Starting phenix.real_space_refine on Sun Aug 24 16:18:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ex7_50032/08_2025/9ex7_50032.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ex7_50032/08_2025/9ex7_50032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ex7_50032/08_2025/9ex7_50032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ex7_50032/08_2025/9ex7_50032.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ex7_50032/08_2025/9ex7_50032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ex7_50032/08_2025/9ex7_50032.map" } resolution = 2.91 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 2 5.21 5 S 93 5.16 5 C 13398 2.51 5 N 3552 2.21 5 O 4010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21055 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 9548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1181, 9548 Classifications: {'peptide': 1181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 40, 'TRANS': 1140} Chain breaks: 1 Chain: "C" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 967 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "D" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 967 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "A" Number of atoms: 9544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1181, 9544 Classifications: {'peptide': 1181} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 1140} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.03, per 1000 atoms: 0.19 Number of scatterers: 21055 At special positions: 0 Unit cell: (97.24, 126.48, 201.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 93 16.00 Mg 2 11.99 O 4010 8.00 N 3552 7.00 C 13398 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=0, symmetry=0 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 674.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4914 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 9 sheets defined 56.2% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'B' and resid 1 through 29 removed outlier: 4.481A pdb=" N ILE B 6 " --> pdb=" O ASN B 2 " (cutoff:3.500A) Proline residue: B 11 - end of helix Processing helix chain 'B' and resid 61 through 75 removed outlier: 3.509A pdb=" N GLN B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 101 removed outlier: 3.524A pdb=" N HIS B 101 " --> pdb=" O TYR B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 134 Processing helix chain 'B' and resid 137 through 148 removed outlier: 3.761A pdb=" N GLY B 148 " --> pdb=" O MET B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 168 removed outlier: 3.610A pdb=" N GLN B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N CYS B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N HIS B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.647A pdb=" N LEU B 185 " --> pdb=" O GLU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 202 removed outlier: 4.035A pdb=" N LEU B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 209 removed outlier: 3.816A pdb=" N TRP B 208 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.512A pdb=" N TYR B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.595A pdb=" N THR B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 258 removed outlier: 3.608A pdb=" N VAL B 252 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN B 258 " --> pdb=" O TYR B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 268 Processing helix chain 'B' and resid 273 through 277 Processing helix chain 'B' and resid 287 through 298 Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.913A pdb=" N ILE B 307 " --> pdb=" O PRO B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 335 removed outlier: 3.820A pdb=" N THR B 321 " --> pdb=" O GLY B 317 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B 322 " --> pdb=" O HIS B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 349 removed outlier: 3.602A pdb=" N LEU B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 373 removed outlier: 3.513A pdb=" N ALA B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 440 Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 459 through 474 removed outlier: 3.627A pdb=" N LEU B 463 " --> pdb=" O ASP B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 499 Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 518 through 529 Processing helix chain 'B' and resid 530 through 533 removed outlier: 4.095A pdb=" N LYS B 533 " --> pdb=" O PRO B 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 530 through 533' Processing helix chain 'B' and resid 536 through 547 Processing helix chain 'B' and resid 565 through 567 No H-bonds generated for 'chain 'B' and resid 565 through 567' Processing helix chain 'B' and resid 568 through 576 Processing helix chain 'B' and resid 591 through 595 Processing helix chain 'B' and resid 626 through 637 Processing helix chain 'B' and resid 646 through 651 Processing helix chain 'B' and resid 662 through 669 Processing helix chain 'B' and resid 688 through 691 removed outlier: 3.511A pdb=" N VAL B 691 " --> pdb=" O SER B 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 688 through 691' Processing helix chain 'B' and resid 695 through 699 removed outlier: 3.715A pdb=" N VAL B 699 " --> pdb=" O TRP B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 740 Processing helix chain 'B' and resid 741 through 746 removed outlier: 3.797A pdb=" N ASN B 746 " --> pdb=" O GLU B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 removed outlier: 3.681A pdb=" N TYR B 756 " --> pdb=" O LYS B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 807 Processing helix chain 'B' and resid 808 through 819 Processing helix chain 'B' and resid 825 through 830 Processing helix chain 'B' and resid 838 through 856 removed outlier: 4.201A pdb=" N ASP B 842 " --> pdb=" O ASN B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 872 removed outlier: 3.688A pdb=" N HIS B 872 " --> pdb=" O LEU B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 909 removed outlier: 3.737A pdb=" N LYS B 899 " --> pdb=" O VAL B 895 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN B 900 " --> pdb=" O ASN B 896 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN B 902 " --> pdb=" O GLU B 898 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 907 " --> pdb=" O ASN B 903 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 908 " --> pdb=" O ILE B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 933 Processing helix chain 'B' and resid 937 through 963 removed outlier: 3.846A pdb=" N ASN B 943 " --> pdb=" O ASP B 939 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 