Starting phenix.real_space_refine on Wed Feb 4 17:40:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7py4_13711/02_2026/7py4_13711.cif Found real_map, /net/cci-nas-00/data/ceres_data/7py4_13711/02_2026/7py4_13711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7py4_13711/02_2026/7py4_13711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7py4_13711/02_2026/7py4_13711.map" model { file = "/net/cci-nas-00/data/ceres_data/7py4_13711/02_2026/7py4_13711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7py4_13711/02_2026/7py4_13711.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 55 5.16 5 Be 1 3.05 5 C 7649 2.51 5 N 1966 2.21 5 O 2160 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11835 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8989 Classifications: {'peptide': 1112} Link IDs: {'PTRANS': 28, 'TRANS': 1083} Chain breaks: 4 Chain: "B" Number of atoms: 2634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2634 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 301} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 110 Unusual residues: {' MG': 1, 'BEF': 1, 'Y01': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.58, per 1000 atoms: 0.22 Number of scatterers: 11835 At special positions: 0 Unit cell: (81.18, 97.68, 180.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 55 16.00 Mg 1 11.99 F 3 9.00 O 2160 8.00 N 1966 7.00 C 7649 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 102 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 402 " - " ASN B 294 " " NAG B 403 " - " ASN B 107 " " NAG C 1 " - " ASN B 180 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 584.8 milliseconds 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2714 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 10 sheets defined 48.8% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 107 through 118 Processing helix chain 'A' and resid 118 through 133 removed outlier: 3.877A pdb=" N LEU A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 174 removed outlier: 3.734A pdb=" N LEU A 145 " --> pdb=" O TRP A 141 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.740A pdb=" N VAL A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 252 through 259 removed outlier: 3.712A pdb=" N THR A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.501A pdb=" N THR A 317 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 366 removed outlier: 4.032A pdb=" N TYR A 335 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 397 removed outlier: 4.084A pdb=" N TRP A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 403 through 422 Processing helix chain 'A' and resid 442 through 448 removed outlier: 4.174A pdb=" N ILE A 448 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 519 removed outlier: 4.275A pdb=" N ILE A 513 " --> pdb=" O ASP A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 534 removed outlier: 4.032A pdb=" N ARG A 525 " --> pdb=" O GLU A 521 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 565 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 635 through 649 Processing helix chain 'A' and resid 662 through 677 Processing helix chain 'A' and resid 682 through 695 removed outlier: 3.603A pdb=" N ILE A 694 " --> pdb=" O VAL A 690 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 695 " --> pdb=" O TYR A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 724 Processing helix chain 'A' and resid 735 through 746 Processing helix chain 'A' and resid 757 through 773 Processing helix chain 'A' and resid 803 through 810 Processing helix chain 'A' and resid 834 through 859 Processing helix chain 'A' and resid 869 through 885 Processing helix chain 'A' and resid 897 through 904 Processing helix chain 'A' and resid 928 through 930 No H-bonds generated for 'chain 'A' and resid 928 through 930' Processing helix chain 'A' and resid 931 through 938 removed outlier: 3.566A pdb=" N LEU A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 969 removed outlier: 3.698A pdb=" N PHE A 961 " --> pdb=" O LYS A 957 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR A 962 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 963 " --> pdb=" O PHE A 959 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL A 964 " --> pdb=" O ALA A 960 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N HIS A 965 " --> pdb=" O PHE A 961 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE A 966 " --> pdb=" O THR A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 972 No H-bonds generated for 'chain 'A' and resid 970 through 972' Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 994 through 1003 removed outlier: 3.531A pdb=" N LEU A 998 " --> pdb=" O SER A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1014 