Starting phenix.real_space_refine on Sat Oct 11 23:36:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xm7_38466/10_2025/8xm7_38466.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xm7_38466/10_2025/8xm7_38466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xm7_38466/10_2025/8xm7_38466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xm7_38466/10_2025/8xm7_38466.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xm7_38466/10_2025/8xm7_38466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xm7_38466/10_2025/8xm7_38466.map" } resolution = 4.91 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2049 atoms to isotropic. 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 3 5.49 5 Mg 1 5.21 5 S 102 5.16 5 C 10947 2.51 5 N 2931 2.21 5 O 3206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17190 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5879 Classifications: {'peptide': 727} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 693} Chain: "B" Number of atoms: 9862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1215, 9862 Classifications: {'peptide': 1215} Link IDs: {'PTRANS': 35, 'TRANS': 1179} Chain: "D" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1416 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 13, 'TRANS': 167} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.31, per 1000 atoms: 0.19 Number of scatterers: 17190 At special positions: 0 Unit cell: (97.09, 174.23, 160.93, 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 102 16.00 P 3 15.00 Mg 1 11.99 O 3206 8.00 N 2931 7.00 C 10947 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 724.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4066 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 11 sheets defined 57.5% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 29 through 41 removed outlier: 3.620A pdb=" N ILE A 33 " --> pdb=" O PRO A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.864A pdb=" N ILE A 69 " --> pdb=" O ARG A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 93 Processing helix chain 'A' and resid 96 through 111 Processing helix chain 'A' and resid 113 through 124 removed outlier: 4.320A pdb=" N GLU A 119 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 135 Processing helix chain 'A' and resid 140 through 167 removed outlier: 4.864A pdb=" N ILE A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 177 through 189 Processing helix chain 'A' and resid 194 through 212 Processing helix chain 'A' and resid 212 through 221 removed outlier: 4.023A pdb=" N GLN A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 234 removed outlier: 3.698A pdb=" N LEU A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 254 removed outlier: 3.555A pdb=" N GLN A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 269 removed outlier: 3.541A pdb=" N GLU A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 287 through 311 removed outlier: 3.908A pdb=" N ASP A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ARG A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 311 " --> pdb=" O ASP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 333 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 344 through 358 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 377 through 390 removed outlier: 3.594A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 402 Processing helix chain 'A' and resid 412 through 429 Processing helix chain 'A' and resid 444 through 448 removed outlier: 3.676A pdb=" N THR A 447 " --> pdb=" O MET A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 470 Processing helix chain 'A' and resid 476 through 493 Processing helix chain 'A' and resid 498 through 509 Processing helix chain 'A' and resid 514 through 527 Processing helix chain 'A' and resid 530 through 540 Processing helix chain 'A' and resid 541 through 559 removed outlier: 3.672A pdb=" N LEU A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.531A pdb=" N ASP A 612 " --> pdb=" O PRO A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 627 Processing helix chain 'A' and resid 634 through 638 Processing helix chain 'A' and resid 658 through 673 removed outlier: 3.654A pdb=" N TYR A 662 " --> pdb=" O ASP A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 696 Processing helix chain 'A' and resid 697 through 702 removed outlier: 3.879A pdb=" N ASP A 700 " --> pdb=" O ARG A 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 104 removed outlier: 3.533A pdb=" N VAL B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 131 removed outlier: 3.817A pdb=" N PHE B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 180 through 206 Processing helix chain 'B' and resid 209 through 219 removed outlier: 4.175A pdb=" N THR B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE B 219 " --> pdb=" O ILE B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 291 Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 378 through 389 Processing helix chain 'B' and resid 409 through 416 Processing helix chain 'B' and resid 521 through 524 Processing helix chain 'B' and resid 537 through 544 Processing helix chain 'B' and resid 583 through 588 Processing helix chain 'B' and resid 591 through 605 Processing helix chain 'B' and resid 634 through 642 Processing helix