Starting phenix.real_space_refine on Mon Jul 28 19:29:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ijm_35489/07_2025/8ijm_35489.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ijm_35489/07_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_35489/07_2025/8ijm_35489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ijm_35489/07_2025/8ijm_35489.map" model { file = "/net/cci-nas-00/data/ceres_data/8ijm_35489/07_2025/8ijm_35489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ijm_35489/07_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-5711/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: 8.70, per 1000 atoms: 0.87 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: 2.44 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: 1.34 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: 2.96 Time building geometry restraints manager: 2.91 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.740 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.080 ------------------------------------------------------------------------------- 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 : 1.290 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 72 average time/residue: 0.3478 time to fit residues: 36.6205 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 : 1.443 ------------------------------------------------------------------------------- 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 = 0.208389 restraints weight = 10543.734| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 1.38 r_work: 0.4084 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3987 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 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 : 1.002 Fit side-chains REVERT: B 91 ARG cc_start: 0.7268 (ttt90) cc_final: 0.7056 (ttt180) REVERT: B 96 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8211 (mttp) REVERT: B 99 GLU cc_start: 0.7658 (tp30) cc_final: 0.7430 (tp30) REVERT: B 129 MET cc_start: 0.8004 (mmm) cc_final: 0.7793 (mmm) outliers start: 22 outliers final: 12 residues processed: 94 average time/residue: 0.2216 time to fit residues: 29.9742 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 : 1.002 ------------------------------------------------------------------------------- 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: 8.9990 chunk 109 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 0.0170 chunk 80 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- 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 = 0.4697 r_free = 0.4697 target = 0.246396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.195647 restraints weight = 11573.867| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 1.97 r_work: 0.3596 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10187 Z= 0.177 Angle : 0.617 13.066 13802 Z= 0.314 Chirality : 0.045 0.171 1575 Planarity : 0.005 0.084 1733 Dihedral : 9.249 131.742 1554 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.89 % Allowed : 13.70 % 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: -0.69 (0.24), residues: 1240 helix: 0.04 (0.23), residues: 526 sheet: -0.50 (0.43), residues: 129 loop : -0.81 (0.25), residues: 585 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 0.019 0.002 TYR A 881 ARG 0.004 0.000 ARG B 182 Details of bonding type rmsd link_NAG-ASN : bond 0.00049 ( 1) link_NAG-ASN : angle 1.84278 ( 3) hydrogen bonds : bond 0.04070 ( 402) hydrogen bonds : angle 5.12118 ( 1155) SS BOND : bond 0.00451 ( 3) SS BOND : angle 0.90857 ( 6) covalent geometry : bond 0.00426 (10181) covalent geometry : angle 0.61596 (13793) Misc. bond : bond 0.00147 ( 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 108 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.2193 (mmp) cc_final: 0.1817 (mmt) REVERT: A 349 LEU cc_start: 0.7637 (mm) cc_final: 0.7038 (tp) REVERT: A 665 GLU cc_start: 0.7217 (mp0) cc_final: 0.6917 (mp0) REVERT: A 776 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: A 950 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8290 (mtpt) REVERT: A 999 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8356 (pm20) REVERT: B 91 ARG cc_start: 0.7895 (ttt90) cc_final: 0.7661 (ttt180) REVERT: B 99 GLU cc_start: 0.7838 (tp30) cc_final: 0.7546 (tp30) outliers start: 31 outliers final: 20 residues processed: 96 average time/residue: 0.2371 time to fit residues: 32.4216 Evaluate side-chains 98 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 711 LEU Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 791 THR 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: 1.9990 chunk 119 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4627 r_free = 0.4627 target = 0.230348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.194117 restraints weight = 10919.852| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 1.54 r_work: 0.3764 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10187 Z= 0.160 Angle : 0.588 13.532 13802 Z= 0.300 Chirality : 0.044 0.176 1575 Planarity : 0.005 0.082 1733 Dihedral : 9.188 138.558 1552 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.36 % Allowed : 14.26 % Favored : 82.39 % 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: -0.60 (0.24), residues: 1240 helix: 0.19 (0.24), residues: 530 sheet: -0.53 (0.42), residues: 137 loop : -0.84 (0.25), residues: 573 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 0.014 0.002 PHE B 186 TYR 0.018 0.002 TYR A 881 ARG 0.003 0.000 ARG B 182 Details of bonding type rmsd link_NAG-ASN : bond 0.00071 ( 1) link_NAG-ASN : angle 1.98197 ( 3) hydrogen bonds : bond 0.03640 ( 402) hydrogen bonds : angle 4.94298 ( 1155) SS BOND : bond 0.00355 ( 3) SS BOND : angle 0.56305 ( 6) covalent geometry : bond 0.00386 (10181) covalent geometry : angle 0.58695 (13793) Misc. bond : bond 0.00139 ( 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 116 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 80 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 LEU cc_start: 0.7742 (mm) cc_final: 0.7048 (tp) REVERT: A 665 GLU cc_start: 0.7359 (mp0) cc_final: 0.7124 (mp0) REVERT: A 708 GLN cc_start: 0.8284 (tm-30) cc_final: 0.8079 (tm-30) REVERT: A 950 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8072 (mtpt) REVERT: A 999 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8439 (pm20) REVERT: B 99 GLU cc_start: 0.7947 (tp30) cc_final: 0.7651 (tp30) outliers start: 36 outliers final: 24 residues processed: 105 average time/residue: 0.2186 time to fit residues: 33.0179 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 : 1.027 ------------------------------------------------------------------------------- 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 711 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 148 VAL 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 72 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.246489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.184804 restraints weight = 11499.779| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 1.54 r_work: 0.3672 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10187 Z= 0.152 Angle : 0.584 13.946 13802 Z= 0.298 Chirality : 0.044 0.180 1575 Planarity : 0.005 0.081 1733 Dihedral : 9.192 140.567 1552 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.98 % Allowed : 15.56 % 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: -0.54 (0.24), residues: 1240 helix: 0.28 (0.24), residues: 532 sheet: -0.53 (0.42), residues: 136 loop : -0.85 (0.25), residues: 572 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 0.017 0.002 PHE A 105 TYR 0.017 0.001 TYR A 881 ARG 0.003 0.000 ARG B 182 Details of bonding type rmsd link_NAG-ASN : bond 0.00062 ( 1) link_NAG-ASN : angle 1.90451 ( 3) hydrogen bonds : bond 0.03470 ( 402) hydrogen bonds : angle 4.86430 ( 1155) SS BOND : bond 0.00344 ( 3) SS BOND : angle 0.58447 ( 6) covalent geometry : bond 0.00366 (10181) covalent geometry : angle 0.58307 (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 113 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.4839 (m-10) cc_final: 0.4637 (m-10) REVERT: A 349 LEU cc_start: 0.7568 (mm) cc_final: 0.6912 (tp) REVERT: A 708 GLN cc_start: 0.8264 (tm-30) cc_final: 0.8041 (tm-30) REVERT: A 950 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8107 (mtpt) REVERT: A 999 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8429 (pm20) REVERT: B 99 GLU cc_start: 0.7872 (tp30) cc_final: 0.7379 (tt0) outliers start: 32 outliers final: 27 residues processed: 101 average time/residue: 0.2292 time to fit residues: 32.9939 Evaluate side-chains 104 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 18 optimal weight: 20.0000 chunk 102 optimal weight: 0.0570 chunk 27 optimal weight: 0.5980 chunk 92 optimal weight: 0.0870 chunk 77 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 36 optimal weight: 0.0370 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 106 optimal weight: 0.0970 overall best weight: 0.1752 ------------------------------------------------------------------------------- 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 = 0.4716 r_free = 0.4716 target = 0.250602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.4169 r_free = 0.4169 target = 0.180019 restraints weight = 11603.482| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 1.83 r_work: 0.3691 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10187 Z= 0.096 Angle : 0.533 13.850 13802 Z= 0.272 Chirality : 0.042 0.187 1575 Planarity : 0.004 0.081 1733 Dihedral : 8.715 133.022 1552 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.80 % Allowed : 16.50 % Favored : 80.71 % 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: -0.27 (0.24), residues: 1240 helix: 0.56 (0.24), residues: 528 sheet: -0.62 (0.42), residues: 148 loop : -0.68 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 902 HIS 0.007 0.001 HIS A 632 PHE 0.014 0.001 PHE A 105 TYR 0.013 0.001 TYR A 881 ARG 0.003 0.000 ARG A 563 Details of bonding type rmsd link_NAG-ASN : bond 0.00507 ( 1) link_NAG-ASN : angle 1.68019 ( 3) hydrogen bonds : bond 0.02748 ( 402) hydrogen bonds : angle 4.60457 ( 1155) SS BOND : bond 0.00136 ( 3) SS BOND : angle 0.35626 ( 6) covalent geometry : bond 0.00213 (10181) covalent geometry : angle 0.53229 (13793) Misc. bond : bond 0.00122 ( 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 114 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 349 LEU cc_start: 0.7681 (mm) cc_final: 0.6897 (tp) REVERT: A 526 ILE cc_start: 0.5008 (OUTLIER) cc_final: 0.4632 (tt) REVERT: A 616 SER cc_start: 0.8465 (t) cc_final: 0.7995 (p) REVERT: A 844 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7960 (mmp) outliers start: 30 outliers final: 21 residues processed: 104 average time/residue: 0.2175 time to fit residues: 32.8630 Evaluate side-chains 97 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 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 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 555 MET 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 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: 0.7980 chunk 18 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN B 104 ASN B 283 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.246053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.189859 restraints weight = 11684.073| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 1.92 r_work: 0.3592 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10187 Z= 0.182 Angle : 0.620 14.630 13802 Z= 0.313 Chirality : 0.045 0.178 1575 Planarity : 0.005 0.080 1733 Dihedral : 9.133 142.970 1552 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.26 % Allowed : 16.31 % Favored : 80.43 % 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: -0.47 (0.24), residues: 1240 helix: 0.37 (0.24), residues: 537 sheet: -0.56 (0.42), residues: 138 loop : -0.82 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 902 HIS 0.008 0.001 HIS A 632 PHE 0.019 0.002 PHE A 105 TYR 0.018 0.002 TYR B 167 ARG 0.007 0.000 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00085 ( 1) link_NAG-ASN : angle 2.03439 ( 3) hydrogen bonds : bond 0.03562 ( 402) hydrogen bonds : angle 4.78052 ( 1155) SS BOND : bond 0.00435 ( 3) SS BOND : angle 0.94418 ( 6) covalent geometry : bond 0.00443 (10181) covalent geometry : angle 0.61936 (13793) Misc. bond : bond 0.00125 ( 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 119 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 84 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 349 LEU cc_start: 0.7598 (mm) cc_final: 0.6825 (tp) REVERT: A 950 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8393 (mtpt) REVERT: A 999 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8369 (pm20) REVERT: B 99 GLU cc_start: 0.7667 (tp30) cc_final: 0.7225 (tt0) outliers start: 35 outliers final: 24 residues processed: 106 average time/residue: 0.2312 time to fit residues: 35.2220 Evaluate side-chains 103 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 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 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 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 148 VAL Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 266 ASN 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 111 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 chunk 108 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.238139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.194767 restraints weight = 11124.260| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 1.83 r_work: 0.3680 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10187 Z= 0.159 Angle : 0.605 14.134 13802 Z= 0.306 Chirality : 0.044 0.186 1575 Planarity : 0.005 0.080 1733 Dihedral : 9.218 146.082 1552 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.52 % Allowed : 16.96 % Favored : 80.52 % 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: -0.42 (0.24), residues: 1240 helix: 0.45 (0.24), residues: 531 sheet: -0.83 (0.41), residues: 146 loop : -0.74 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 902 HIS 0.007 0.001 HIS A 632 PHE 0.019 0.001 PHE A 128 TYR 0.017 0.002 TYR A 881 ARG 0.007 0.000 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00095 ( 1) link_NAG-ASN : angle 2.10261 ( 3) hydrogen bonds : bond 0.03355 ( 402) hydrogen bonds : angle 4.77558 ( 1155) SS BOND : bond 0.00312 ( 3) SS BOND : angle 0.59819 ( 6) covalent geometry : bond 0.00386 (10181) covalent geometry : angle 0.60378 (13793) Misc. bond : bond 0.00090 ( 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 105 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 349 LEU cc_start: 0.7544 (mm) cc_final: 0.6864 (tp) REVERT: A 950 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8317 (mtpt) REVERT: A 999 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8345 (pm20) REVERT: B 99 GLU cc_start: 0.7609 (tp30) cc_final: 0.7248 (tt0) outliers start: 27 outliers final: 21 residues processed: 96 average time/residue: 0.2240 time to fit residues: 31.2280 Evaluate side-chains 99 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 148 LEU 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 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 999 GLN 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 63 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.230984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.193457 restraints weight = 10962.766| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 1.63 r_work: 0.3754 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10187 Z= 0.146 Angle : 0.600 15.090 13802 Z= 0.302 Chirality : 0.044 0.185 1575 Planarity : 0.004 0.079 1733 Dihedral : 9.129 148.208 1552 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.61 % Allowed : 16.68 % Favored : 80.71 % 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: -0.37 (0.24), residues: 1240 helix: 0.51 (0.24), residues: 531 sheet: -0.81 (0.42), residues: 146 loop : -0.72 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 902 HIS 0.007 0.001 HIS A 632 PHE 0.020 0.001 PHE A 105 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 0.00106 ( 1) link_NAG-ASN : angle 2.05512 ( 3) hydrogen bonds : bond 0.03264 ( 402) hydrogen bonds : angle 4.72671 ( 1155) SS BOND : bond 0.00289 ( 3) SS BOND : angle 0.51744 ( 6) covalent geometry : bond 0.00354 (10181) covalent geometry : angle 0.59945 (13793) Misc. bond : bond 0.00095 ( 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 105 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 349 LEU cc_start: 0.7504 (mm) cc_final: 0.6894 (tp) REVERT: A 999 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8303 (pm20) REVERT: B 99 GLU cc_start: 0.7411 (tp30) cc_final: 0.7106 (tt0) outliers start: 28 outliers final: 25 residues processed: 96 average time/residue: 0.2217 time to fit residues: 30.7897 Evaluate side-chains 100 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 148 LEU Chi-restraints excluded: chain A residue 150 LEU 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 203 VAL 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 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 998 VAL Chi-restraints excluded: chain A residue 999 GLN 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: 0.8980 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 122 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.230889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.194254 restraints weight = 11010.374| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 1.61 r_work: 0.3770 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10187 Z= 0.146 Angle : 0.605 15.077 13802 Z= 0.304 Chirality : 0.044 0.188 1575 Planarity : 0.005 0.079 1733 Dihedral : 9.113 152.011 1552 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.52 % Allowed : 16.78 % Favored : 80.71 % 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: -0.33 (0.24), residues: 1240 helix: 0.55 (0.24), residues: 531 sheet: -0.81 (0.42), residues: 146 loop : -0.71 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 902 HIS 0.007 0.001 HIS A 632 PHE 0.016 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 0.00110 ( 1) link_NAG-ASN : angle 2.11228 ( 3) hydrogen bonds : bond 0.03270 ( 402) hydrogen bonds : angle 4.70765 ( 1155) SS BOND : bond 0.00303 ( 3) SS BOND : angle 0.53021 ( 6) covalent geometry : bond 0.00356 (10181) covalent geometry : angle 0.60387 (13793) Misc. bond : bond 0.00090 ( 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 105 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.1034 (OUTLIER) cc_final: 0.0482 (tpt) REVERT: A 349 LEU cc_start: 0.7501 (mm) cc_final: 0.6918 (tp) REVERT: A 670 ARG cc_start: 0.7809 (tpm170) cc_final: 0.7528 (tpm170) REVERT: A 999 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8308 (pm20) REVERT: B 99 GLU cc_start: 0.7413 (tp30) cc_final: 0.7109 (tt0) outliers start: 27 outliers final: 24 residues processed: 96 average time/residue: 0.2253 time to fit residues: 31.0596 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 : 1.015 ------------------------------------------------------------------------------- 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 148 LEU Chi-restraints excluded: chain A residue 150 LEU 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 203 VAL 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 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 998 VAL Chi-restraints excluded: chain A residue 999 GLN 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 14 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 2 optimal weight: 20.0000 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 33 optimal weight: 0.0770 chunk 81 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.231528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.191767 restraints weight = 10918.064| |-----------------------------------------------------------------------------| r_work (start): 0.4337 rms_B_bonded: 1.72 r_work: 0.3746 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2000 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= 0.137 Angle : 0.597 15.354 13802 Z= 0.300 Chirality : 0.043 0.192 1575 Planarity : 0.005 0.079 1733 Dihedral : 9.012 155.084 1552 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.52 % Allowed : 16.78 % Favored : 80.71 % 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: -0.29 (0.24), residues: 1240 helix: 0.61 (0.24), residues: 531 sheet: -0.82 (0.41), residues: 146 loop : -0.69 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 902 HIS 0.010 0.001 HIS A 632 PHE 0.023 0.001 PHE A 105 TYR 0.016 0.001 TYR A 881 ARG 0.010 0.000 ARG A 397 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 1) link_NAG-ASN : angle 2.13760 ( 3) hydrogen bonds : bond 0.03145 ( 402) hydrogen bonds : angle 4.65968 ( 1155) SS BOND : bond 0.00246 ( 3) SS BOND : angle 0.43324 ( 6) covalent geometry : bond 0.00329 (10181) covalent geometry : angle 0.59648 (13793) Misc. bond : bond 0.00086 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5343.68 seconds wall clock time: 92 minutes 18.28 seconds (5538.28 seconds total)