removed outlier: 3.542A pdb=" N ARG A1014 " --> pdb=" O LYS A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1018 Processing helix chain 'A' and resid 1019 through 1024 Processing helix chain 'A' and resid 1031 through 1057 Proline residue: A1051 - end of helix removed outlier: 4.131A pdb=" N GLN A1057 " --> pdb=" O GLY A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1092 removed outlier: 3.787A pdb=" N GLY A1089 " --> pdb=" O ASN A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1118 removed outlier: 4.333A pdb=" N ILE A1107 " --> pdb=" O ILE A1103 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A1108 " --> pdb=" O PHE A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1126 Processing helix chain 'A' and resid 1134 through 1140 Processing helix chain 'A' and resid 1142 through 1171 Proline residue: A1159 - end of helix Processing helix chain 'A' and resid 1173 through 1181 Processing helix chain 'A' and resid 1182 through 1185 removed outlier: 3.722A pdb=" N LEU A1185 " --> pdb=" O ARG A1182 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1182 through 1185' Processing helix chain 'A' and resid 1216 through 1223 Processing helix chain 'B' and resid 46 through 74 removed outlier: 3.550A pdb=" N VAL B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Proline residue: B 52 - end of helix Proline residue: B 63 - end of helix Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.637A pdb=" N SER B 96 " --> pdb=" O LYS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 136 Processing helix chain 'B' and resid 141 through 145 Processing helix chain 'B' and resid 146 through 151 removed outlier: 3.786A pdb=" N LEU B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.622A pdb=" N CYS B 157 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 removed outlier: 3.579A pdb=" N ASN B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'B' and resid 222 through 227 removed outlier: 3.564A pdb=" N PHE B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 removed outlier: 3.679A pdb=" N LEU B 243 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP B 244 " --> pdb=" O TYR B 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 240 through 244' Processing helix chain 'B' and resid 254 through 262 removed outlier: 3.801A pdb=" N TRP B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 350 removed outlier: 3.806A pdb=" N GLY B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 67 removed outlier: 4.380A pdb=" N GLY A 277 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190 removed outlier: 11.898A pdb=" N THR A 177 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N LYS A 203 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU A 179 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N PHE A 305 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N SER A 217 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N HIS A 307 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 240 removed outlier: 3.890A pdb=" N TYR A 225 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 426 through 427 removed outlier: 3.629A pdb=" N TYR A 427 " --> pdb=" O THR A 432 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 754 through 756 removed outlier: 6.062A pdb=" N THR A 754 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE A 800 " --> pdb=" O THR A 754 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N CYS A 756 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N THR A 802 " --> pdb=" O CYS A 756 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A 862 " --> pdb=" O ARG A 797 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE A 728 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N CYS A 865 " --> pdb=" O ILE A 728 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 730 " --> pdb=" O CYS A 865 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE A 451 " --> pdb=" O TRP A 729 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU A 731 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N SER A 453 " --> pdb=" O LEU A 731 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR A 450 " --> pdb=" O LEU A 889 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE A 891 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N PHE A 452 " --> pdb=" O ILE A 891 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR A 888 " --> pdb=" O ILE A 906 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N VAL A 908 " --> pdb=" O THR A 888 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA A 890 " --> pdb=" O VAL A 908 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE A 910 " --> pdb=" O ALA A 890 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N