chain 'B' and resid 649 through 658 removed outlier: 4.202A pdb=" N MET B 658 " --> pdb=" O LEU B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 667 removed outlier: 3.771A pdb=" N LYS B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 683 Processing helix chain 'B' and resid 686 through 706 removed outlier: 3.780A pdb=" N ASP B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 711 removed outlier: 5.503A pdb=" N HIS B 711 " --> pdb=" O LYS B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 724 removed outlier: 3.888A pdb=" N LYS B 722 " --> pdb=" O THR B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 743 Processing helix chain 'B' and resid 746 through 758 removed outlier: 3.774A pdb=" N GLU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 778 Processing helix chain 'B' and resid 783 through 804 Processing helix chain 'B' and resid 805 through 820 removed outlier: 4.360A pdb=" N ALA B 809 " --> pdb=" O PRO B 805 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LYS B 811 " --> pdb=" O GLU B 807 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 831 removed outlier: 3.927A pdb=" N LEU B 829 " --> pdb=" O ASN B 825 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 830 " --> pdb=" O ASP B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 846 Processing helix chain 'B' and resid 852 through 866 removed outlier: 3.774A pdb=" N SER B 866 " --> pdb=" O LYS B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 891 Proline residue: B 880 - end of helix removed outlier: 3.576A pdb=" N ASP B 891 " --> pdb=" O SER B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 915 removed outlier: 4.667A pdb=" N ALA B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 910 " --> pdb=" O LEU B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 919 removed outlier: 4.176A pdb=" N GLY B 919 " --> pdb=" O LYS B 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 916 through 919' Processing helix chain 'B' and resid 921 through 943 removed outlier: 5.704A pdb=" N ARG B 934 " --> pdb=" O GLU B 930 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ARG B 935 " --> pdb=" O ARG B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 964 removed outlier: 3.817A pdb=" N PHE B 953 " --> pdb=" O HIS B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 970 Processing helix chain 'B' and resid 978 through 998 removed outlier: 3.639A pdb=" N ILE B 982 " --> pdb=" O THR B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1033 Processing helix chain 'B' and resid 1034 through 1037 Processing helix chain 'B' and resid 1042 through 1055 removed outlier: 3.591A pdb=" N TYR B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1063 Processing helix chain 'B' and resid 1065 through 1077 removed outlier: 3.822A pdb=" N ARG B1069 " --> pdb=" O SER B1065 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASN B1070 " --> pdb=" O GLN B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1095 removed outlier: 4.153A pdb=" N GLU B1082 " --> pdb=" O ASP B1078 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY B1095 " --> pdb=" O TRP B1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1100 Processing helix chain 'B' and resid 1101 through 1106 Processing helix chain 'B' and resid 1107 through 1114 removed outlier: 4.087A pdb=" N GLU B1111 " --> pdb=" O GLY B1107 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B1112 " --> pdb=" O PRO B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1118 through 1125 Processing helix chain 'B' and resid 1125 through 1140 removed outlier: 3.882A pdb=" N PHE B1129 " --> pdb=" O ILE B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1162 removed outlier: 3.676A pdb=" N GLU B1150 " --> pdb=" O MET B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1165 through 1183 Processing helix chain 'B' and resid 1185 through 1212 Processing helix chain 'D' and resid 15 through 25 Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 86 through 94 removed outlier: 3.544A pdb=" N TYR D 90 " --> pdb=" O SER D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 105 Processing helix chain 'D' and resid 116 through 120 Processing helix chain 'D' and resid 122 through 132 Processing helix chain 'D' and resid 138 through 149 Processing helix chain 'D' and resid 164 through 178 removed outlier: 4.007A pdb=" N VAL D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 25 removed outlier: 4.054A pdb=" N TRP A 14 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE A 12 " --> pdb=" O PRO A 19 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU A 21 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL A 10 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU A 23 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL A 8 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N LEU A 75 " --> pdb=" O LYS A 9 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA A 11 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU A 77 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLU A 13 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N THR A 79 " --> pdb=" O GLU A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 561 through 562 Processing sheet with id=AA3, first strand: chain 'A' and resid 578 through 579 Processing sheet