle 4.69040 / 3.39 ( 1155) Misc. bond : bond 0.00027 / 0.02 ( 2) link_NAG-ASN : bond 0.00198 / 0.12 ( 1) link_NAG-ASN : angle 1.95323 / 0.77 ( 3) *********************** 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 102 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 71 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 950 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8372 (mtpt) REVERT: A 999 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8350 (pm20) outliers start: 31 outliers final: 27 residues processed: 91 average time/residue: 0.0946 time to fit residues: 12.5047 Evaluate side-chains 100 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 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 564 VAL 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 80 ILE 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 20 optimal weight: 9.9990 chunk 122 optimal weight: 0.6980 chunk 17 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.0770 chunk 120 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 97 optimal weight: 0.2980 chunk 96 optimal weight: 0.2980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.248008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.4219 r_free = 0.4219 target = 0.187231 restraints weight = 11371.222| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 1.65 r_work: 0.3714 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10187 Z= 0.113 Angle : 0.575 15.059 13802 Z= 0.288 Chirality : 0.042 0.183 1575 Planarity : 0.004 0.081 1733 Dihedral : 7.299 110.416 1425 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.42 % Allowed : 17.52 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.24), residues: 1240 helix: 0.66 (0.24), residues: 534 sheet: -0.76 (0.43), residues: 138 loop : -0.58 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 91 TYR 0.015 0.001 TYR A 881 PHE 0.018 0.001 PHE A 105 TRP 0.010 0.001 TRP A 902 HIS 0.009 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (10181) covalent geometry : angle 0.57438 / 0.29 (13793) SS BOND : bond 0.00181 / 0.10 ( 3) SS BOND : angle 0.26297 / 0.15 ( 6) hydrogen bonds : bond 0.02948 / 2.01 ( 402) hydrogen bonds : angle 4.57643 / 3.31 ( 1155) Misc. bond : bond 0.00022 / 0.01 ( 2) link_NAG-ASN : bond 0.00324 / 0.20 ( 1) link_NAG-ASN : angle 1.84953 / 0.72 ( 3) ********************** 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 99 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 616 SER cc_start: 0.8590 (t) cc_final: 0.8126 (p) REVERT: A 670 ARG cc_start: 0.8130 (tpm170) cc_final: 0.7785 (tpm170) REVERT: A 824 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7723 (mt) REVERT: A 950 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8338 (mtpt) REVERT: A 999 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8381 (pm20) outliers start: 26 outliers final: 22 residues processed: 90 average time/residue: 0.0804 time to fit residues: 10.6380 Evaluate side-chains 96 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 124 CYS 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 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 564 VAL 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 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 55 optimal weight: 0.0040 chunk 62 optimal weight: 4.9990 chunk 43 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 105 optimal weight: 0.0670 chunk 59 optimal weight: 1.9990 overall best weight: 0.4732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 569 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.233163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.193882 restraints weight = 10964.403| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 1.67 r_work: 0.3766 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10187 Z= 0.122 Angle : 0.584 15.300 13802 Z= 0.293 Chirality : 0.043 0.178 1575 Planarity : 0.004 0.079 1733 Dihedral : 7.266 110.180 1425 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.42 % Allowed : 17.71 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.24), residues: 1240 helix: 0.66 (0.24), residues: 534 sheet: -0.78 (0.44), residues: 136 loop : -0.59 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 91 TYR 0.016 0.001 TYR A 881 PHE 0.016 0.001 PHE A 128 TRP 0.011 0.001 TRP A 902 HIS 0.008 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (10181) covalent geometry : angle 0.58364 / 0.29 (13793) SS BOND : bond 0.00222 / 0.12 ( 3) SS BOND : angle 0.33763 / 0.21 ( 6) hydrogen bonds : bond 0.03035 / 2.05 ( 402) hydrogen bonds : angle 4.55689 / 3.29 ( 1155) Misc. bond : bond 0.00022 / 0.01 ( 2) link_NAG-ASN : bond 0.00238 / 0.15 ( 1) link_NAG-ASN : angle 1.83182 / 0.71 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2134.01 seconds wall clock time: 37 minutes 14.46 seconds (2234.46 seconds total)