GLY A 892 " --> pdb=" O ILE A 910 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE A 926 " --> pdb=" O GLY A 909 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 474 through 476 removed outlier: 4.960A pdb=" N ILE A 463 " --> pdb=" O LYS A 709 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA A 705 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N CYS A 469 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA A 703 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE A 471 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N LEU A 701 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU A 656 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA A 703 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A 654 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA A 705 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ARG A 652 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE A 614 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG A 608 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL A 590 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 540 Processing sheet with id=AA8, first strand: chain 'A' and resid 567 through 572 removed outlier: 3.738A pdb=" N LEU A 570 " --> pdb=" O THR A 578 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR A 578 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 78 through 81 removed outlier: 5.733A pdb=" N TYR B 122 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU B 272 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU B 124 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ARG B 270 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 102 through 110 removed outlier: 4.134A pdb=" N CYS B 102 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B 295 " --> pdb=" O CYS B 104 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG B 290 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 182 " --> pdb=" O THR B 296 " (cutoff:3.500A) 541 hydrogen bonds defined for protein. 1536 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: 2.05 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2282 1.33 - 1.45: 3007 1.45 - 1.57: 6743 1.57 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 12117 Sorted by residual: bond pdb=" CAX Y01 A1303 " pdb=" OAH Y01 A1303 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" CAX Y01 B 401 " pdb=" OAH Y01 B 401 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" CAX Y01 A1304 " pdb=" OAH Y01 A1304 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" CAX Y01 A1305 " pdb=" OAH Y01 A1305 " ideal model delta sigma weight residual 1.248 1.341 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" F2 BEF A1302 " pdb="BE BEF A1302 " ideal model delta sigma weight residual 1.476 1.559 -0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 12112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 16273 2.45 - 4.90: 139 4.90 - 7.34: 19 7.34 - 9.79: 6 9.79 - 12.24: 1 Bond angle restraints: 16438 Sorted by residual: angle pdb=" F2 BEF A1302 " pdb="BE BEF A1302 " pdb=" F3 BEF A1302 " ideal model delta sigma weight residual 119.96 107.72 12.24 3.00e+00 1.11e-01 1.67e+01 angle pdb=" F1 BEF A1302 " pdb="BE BEF A1302 " pdb=" F3 BEF A1302 " ideal model delta sigma weight residual 120.12 110.60 9.52 3.00e+00 1.11e-01 1.01e+01 angle pdb=" CAM Y01 A1305 " pdb=" CAY Y01 A1305 " pdb=" OAW Y01 A1305 " ideal model delta sigma weight residual 111.19 120.15 -8.96 3.00e+00 1.11e-01 8.91e+00 angle pdb=" CAM Y01 A1304 " pdb=" CAY Y01 A1304 " pdb=" OAW Y01 A1304 " ideal model delta sigma weight residual 111.19 120.11 -8.92 3.00e+00 1.11e-01 8.84e+00 angle pdb=" CAM Y01 B 401 " pdb=" CAY Y01 B 401 " pdb=" OAW Y01 B 401 " ideal model delta sigma weight residual 111.19 119.88 -8.69 3.00e+00 1.11e-01 8.38e+00 ... (remaining 16433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.99: 7093 23.99 - 47.98: 311 47.98 - 71.97: 25 71.97 - 95.95: 23 95.95 - 119.94: 11 Dihedral angle restraints: 7463 sinusoidal: 3253 harmonic: 4210 Sorted by residual: dihedral pdb=" O3 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" C4 NAG C 1 " pdb=" O4 NAG C 1 " ideal model delta sinusoidal sigma weight residual 295.45 175.51 119.94 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C2 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" C4 NAG C 1 " pdb=" O4 NAG C 1 " ideal model delta sinusoidal sigma weight residual 175.11 55.35 119.76 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C5 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" C4 NAG C 1 " pdb=" O3 NAG C 1 " ideal model delta sinusoidal sigma weight residual -174.13 -56.61 -117.52 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 