with id=AA4, first strand: chain 'A' and resid 616 through 618 Processing sheet with id=AA5, first strand: chain 'B' and resid 13 through 14 removed outlier: 3.796A pdb=" N LEU B 38 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ARG B 46 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N MET B 40 " --> pdb=" O TRP B 44 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N TRP B 44 " --> pdb=" O MET B 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 339 through 347 removed outlier: 9.566A pdb=" N GLU B 340 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 9.874A pdb=" N LEU B 405 " --> pdb=" O GLU B 340 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LYS B 342 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU B 403 " --> pdb=" O LYS B 342 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N TYR B 222 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 252 through 253 Processing sheet with id=AA8, first strand: chain 'B' and resid 252 through 253 removed outlier: 6.825A pdb=" N LEU B 296 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL B 326 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N CYS B 298 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL B 324 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ILE B 300 " --> pdb=" O PHE B 322 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 484 through 485 removed outlier: 6.223A pdb=" N TRP B 509 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N HIS B 452 " --> pdb=" O TRP B 509 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLN B 621 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ASP B 618 " --> pdb=" O VAL B 571 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 571 " --> pdb=" O ASP B 618 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 495 through 497 removed outlier: 7.451A pdb=" N HIS B 533 " --> pdb=" O ALA B 546 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ALA B 546 " --> pdb=" O HIS B 533 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 37 through 46 removed outlier: 3.736A pdb=" N ILE D 4 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N VAL D 77 " --> pdb=" O SER D 3 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS D 5 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL D 79 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL D 7 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N CYS D 81 " --> pdb=" O VAL D 7 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL D 9 " --> pdb=" O CYS D 81 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N SER D 83 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N LEU D 155 " --> pdb=" O ILE D 110 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU D 112 " --> pdb=" O LEU D 155 " (cutoff:3.500A) 926 hydrogen bonds defined for protein. 2676 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.23 Time building geometry restraints manager: 2.19 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: 4351 1.33 - 1.45: 3260 1.45 - 1.57: 9744 1.57 - 1.69: 5 1.69 - 1.81: 172 Bond restraints: 17532 Sorted by residual: bond pdb=" CG1 ILE B 863 " pdb=" CD1 ILE B 863 " ideal model delta sigma weight residual 1.513 1.411 0.102 3.90e-02 6.57e+02 6.85e+00 bond pdb=" CB ARG B 931 " pdb=" CG ARG B 931 " ideal model delta sigma weight residual 1.520 1.450 0.070 3.00e-02 1.11e+03 5.47e+00 bond pdb=" C ILE A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.28e-02 6.10e+03 4.16e+00 bond pdb=" CA ALA B1003 " pdb=" C ALA B1003 " ideal model delta sigma weight residual 1.524 1.479 0.044 2.25e-02 1.98e+03 3.86e+00 bond pdb=" CG GLN B1157 " pdb=" CD GLN B1157 " ideal model delta sigma weight residual 1.516 1.472 0.044 2.50e-02 1.60e+03 3.03e+00 ... (remaining 17527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 22751 2.28 - 4.57: 817 4.57 - 6.85: 95 6.85 - 9.14: 20 9.14 - 11.42: 5 Bond angle restraints: 23688 Sorted by residual: angle pdb=" N ILE B 204 " pdb=" CA ILE B 204 " pdb=" C ILE B 204 " ideal model delta sigma weight residual 113.53 106.75 6.78 9.80e-01 1.04e+00 4.79e+01 angle pdb=" C LYS A 253 " pdb=" N ALA A 254 " pdb=" CA ALA A 254 " ideal model delta sigma weight residual 120.68 110.18 10.50 1.52e+00 4.33e-01 4.77e+01 angle pdb=" C ARG B 103 " pdb=" N LYS B 104 " pdb=" CA LYS B 104 " ideal model delta sigma weight residual 122.66 113.63 9.03 1.63e+00 3.76e-01 3.07e+01 angle pdb=" C LEU A 228 " pdb=" N ILE A 229 " pdb=" CA ILE A 229 " ideal model delta sigma weight residual 120.24 123.19 -2.95 6.30e-01 2.52e+00 2.20e+01 angle pdb=" C LYS B1184 " pdb=" N TYR B1185 " pdb=" CA TYR B1185 " ideal model delta sigma weight residual 121.54 129.64 -8.10 1.91e+00 2.74e-01 1.80e+01 ... (remaining 23683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.60: 10423 30.60 - 61.20: 262 61.20 - 91.80: 38 91.80 - 122.40: 2 122.40 - 153.00: 1 Dihedral angle restraints: 10726 sinusoidal: 4475 harmonic: 6251 Sorted by residual: dihedral pdb=" CA VAL D 36 " pdb=" C VAL D 36 " pdb=" N PHE D 37 " pdb=" CA PHE D 37 " ideal model delta harmonic sigma weight residual 180.00 135.90 44.10 0 5.00e+00 4.00e-02 7.78e+01 dihedral pdb=" C4' GTP D 202 " pdb=" C5' GTP D 202 " pdb=" O5' GTP D 202 " pdb=" PA GTP D 202 " ideal model delta sinusoidal sigma weight residual 260.87 107.87 153.00 1 2.00e+01 2.50e-03 4.54e+01 dihedral pdb=" CA ARG B 870 " pdb=" C ARG B 870 " pdb=" N GLN B 871 " pdb=" CA GLN B 871 " ideal model delta harmonic sigma weight residual -180.00 -148.19 -31.81 0 5.00e+00 4.00e-02 4.05e+01 ... (remaining 10723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1831 0.050 - 0.101: 660 0.101 - 0.151: 149 0.151 - 0.201: 12 0.201 - 0.251: 6 Chirality restraints: 2658 Sorted by residual: chirality pdb=" CG LEU A 159 " pdb=" CB LEU A 159 " pdb=" CD1 LEU A 159 " pdb=" CD2 LEU A 159 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CG LEU B 879 " pdb=" CB LEU B 879 " pdb=" CD1 LEU B 879 " pdb=" CD2 LEU B 879 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA PHE B1031 " pdb=" N PHE B1031 " pdb=" C PHE B1031 " pdb=" CB PHE B1031 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 2655 not shown) Planarity restraints: 3037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 59 " 0.029 2.00e-02 2.50e+03 2.44e-02 1.04e+01 pdb=" CG PHE B 59 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE B 59 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 59 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 59 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 59 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE B 59 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1043 " 0.018 2.00e-02 2.50e+03 1.73e-02 7.50e+00 pdb=" CG TRP B1043 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP B1043 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B1043 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B1043 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B1043 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B1043 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1043 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1043 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP B1043 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 87 " -0.045 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO D 88 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 88 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 88 " -0.038 5.00e-02 4.00e+02 ... (remaining 3034 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 439 2.59 - 3.17: 18389 3.17 - 3.74: 31579 3.74 - 4.32: 44210 4.32 - 4.90: 64094 Nonbonded interactions: 158711 Sorted by model distance: nonbonded pdb="MG MG D 201 " pdb=" O2G GTP D 202 " model vdw 2.009 2.170 nonbonded pdb=" O THR B 330 " pdb=" ND1 HIS B 334 " model vdw 2.029 3.120 nonbonded pdb=" O LEU B1120 " pdb=" OG1 THR B1124 " model vdw 2.033 3.040 nonbonded pdb=" O PHE B 843 " pdb=" OG SER B 846 " model vdw 2.036 3.040 nonbonded pdb=" OG SER A 643 " pdb=" OD1 ASN A 653 " model vdw 2.053 3.040 ... (remaining 158706 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 group one per residue 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.750 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 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 0.102 17533 Z= 0.330 Angle : 1.013 11.424 23688 Z= 0.577 Chirality : 0.053 0.251 2658 Planarity : 0.006 0.068 3037 Dihedral : 14.707 153.003 6660 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 51.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -2.89 (0.17), residues: 2117 helix: -1.65 (0.14), residues: 1051 sheet: -1.88 (0.32), residues: 215 loop : -2.08 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 945 TYR 0.032 0.003 TYR B 778 PHE 0.055 0.004 PHE B 59 TRP 0.045 0.004 TRP B1043 HIS 0.014 0.003 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00663 (17532) covalent geometry : angle 1.01340 (23688) hydrogen bonds : bond 0.17171 ( 924) hydrogen bonds : angle 8.22883 ( 2676) Misc. bond : bond 0.00138 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.2627 (tpt) cc_final: 0.2263 (tpt) REVERT: B 40 MET cc_start: 0.8461 (mmp) cc_final: 0.8256 (mmt) REVERT: B 521 GLU cc_start: 0.9764 (mt-10) cc_final: 0.9531 (mp0) REVERT: B 681 MET cc_start: 0.9454 (mmp) cc_final: 0.9193 (mmm) REVERT: B 764 PHE cc_start: 0.9025 (t80) cc_final: 0.8721 (t80) REVERT: B 1011 MET cc_start: 0.9728 (mmp) cc_final: 0.9447 (mmm) REVERT: B 1090 MET cc_start: 0.9177 (mmp) cc_final: 0.8899 (mmm) REVERT: B 1132 MET cc_start: 0.9432 (tmm) cc_final: 0.9109 (tmm) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1225 time to fit residues: 19.9284 Evaluate side-chains 87 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.0070 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 20.0000 overall best weight: 2.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 HIS A 487 GLN A 566 ASN A 601 HIS A 633 GLN A 634 ASN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 GLN B 213 GLN B 227 ASN ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 HIS B 537 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 GLN ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 743 ASN B1035 GLN B1066 GLN ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1149 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.069065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.048645 restraints weight = 192865.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.048308 restraints weight = 105327.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.049654 restraints weight = 71344.