7460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1814 0.129 - 0.258: 21 0.258 - 0.387: 1 0.387 - 0.516: 4 0.516 - 0.644: 1 Chirality restraints: 1841 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN B 180 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" CBG Y01 B 401 " pdb=" CAQ Y01 B 401 " pdb=" CBD Y01 B 401 " pdb=" CBI Y01 B 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.76 0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CBG Y01 A1305 " pdb=" CAQ Y01 A1305 " pdb=" CBD Y01 A1305 " pdb=" CBI Y01 A1305 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 1838 not shown) Planarity restraints: 2067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 108 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO A 109 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 169 " -0.033 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO B 170 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 170 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 170 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1184 " -0.150 9.50e-02 1.11e+02 6.74e-02 3.18e+00 pdb=" NE ARG A1184 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A1184 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A1184 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A1184 " -0.002 2.00e-02 2.50e+03 ... (remaining 2064 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 19 2.30 - 2.95: 5660 2.95 - 3.60: 16525 3.60 - 4.25: 26530 4.25 - 4.90: 46813 Nonbonded interactions: 95547 Sorted by model distance: nonbonded pdb=" OD2 ASP A 454 " pdb=" F3 BEF A1302 " model vdw 1.650 2.990 nonbonded pdb=" O LEU A 441 " pdb=" OH TYR A 924 " model vdw 1.963 3.040 nonbonded pdb=" O ASN B 298 " pdb=" O3 NAG C 1 " model vdw 1.964 3.040 nonbonded pdb=" O LEU A 445 " pdb=" OH TYR A1019 " model vdw 2.078 3.040 nonbonded pdb=" O THR A 456 " pdb="MG MG A1301 " model vdw 2.085 2.170 ... (remaining 95542 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=0.00 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: 6.910 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.980 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 : 0.007 0.677 12126 Z= 0.638 Angle : 0.610 12.241 16459 Z= 0.276 Chirality : 0.051 0.644 1841 Planarity : 0.003 0.067 2064 Dihedral : 14.524 119.943 4740 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.08 % Allowed : 0.08 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.83 (0.23), residues: 1427 helix: 1.85 (0.23), residues: 607 sheet: 0.70 (0.37), residues: 202 loop : -0.82 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1184 TYR 0.010 0.001 TYR B 121 PHE 0.012 0.001 PHE A1072 TRP 0.010 0.001 TRP B 317 HIS 0.002 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00363 (12117) covalent geometry : angle 0.58578 (16438) SS BOND : bond 0.00322 ( 3) SS BOND : angle 0.66933 ( 6) hydrogen bonds : bond 0.13189 ( 541) hydrogen bonds : angle 5.40561 ( 1536) Misc. bond : bond 0.67674 ( 1) link_BETA1-4 : bond 0.01852 ( 2) link_BETA1-4 : angle 7.07869 ( 6) link_NAG-ASN : bond 0.01079 ( 3) link_NAG-ASN : angle 4.57856 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 228 THR cc_start: 0.8219 (p) cc_final: 0.8019 (p) REVERT: A 1000 MET cc_start: 0.8081 (tmm) cc_final: 0.7690 (ttp) REVERT: B 242 MET cc_start: 0.8445 (mpp) cc_final: 0.7840 (mpp) outliers start: 1 outliers final: 1 residues processed: 142 average time/residue: 0.1054 time to fit residues: 21.5807 Evaluate side-chains 118 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 958 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0070 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 479 HIS B 152 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.167400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.123423 restraints weight = 14086.791| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.32 r_work: 0.3450 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12126 Z= 0.127 Angle : 0.590 13.655 16459 Z= 0.287 Chirality : 0.045 0.532 1841 Planarity : 0.004 0.044 2064 Dihedral : 11.339 107.758 1965 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.63 % Allowed : 5.06 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.84 (0.23), residues: 1427 helix: 1.73 (0.22), residues: 632 sheet: 0.83 (0.37), residues: 196 loop : -0.82 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1184 TYR 0.019 0.001 TYR B 241 PHE 0.020 0.001 PHE A 666 TRP 0.012 0.001 TRP B 260 HIS 0.002 0.001 HIS A1123 Details of bonding type rmsd covalent geometry : bond 0.00293 (12117) covalent geometry : angle 0.55459 (16438) SS BOND : bond 0.00171 ( 3) SS BOND : angle 0.73116 ( 6) hydrogen bonds : bond 0.04330 ( 541) hydrogen bonds : angle 4.42706 ( 