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.049760 restraints weight = 46768.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.049988 restraints weight = 41911.445| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17533 Z= 0.187 Angle : 0.772 7.987 23688 Z= 0.409 Chirality : 0.047 0.225 2658 Planarity : 0.006 0.114 3037 Dihedral : 8.437 145.944 2300 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 27.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.57 % Allowed : 6.56 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -2.36 (0.17), residues: 2117 helix: -1.11 (0.14), residues: 1124 sheet: -1.77 (0.33), residues: 206 loop : -1.99 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 120 TYR 0.031 0.002 TYR B 719 PHE 0.040 0.002 PHE B 114 TRP 0.018 0.002 TRP B1043 HIS 0.008 0.002 HIS B 154 Details of bonding type rmsd covalent geometry : bond 0.00397 (17532) covalent geometry : angle 0.77246 (23688) hydrogen bonds : bond 0.05468 ( 924) hydrogen bonds : angle 6.68777 ( 2676) Misc. bond : bond 0.00119 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 595 MET cc_start: 0.9176 (mtm) cc_final: 0.8888 (mtt) REVERT: B 681 MET cc_start: 0.9641 (mmp) cc_final: 0.9336 (mmm) REVERT: B 990 PHE cc_start: 0.9331 (m-80) cc_final: 0.9004 (m-80) REVERT: B 1009 MET cc_start: 0.9590 (ppp) cc_final: 0.9141 (ppp) REVERT: B 1011 MET cc_start: 0.9724 (mmp) cc_final: 0.9390 (mmm) REVERT: B 1090 MET cc_start: 0.9358 (mmp) cc_final: 0.9147 (mmm) REVERT: B 1110 LEU cc_start: 0.9897 (mm) cc_final: 0.9684 (mt) REVERT: B 1131 MET cc_start: 0.9604 (pmm) cc_final: 0.9355 (pmm) REVERT: B 1132 MET cc_start: 0.9439 (tmm) cc_final: 0.9186 (tmm) REVERT: B 1158 GLU cc_start: 0.9276 (tp30) cc_final: 0.8894 (tp30) outliers start: 11 outliers final: 4 residues processed: 124 average time/residue: 0.1279 time to fit residues: 25.2362 Evaluate side-chains 100 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 21 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 99 optimal weight: 30.0000 chunk 87 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 206 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 576 ASN ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.057964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.032607 restraints weight = 196553.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.033563 restraints weight = 138092.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.034295 restraints weight = 106720.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.034863 restraints weight = 87521.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.035164 restraints weight = 75284.874| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5849 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17533 Z= 0.230 Angle : 0.772 13.916 23688 Z= 0.408 Chirality : 0.047 0.205 2658 Planarity : 0.006 0.099 3037 Dihedral : 8.244 145.492 2300 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 31.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.21 % Allowed : 6.61 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -2.24 (0.17), residues: 2117 helix: -0.98 (0.14), residues: 1114 sheet: -1.73 (0.33), residues: 206 loop : -1.98 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 875 TYR 0.026 0.002 TYR B 719 PHE 0.036 0.003 PHE D 37 TRP 0.016 0.002 TRP A 41 HIS 0.020 0.002 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00475 (17532) covalent geometry : angle 0.77174 (23688) hydrogen bonds : bond 0.05258 ( 924) hydrogen bonds : angle 6.62645 ( 2676) Misc. bond : bond 0.00186 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 579 MET cc_start: 0.0330 (mtm) cc_final: 0.0007 (mtp) REVERT: B 595 MET cc_start: 0.6681 (mtm) cc_final: 0.6433 (mtt) REVERT: B 680 MET cc_start: 0.9137 (ppp) cc_final: 0.8892 (ppp) REVERT: B 957 MET cc_start: 0.9167 (ptp) cc_final: 0.8893 (ptp) outliers start: 4 outliers final: 2 residues processed: 114 average time/residue: 0.1277 time to fit residues: 23.1934 Evaluate side-chains 95 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 27 optimal weight: 8.9990 chunk 127 optimal weight: 0.4980 chunk 125 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 30.0000 chunk 35 optimal weight: 9.9990 chunk 132 optimal weight: 0.3980 chunk 146 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 ASN B 376 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.068555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.048595 restraints weight = 195722.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.047684 restraints weight = 107322.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.049025 restraints weight = 73563.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.049070 restraints weight = 48830.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.049365 restraints weight = 42683.174| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17533 Z= 0.189 Angle : 0.733 11.218 23688 Z= 0.385 Chirality : 0.046 0.196 2658 Planarity : 0.005 0.073 3037 Dihedral : 8.096 143.000 2300 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 28.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.10 % Allowed : 4.64 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -1.94 (0.17), residues: 2117 helix: -0.76 (0.14), residues: 1130 sheet: -1.49 (0.35), residues: 188 loop : -1.84 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 931 TYR 0.027 0.002 TYR B 719 PHE 0.034 0.002 PHE D 37 TRP 0.014 0.002 TRP A 41 HIS 0.006 0.001 HIS B 154 Details of bonding type rmsd covalent geometry : bond 0.00398 (17532) covalent geometry : angle 0.73315 (23688) hydrogen bonds : bond 0.04884 ( 924) hydrogen bonds : angle 6.41989 ( 2676) Misc. bond : bond 0.00158 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4067 (mmm) cc_final: 0.2430 (ttt) REVERT: B 579 MET cc_start: 0.4116 (mtm) cc_final: 0.3824 (mtp) REVERT: B 595 MET cc_start: 0.9038 (mtm) cc_final: 0.8729 (mtp) REVERT: B 640 LEU cc_start: 0.9256 (tt) cc_final: 0.8802 (mt) REVERT: B 681 MET cc_start: 0.9396 (mmm) cc_final: 0.9152 (mmm) REVERT: B 943 MET cc_start: 0.8712 (ttp) cc_final: 0.8221 (ppp) REVERT: B 990 PHE cc_start: 0.9528 (m-10) cc_final: 0.9311 (m-80) REVERT: B 1011 MET cc_start: 0.9738 (mmp) cc_final: 0.9435 (mmm) REVERT: B 1110 LEU cc_start: 0.9705 (mt) cc_final: 0.9500 (mt) REVERT: B 1158 GLU cc_start: 0.9341 (tp30) cc_final: 0.8951 (tp30) outliers start: 2 outliers final: 1 residues processed: 111 average time/residue: 0.1334 time to fit residues: 23.5842 Evaluate side-chains 94 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 188 optimal weight: 8.9990 chunk 95 optimal weight: 20.0000 chunk 22 optimal weight: 40.0000 chunk 50 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 61 optimal weight: 30.0000 chunk 25 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 HIS ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 HIS ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 GLN ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1060 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.057459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.028921 restraints weight = 187105.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.029612 restraints weight = 137800.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.030202 restraints weight = 110354.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.030604 restraints weight = 94084.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.030991 restraints weight = 83891.606| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5923 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17533 Z= 0.234 Angle : 0.776 10.388 23688 Z= 0.407 Chirality : 0.047 0.195 2658 Planarity : 0.005 0.072 3037 Dihedral : 8.154 143.991 2300 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 30.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -2.00 (0.17), residues: 2117 helix: -0.76 (0.15), residues: 1116 sheet: -1.53 (0.36), residues: 179 loop : -1.94 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B1015 TYR 0.025 0.002 TYR B 719 PHE 0.038 0.003 PHE B 59 TRP 0.015 0.002 TRP A 41 HIS 0.006 0.001 HIS B 567 Details of bonding type rmsd covalent geometry : bond 0.00478 (17532) covalent geometry : angle 0.77613 (23688) hydrogen bonds : bond 0.04975 ( 924) hydrogen bonds : angle 6.48786 ( 2676) Misc. bond : bond 0.00162 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 579 MET cc_start: 0.0124 (mtm) cc_final: -0.0228 (mtp) REVERT: B 595 MET cc_start: 0.6486 (mtm) cc_final: 0.6203 (mtp) REVERT: B 631 LEU cc_start: 0.6949 (mt) cc_final: 0.6682 (mt) REVERT: B 929 MET cc_start: 0.3072 (ttp) cc_final: 0.2833 (ttp) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1281 time to fit residues: 23.5248 Evaluate side-chains 90 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 62 optimal weight: 30.0000 chunk 201 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 799 ASN ** B 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1060 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.066323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.044365 restraints weight = 197356.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.045468 restraints weight = 102173.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.046165 restraints weight = 63186.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.046402 restraints weight = 46938.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.047281 restraints weight = 38953.484| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17533 Z= 0.247 Angle : 0.789 9.973 23688 Z= 0.415 Chirality : 0.047 0.182 2658 Planarity : 0.006 0.081 3037 Dihedral : 8.177 144.607 2300 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 32.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.05 % Allowed : 3.59 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -2.11 (0.17), residues: 2117 helix: -0.84 (0.14), residues: 1118 sheet: -1.47 (0.36), residues: 184 loop : -2.05 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 329 TYR 0.029 0.002 TYR D 72 PHE 0.043 0.003 PHE B 59 TRP 0.016 0.002 TRP A 41 HIS 0.006 0.002 HIS B 567 Details of bonding type rmsd covalent geometry : bond 0.00504 (17532) covalent geometry : angle 0.78923 (23688) hydrogen bonds : bond 0.04936 ( 924) hydrogen bonds : angle 6.50039 ( 2676) Misc. bond : bond 0.00140 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 ASP cc_start: 0.8475 (p0) cc_final: 0.8092 (t0) REVERT: B 40 MET cc_start: 0.8593 (mmp) cc_final: 0.8322 (mmm) REVERT: B 764 PHE cc_start: 0.8933 (t80) cc_final: 