1536) Misc. bond : bond 0.00017 ( 1) link_BETA1-4 : bond 0.01143 ( 2) link_BETA1-4 : angle 5.98560 ( 6) link_NAG-ASN : bond 0.01538 ( 3) link_NAG-ASN : angle 7.07870 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 206 ASP cc_start: 0.7977 (m-30) cc_final: 0.7534 (m-30) REVERT: A 1000 MET cc_start: 0.8407 (tmm) cc_final: 0.8101 (ttp) REVERT: B 224 GLU cc_start: 0.8222 (tp30) cc_final: 0.7964 (tp30) REVERT: B 242 MET cc_start: 0.8617 (mpp) cc_final: 0.7862 (mpp) outliers start: 8 outliers final: 4 residues processed: 132 average time/residue: 0.0991 time to fit residues: 19.2232 Evaluate side-chains 116 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 1025 ASP Chi-restraints excluded: chain A residue 1113 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 4 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 80 optimal weight: 0.0970 chunk 21 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 HIS B 74 ASN B 249 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.164481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.123156 restraints weight = 14172.531| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.28 r_work: 0.3370 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12126 Z= 0.187 Angle : 0.611 14.221 16459 Z= 0.299 Chirality : 0.045 0.527 1841 Planarity : 0.004 0.042 2064 Dihedral : 10.174 106.103 1963 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.27 % Allowed : 7.28 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.23), residues: 1427 helix: 1.53 (0.21), residues: 630 sheet: 0.81 (0.37), residues: 197 loop : -0.92 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 166 TYR 0.015 0.001 TYR B 241 PHE 0.022 0.002 PHE A 666 TRP 0.013 0.001 TRP B 260 HIS 0.004 0.001 HIS A1213 Details of bonding type rmsd covalent geometry : bond 0.00463 (12117) covalent geometry : angle 0.57944 (16438) SS BOND : bond 0.00228 ( 3) SS BOND : angle 0.78238 ( 6) hydrogen bonds : bond 0.04675 ( 541) hydrogen bonds : angle 4.36122 ( 1536) Misc. bond : bond 0.00123 ( 1) link_BETA1-4 : bond 0.01503 ( 2) link_BETA1-4 : angle 5.95266 ( 6) link_NAG-ASN : bond 0.01438 ( 3) link_NAG-ASN : angle 6.81709 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.428 Fit side-chains REVERT: A 357 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8608 (mt) REVERT: A 514 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: A 1000 MET cc_start: 0.8350 (tmm) cc_final: 0.8037 (ttp) REVERT: A 1215 ARG cc_start: 0.8343 (ptm160) cc_final: 0.7969 (ptp90) REVERT: B 222 ASN cc_start: 0.8252 (t0) cc_final: 0.7976 (p0) REVERT: B 242 MET cc_start: 0.8632 (mpp) cc_final: 0.7881 (mpp) outliers start: 16 outliers final: 9 residues processed: 137 average time/residue: 0.0931 time to fit residues: 18.5954 Evaluate side-chains 129 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 1025 ASP Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain B residue 53 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 66 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.0970 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 41 optimal weight: 0.2980 chunk 89 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 HIS A 848 GLN B 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.166340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.126741 restraints weight = 14012.467| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.29 r_work: 0.3424 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12126 Z= 0.104 Angle : 0.537 14.049 16459 Z= 0.263 Chirality : 0.043 0.503 1841 Planarity : 0.003 0.036 2064 Dihedral : 9.212 102.873 1963 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.71 % Allowed : 9.02 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.91 (0.23), residues: 1427 helix: 1.76 (0.22), residues: 640 sheet: 0.95 (0.37), residues: 199 loop : -0.82 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 166 TYR 0.012 0.001 TYR B 121 PHE 0.014 0.001 PHE A 955 TRP 0.013 0.001 TRP B 317 HIS 0.002 0.000 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00234 (12117) covalent geometry : angle 0.50302 (16438) SS BOND : bond 0.00185 ( 3) SS BOND : angle 0.65024 ( 6) hydrogen bonds : bond 0.03592 ( 541) hydrogen bonds : angle 4.16122 ( 1536) Misc. bond : bond 0.00032 ( 1) link_BETA1-4 : bond 0.01382 ( 2) link_BETA1-4 : angle 5.85039 ( 6) link_NAG-ASN : bond 0.01591 ( 3) link_NAG-ASN : angle 6.54627 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.336 Fit side-chains REVERT: A 514 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: A 1000 MET cc_start: 0.8257 (tmm) cc_final: 0.8000 (ttp) REVERT: A 1215 ARG cc_start: 0.8318 (ptm160) cc_final: 0.7926 (ptp90) REVERT: B 242 MET cc_start: 0.8611 (mpp) cc_final: 