0.8586 (t80) REVERT: B 929 MET cc_start: 0.8662 (ttp) cc_final: 0.8435 (ttp) REVERT: B 958 ILE cc_start: 0.9761 (pt) cc_final: 0.9488 (pt) REVERT: B 1009 MET cc_start: 0.9540 (ppp) cc_final: 0.9100 (ppp) REVERT: B 1011 MET cc_start: 0.9730 (mmp) cc_final: 0.9434 (mmm) REVERT: B 1158 GLU cc_start: 0.9285 (tp30) cc_final: 0.8930 (tp30) outliers start: 1 outliers final: 1 residues processed: 111 average time/residue: 0.1264 time to fit residues: 23.1153 Evaluate side-chains 93 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 201 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 71 optimal weight: 0.5980 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN B 452 HIS ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 GLN ** B1060 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.057491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.032179 restraints weight = 196715.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.033108 restraints weight = 138977.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.033837 restraints weight = 107397.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.034390 restraints weight = 87835.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.034749 restraints weight = 75458.893| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5877 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17533 Z= 0.238 Angle : 0.792 9.498 23688 Z= 0.418 Chirality : 0.047 0.178 2658 Planarity : 0.006 0.072 3037 Dihedral : 8.199 144.617 2300 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 30.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -2.19 (0.17), residues: 2117 helix: -0.90 (0.14), residues: 1136 sheet: -1.45 (0.37), residues: 179 loop : -2.12 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 329 TYR 0.027 0.002 TYR B 719 PHE 0.038 0.003 PHE B 59 TRP 0.011 0.002 TRP A 41 HIS 0.006 0.002 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00487 (17532) covalent geometry : angle 0.79173 (23688) hydrogen bonds : bond 0.04917 ( 924) hydrogen bonds : angle 6.52483 ( 2676) Misc. bond : bond 0.00122 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 680 MET cc_start: 0.9252 (ppp) cc_final: 0.9037 (ppp) REVERT: B 764 PHE cc_start: 0.8282 (t80) cc_final: 0.7907 (t80) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1183 time to fit residues: 22.5727 Evaluate side-chains 93 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 207 optimal weight: 20.0000 chunk 29 optimal weight: 50.0000 chunk 74 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 15 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 144 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** 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 = 0.3691 r_free = 0.3691 target = 0.068552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.048205 restraints weight = 193121.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.047958 restraints weight = 102882.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.049228 restraints weight = 72086.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.049321 restraints weight = 46893.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.049543 restraints weight = 42512.601| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17533 Z= 0.163 Angle : 0.738 9.051 23688 Z= 0.383 Chirality : 0.046 0.208 2658 Planarity : 0.005 0.072 3037 Dihedral : 8.012 139.516 2300 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 24.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -1.79 (0.18), residues: 2117 helix: -0.54 (0.15), residues: 1128 sheet: -1.20 (0.39), residues: 173 loop : -2.01 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 329 TYR 0.026 0.002 TYR B 719 PHE 0.031 0.002 PHE B 59 TRP 0.010 0.002 TRP A 41 HIS 0.004 0.001 HIS B 567 Details of bonding type rmsd covalent geometry : bond 0.00351 (17532) covalent geometry : angle 0.73790 (23688) hydrogen bonds : bond 0.04533 ( 924) hydrogen bonds : angle 6.25780 ( 2676) Misc. bond : bond 0.00082 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 595 MET cc_start: 0.9223 (mtm) cc_final: 0.8956 (mtm) REVERT: B 958 ILE cc_start: 0.9761 (pt) cc_final: 0.9506 (pt) REVERT: B 990 PHE cc_start: 0.9603 (m-80) cc_final: 0.9189 (m-80) REVERT: B 1009 MET cc_start: 0.9596 (ppp) cc_final: 0.9324 (ppp) REVERT: B 1011 MET cc_start: 0.9714 (mmp) cc_final: 0.9416 (mmm) REVERT: B 1090 MET cc_start: 0.9359 (mmp) cc_final: 0.9007 (mmm) REVERT: B 1158 GLU cc_start: 0.9362 (tp30) cc_final: 0.8975 (tp30) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1259 time to fit residues: 24.6367 Evaluate side-chains 98 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 90 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 74 optimal weight: 0.0870 chunk 82 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 151 optimal weight: 5.9990 chunk 46 optimal weight: 30.0000 chunk 124 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 133 optimal weight: 30.0000 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN B 130 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.057747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.029057 restraints weight = 183002.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.029894 restraints weight = 134661.