0.7871 (mpp) outliers start: 9 outliers final: 6 residues processed: 134 average time/residue: 0.0912 time to fit residues: 17.9903 Evaluate side-chains 127 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 1025 ASP Chi-restraints excluded: chain A residue 1059 VAL Chi-restraints excluded: chain B residue 148 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 99 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 137 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 HIS B 235 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.161864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.122150 restraints weight = 14152.908| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.15 r_work: 0.3372 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12126 Z= 0.199 Angle : 0.605 14.295 16459 Z= 0.297 Chirality : 0.045 0.530 1841 Planarity : 0.004 0.050 2064 Dihedral : 9.313 104.209 1963 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.34 % Allowed : 10.21 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.23), residues: 1427 helix: 1.52 (0.21), residues: 637 sheet: 0.82 (0.37), residues: 200 loop : -0.91 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 166 TYR 0.014 0.001 TYR B 134 PHE 0.018 0.002 PHE A 527 TRP 0.013 0.001 TRP B 260 HIS 0.004 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00491 (12117) covalent geometry : angle 0.57186 (16438) SS BOND : bond 0.00155 ( 3) SS BOND : angle 0.72053 ( 6) hydrogen bonds : bond 0.04611 ( 541) hydrogen bonds : angle 4.24572 ( 1536) Misc. bond : bond 0.00137 ( 1) link_BETA1-4 : bond 0.01660 ( 2) link_BETA1-4 : angle 5.75918 ( 6) link_NAG-ASN : bond 0.01787 ( 3) link_NAG-ASN : angle 7.00663 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.423 Fit side-chains REVERT: A 514 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7441 (mp0) REVERT: A 1000 MET cc_start: 0.8347 (tmm) cc_final: 0.7976 (ttp) REVERT: A 1215 ARG cc_start: 0.8345 (ptm160) cc_final: 0.7974 (ptp90) REVERT: B 242 MET cc_start: 0.8627 (mpp) cc_final: 0.7899 (mpp) outliers start: 17 outliers final: 13 residues processed: 128 average time/residue: 0.0949 time to fit residues: 17.9561 Evaluate side-chains 128 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 1025 ASP Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 240 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 67 optimal weight: 0.8980 chunk 131 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.164187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.123976 restraints weight = 14130.399| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.14 r_work: 0.3403 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12126 Z= 0.117 Angle : 0.544 13.990 16459 Z= 0.265 Chirality : 0.043 0.508 1841 Planarity : 0.003 0.037 2064 Dihedral : 9.075 101.903 1963 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.34 % Allowed : 10.68 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.87 (0.23), residues: 1427 helix: 1.73 (0.22), residues: 642 sheet: 0.87 (0.37), residues: 199 loop : -0.84 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 166 TYR 0.012 0.001 TYR B 121 PHE 0.014 0.001 PHE A 955 TRP 0.012 0.001 TRP B 260 HIS 0.002 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00273 (12117) covalent geometry : angle 0.50498 (16438) SS BOND : bond 0.00204 ( 3) SS BOND : angle 0.61846 ( 6) hydrogen bonds : bond 0.03848 ( 541) hydrogen bonds : angle 4.10491 ( 1536) Misc. bond : bond 0.00051 ( 1) link_BETA1-4 : bond 0.01366 ( 2) link_BETA1-4 : angle 5.82351 ( 6) link_NAG-ASN : bond 0.01728 ( 3) link_NAG-ASN : angle 7.20278 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.433 Fit side-chains REVERT: A 514 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: A 1000 MET cc_start: 0.8304 (tmm) cc_final: 0.8019 (ttp) REVERT: A 1168 MET cc_start: 0.7649 (ttm) cc_final: 0.7422 (ttp) REVERT: A 1215 ARG cc_start: 0.8333 (ptm160) cc_final: 0.7939 (ptp90) REVERT: B 224 GLU cc_start: 0.8103 (tp30) cc_final: 0.7500 (tp30) REVERT: B 242 MET cc_start: 0.8639 (mpp) cc_final: 0.7880 (mpp) outliers start: 17 outliers final: 13 residues processed: 132 average time/residue: 0.0978 time to fit residues: 19.0223 Evaluate side-chains 132 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 1025 ASP Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 240 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 29 optimal weight: 0.0970 chunk 129 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 479 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.161840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.123282 restraints weight = 13893.383| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.12 r_work: 0.3357 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12126 Z= 0.143 Angle : 0.555 14.057 16459 Z= 0.272 Chirality : 0.044 0.515 1841 Planarity : 0.004 0.051 2064 Dihedral : 9.075 101.793 1963 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.50 % Allowed : 11.71 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.81 (0.23), residues: 1427 helix: 1.68 (0.21), residues: 642 sheet: 0.86 (0.37), residues: 199 loop : -0.88 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 166 TYR 0.013 0.001 TYR B 121 PHE 0.015 0.001 PHE A 527 TRP 0.012 0.001 TRP B 260 HIS 0.002 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00348 (12117) covalent geometry : angle 0.52268 (16438) SS BOND : bond 0.00132 ( 3) SS BOND : angle 0.65241 ( 6) hydrogen bonds : bond 0.04072 ( 541) hydrogen bonds : angle 4.07682 ( 1536) Misc. bond : bond 0.00076 ( 1) link_BETA1-4 : bond 0.01505 ( 2) link_BETA1-4 : angle 5.77369 ( 6) link_NAG-ASN : bond 0.01537 ( 3) link_NAG-ASN : angle 6.45200 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.459 Fit side-chains REVERT: A 514 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: A 1000 MET cc_start: 0.8372 (tmm) cc_final: 0.8009 (ttp) REVERT: A 1168 MET cc_start: 0.7708 (ttm) cc_final: 0.7479 (ttp) REVERT: A 1215 ARG cc_start: 0.8311 (ptm160) cc_final: 0.7925 (ptp90) REVERT: B 242 MET cc_start: 0.8655 (mpp) cc_final: 0.7884 (mpp) outliers start: 19 outliers final: 17 residues processed: 131 average time/residue: 0.0932 time to fit residues: 18.1468 Evaluate side-chains 132 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1025 ASP Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 240 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 64 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 136 optimal weight: 0.2980 chunk 14 optimal weight: 0.0870 chunk 38 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.165419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.125316 restraints weight = 14042.070| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.17 r_work: 0.3425 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12126 Z= 0.105 Angle : 0.534 13.790 16459 Z= 0.259 Chirality : 0.042 0.496 1841 Planarity : 0.003 0.042 2064 Dihedral : 8.917 99.157 1963 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.42 % Allowed : 12.10 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.23), residues: 1427 helix: 1.89 (0.22), residues: 642 sheet: 0.80 (0.37), residues: 204 loop : -0.79 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 166 TYR 0.012 0.001 TYR B 121 PHE 0.011 0.001 PHE A 527 TRP 0.012 0.001 TRP B 317 HIS 0.002 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00240 (12117) covalent geometry : angle 0.49487 (16438) SS BOND : bond 0.00188 ( 3) SS BOND : angle 0.52549 ( 6) hydrogen bonds : bond 0.03511 ( 541) hydrogen bonds : angle 3.96557 ( 1536) Misc. bond : bond 0.00033 ( 1) link_BETA1-4 : bond 0.01488 ( 2) link_BETA1-4 : angle 5.89202 ( 6) link_NAG-ASN : bond 0.01931 ( 3) link_NAG-ASN : angle 7.12273 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.419 Fit side-chains REVERT: A 514 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: A 1000 MET cc_start: 0.8284 (tmm) cc_final: 0.8003 (ttp) REVERT: A 1168 MET cc_start: 0.7649 (ttm) cc_final: 0.7435 (ttp) REVERT: A 1215 ARG cc_start: 0.8281 (ptm160) cc_final: 0.7886 (ptp90) REVERT: B 224 GLU cc_start: 0.8104 (tp30) cc_final: 0.7488 (tp30) REVERT: B 242 MET cc_start: 0.8654 (mpp) cc_final: 0.7885 (mpp) outliers start: 18 outliers final: 16 residues processed: 139 average time/residue: 0.0922 time to fit residues: 19.0174 Evaluate side-chains 139 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1025 ASP Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 240 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 102 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 HIS A 989 ASN B 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.160306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.120964 restraints weight = 13981.376| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.09 r_work: 0.3362 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.005 0.038 12126 Z= 0.202 Angle : 0.607 14.222 16459 Z= 0.299 Chirality : 0.046 0.524 1841 Planarity : 0.004 0.053 2064 Dihedral : 9.211 102.267 1963 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.50 % Allowed : 12.66 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.23), residues: 1427 helix: 1.61 (0.21), residues: 637 sheet: 0.74 (0.37), residues: 204 loop : -0.88 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 166 TYR 0.014 0.001 TYR B 122 PHE 0.018 0.002 PHE A 527 TRP 0.015 0.001 TRP A 281 HIS 0.003 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00500 (12117) covalent geometry : angle 0.57293 (16438) SS BOND : bond 0.00247 ( 3) SS BOND : angle 1.36155 ( 6) hydrogen bonds : bond 0.04590 ( 541) hydrogen bonds : angle 4.15382 ( 1536) Misc. bond : bond 0.00125 ( 1) link_BETA1-4 : bond 0.01473 ( 2) link_BETA1-4 : angle 5.85122 ( 6) link_NAG-ASN : bond 0.02244 ( 3) link_NAG-ASN : angle 7.11944 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.462 Fit side-chains REVERT: A 206 ASP cc_start: 0.7775 (m-30) cc_final: 0.7288 (m-30) REVERT: A 514 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: A 1000 MET cc_start: 0.8345 (tmm) cc_final: 0.7961 (ttp) REVERT: A 1215 ARG cc_start: 0.8304 (ptm160) cc_final: 0.7907 (ptp90) REVERT: B 113 SER cc_start: 0.8285 (p) cc_final: 0.8021 (p) REVERT: B 242 MET cc_start: 0.8676 (mpp) cc_final: 0.7901 (mpp) outliers start: 19 outliers final: 17 residues processed: 133 average time/residue: 0.1060 time to fit residues: 20.8566 Evaluate side-chains 133 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1025 ASP Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 240 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 109 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 55 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 HIS B 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.163088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.124106 restraints weight = 13915.465| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.10 r_work: 0.3403 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12126 Z= 0.117 Angle : 0.564 16.815 16459 Z= 0.272 Chirality : 0.044 0.616 1841 Planarity : 0.003 0.043 2064 Dihedral : 9.019 99.335 1963 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.50 % Allowed : 12.90 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1427 helix: 1.86 (0.22), residues: 639 sheet: 0.81 (0.37), residues: 204 loop : -0.83 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 166 TYR 0.013 0.001 TYR B 121 PHE 0.015 0.001 PHE A 955 TRP 0.016 0.001 TRP A 281 HIS 0.002 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00269 (12117) covalent geometry : angle 0.51897 (16438) SS BOND : bond 0.00284 ( 3) SS BOND : angle 1.51962 ( 6) hydrogen bonds : bond 0.03738 ( 541) hydrogen bonds : angle 4.04181 ( 1536) Misc. bond : bond 0.00039 ( 1) link_BETA1-4 : bond 0.01385 ( 2) link_BETA1-4 : angle 6.04247 ( 6) link_NAG-ASN : bond 0.03209 ( 3) link_NAG-ASN : angle 8.01139 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.420 Fit side-chains REVERT: A 206 ASP cc_start: 0.7719 (m-30) cc_final: 0.7249 (m-30) REVERT: A 514 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: A 1000 MET cc_start: 0.8310 (tmm) cc_final: 0.7991 (ttp) REVERT: A 1215 ARG cc_start: 0.8297 (ptm160) cc_final: 0.7899 (ptp90) REVERT: B 113 SER cc_start: 0.8259 (p) cc_final: 0.7987 (p) REVERT: B 242 MET cc_start: 0.8681 (mpp) cc_final: 0.7900 (mpp) outliers start: 19 outliers final: 18 residues processed: 137 average time/residue: 0.0953 time to fit residues: 19.3404 Evaluate side-chains 141 residues out of total 1264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1025 ASP Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 240 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 10 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 108 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 HIS B 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.161889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.122608 restraints weight = 13982.271| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.12 r_work: 0.3378 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12126 Z= 0.152 Angle : 0.574 14.006 16459 Z= 0.281 Chirality : 0.045 0.578 1841 Planarity : 0.004 0.052 2064 Dihedral : 9.018 100.282 1963 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.50 % Allowed : 13.45 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.85 (0.23), residues: 1427 helix: 1.75 (0.21), residues: 639 sheet: 0.80 (0.37), residues: 204 loop : -0.87 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 631 TYR 0.013 0.001 TYR B 121 PHE 0.015 0.001 PHE A 527 TRP 0.014 0.001 TRP A 281 HIS 0.002 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00367 (12117) covalent geometry : angle 0.53650 (16438) SS BOND : bond 0.00257 ( 3) SS BOND : angle 1.48660 ( 6) hydrogen bonds : bond 0.04126 ( 541) hydrogen bonds : angle 4.06867 ( 1536) Misc. bond : bond 0.00074 ( 1) link_BETA1-4 : bond 0.01432 ( 2) link_BETA1-4 : angle 5.98738 ( 6) link_NAG-ASN : bond 0.02625 ( 3) link_NAG-ASN : angle 7.15152 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2662.91 seconds wall clock time: 46 minutes 27.76 seconds (2787.76 seconds total)