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.030436 restraints weight = 108746.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.030953 restraints weight = 92274.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.031375 restraints weight = 81817.107| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5968 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17533 Z= 0.229 Angle : 0.792 10.355 23688 Z= 0.417 Chirality : 0.047 0.185 2658 Planarity : 0.006 0.071 3037 Dihedral : 8.102 141.501 2300 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 30.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 0.05 % Allowed : 1.04 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -1.89 (0.17), residues: 2117 helix: -0.64 (0.15), residues: 1131 sheet: -1.15 (0.39), residues: 171 loop : -2.04 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 935 TYR 0.024 0.002 TYR B 719 PHE 0.036 0.003 PHE B1147 TRP 0.012 0.002 TRP B1043 HIS 0.008 0.002 HIS B 924 Details of bonding type rmsd covalent geometry : bond 0.00471 (17532) covalent geometry : angle 0.79236 (23688) hydrogen bonds : bond 0.04752 ( 924) hydrogen bonds : angle 6.35175 ( 2676) Misc. bond : bond 0.00072 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 680 MET cc_start: 0.9320 (ppp) cc_final: 0.8936 (ppp) REVERT: B 764 PHE cc_start: 0.8301 (t80) cc_final: 0.8079 (t80) outliers start: 1 outliers final: 0 residues processed: 117 average time/residue: 0.1189 time to fit residues: 22.8535 Evaluate side-chains 94 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 14 optimal weight: 0.4980 chunk 146 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 205 optimal weight: 8.9990 chunk 188 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN A 292 HIS ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN B 130 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.058474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.032851 restraints weight = 191030.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.033826 restraints weight = 133845.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.034580 restraints weight = 103184.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.035038 restraints weight = 84570.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.035571 restraints weight = 73321.306| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5841 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17533 Z= 0.180 Angle : 0.756 12.510 23688 Z= 0.394 Chirality : 0.047 0.181 2658 Planarity : 0.005 0.072 3037 Dihedral : 8.015 138.587 2300 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 26.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.10 % Allowed : 0.68 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -1.74 (0.18), residues: 2117 helix: -0.47 (0.15), residues: 1132 sheet: -1.09 (0.40), residues: 173 loop : -2.05 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 935 TYR 0.026 0.002 TYR B 719 PHE 0.027 0.002 PHE B 59 TRP 0.011 0.002 TRP A 41 HIS 0.006 0.001 HIS B 924 Details of bonding type rmsd covalent geometry : bond 0.00380 (17532) covalent geometry : angle 0.75641 (23688) hydrogen bonds : bond 0.04558 ( 924) hydrogen bonds : angle 6.19794 ( 2676) Misc. bond : bond 0.00066 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 353 MET cc_start: 0.5662 (mpp) cc_final: 0.5322 (mmm) outliers start: 2 outliers final: 2 residues processed: 122 average time/residue: 0.1293 time to fit residues: 25.4261 Evaluate side-chains 97 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 104 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 97 optimal weight: 40.0000 chunk 191 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 60 optimal weight: 0.0470 chunk 178 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 overall best weight: 2.7284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN ** D 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.067749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.047712 restraints weight = 195529.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.047314 restraints weight = 103125.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.048670 restraints weight = 73855.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.048684 restraints weight = 47612.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.048852 restraints weight = 44417.576| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17533 Z= 0.173 Angle : 0.770 12.898 23688 Z= 0.402 Chirality : 0.047 0.281 2658 Planarity : 0.005 0.072 3037 Dihedral : 7.935 136.499 2300 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 26.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -1.67 (0.18), residues: 2117 helix: -0.44 (0.15), residues: 1134 sheet: -0.99 (0.41), residues: 173 loop : -1.99 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 193 TYR 0.024 0.002 TYR B 719 PHE 0.031 0.002 PHE B 694 TRP 0.021 0.002 TRP D 56 HIS 0.006 0.001 HIS B 924 Details of bonding type rmsd covalent geometry : bond 0.00369 (17532) covalent geometry : angle 0.77046 (23688) hydrogen bonds : bond 0.04672 ( 924) hydrogen bonds : angle 6.20338 ( 2676) Misc. bond : bond 0.00055 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3636.61 seconds wall clock time: 63 minutes 54.03 seconds (3834.03 seconds total)