989 removed outlier: 3.577A pdb=" N GLY B 989 " --> pdb=" O LEU B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1026 Processing helix chain 'B' and resid 1030 through 1043 removed outlier: 3.510A pdb=" N CYS B1043 " --> pdb=" O ALA B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1066 Processing helix chain 'B' and resid 1067 through 1075 Processing helix chain 'B' and resid 1099 through 1101 No H-bonds generated for 'chain 'B' and resid 1099 through 1101' Processing helix chain 'B' and resid 1104 through 1114 removed outlier: 4.134A pdb=" N ARG B1108 " --> pdb=" O ALA B1104 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL B1114 " --> pdb=" O ARG B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1135 removed outlier: 3.651A pdb=" N GLN B1131 " --> pdb=" O ARG B1127 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B1132 " --> pdb=" O LEU B1128 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP B1133 " --> pdb=" O ASN B1129 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1169 removed outlier: 3.578A pdb=" N LYS B1144 " --> pdb=" O ALA B1140 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER B1149 " --> pdb=" O ARG B1145 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B1150 " --> pdb=" O GLU B1146 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE B1151 " --> pdb=" O ARG B1147 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS B1152 " --> pdb=" O ASP B1148 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP B1169 " --> pdb=" O ARG B1165 " (cutoff:3.500A) Processing helix chain 'B' and resid 1179 through 1184 Processing helix chain 'B' and resid 1193 through 1199 removed outlier: 3.585A pdb=" N ILE B1197 " --> pdb=" O ASP B1193 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 27 removed outlier: 3.633A pdb=" N VAL C 11 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP C 27 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 44 removed outlier: 3.674A pdb=" N ALA C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 58 removed outlier: 3.711A pdb=" N ALA C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 72 removed outlier: 3.609A pdb=" N LEU C 71 " --> pdb=" O ASP C 68 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N MET C 72 " --> pdb=" O SER C 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 68 through 72' Processing helix chain 'C' and resid 77 through 97 removed outlier: 4.199A pdb=" N ILE C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP C 97 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 113 removed outlier: 3.641A pdb=" N LEU C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 27 removed outlier: 3.626A pdb=" N VAL D 11 " --> pdb=" O THR D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 44 removed outlier: 4.471A pdb=" N ALA D 37 " --> pdb=" O ASP D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 58 removed outlier: 3.571A pdb=" N ALA D 58 " --> pdb=" O PHE D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 72 removed outlier: 3.711A pdb=" N LEU D 71 " --> pdb=" O ASP D 68 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET D 72 " --> pdb=" O SER D 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 68 through 72' Processing helix chain 'D' and resid 78 through 97 removed outlier: 3.855A pdb=" N ASP D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 111 removed outlier: 3.675A pdb=" N LEU D 102 " --> pdb=" O ALA D 98 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 117 removed outlier: 6.248A pdb=" N ASP D 115 " --> pdb=" O TYR D 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 29 removed outlier: 4.150A pdb=" N ILE A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 7 " --> pdb=" O THR A 3 " (cutoff:3.500A) Proline residue: A 11 - end of helix Processing helix chain 'A' and resid 60 through 75 removed outlier: 4.450A pdb=" N ARG A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 102 Processing helix chain 'A' and resid 120 through 124 removed outlier: 3.511A pdb=" N ASP A 124 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 137 through 148 Processing helix chain 'A' and resid 153 through 167 Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 194 through 203 removed outlier: 4.140A pdb=" N GLY A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 212 through 230 removed outlier: 3.735A pdb=" N TYR A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU A 224 " --> pdb=" O PHE A 220 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LYS A 225 " --> pdb=" O TYR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 260 removed outlier: 3.600A pdb=" N VAL A 252 " --> pdb=" O PRO A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 268 removed outlier: 3.803A pdb=" N TYR A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.926A pdb=" N LYS A 274 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASP A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 271 through 275' Processing helix chain 'A' and resid 287 through 298 Processing helix chain 'A' and resid 303 through 307 removed outlier: 4.178A pdb=" N ILE A 307 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 335 Processing helix chain 'A' and resid 339 through 349 removed outlier: 4.363A pdb=" N GLN A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 432 through 443 Processing helix chain 'A' and resid 445 through 450 removed outlier: 4.292A pdb=" N LEU A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 456 through 459 removed outlier: 3.577A pdb=" N ASP A 459 " --> pdb=" O PRO A 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 456 through 459' Processing helix chain 'A' and resid 460 through 475 removed outlier: 4.478A pdb=" N VAL A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 499 Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 518 through 528 Processing helix chain 'A' and resid 535 through 547 removed outlier: 3.670A pdb=" N MET A 539 " --> pdb=" O ASP A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 579 Processing helix chain 'A' and resid 626 through 637 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 662 through 670 removed outlier: 3.981A pdb=" N LEU A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 695 through 699 removed outlier: 3.635A pdb=" N GLU A 698 " --> pdb=" O ARG A 695 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 699 " --> pdb=" O TRP A 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 695 through 699' Processing helix chain 'A' and resid 737 through 740 Processing helix chain 'A' and resid 798 through 807 Processing helix chain 'A' and resid 808 through 819 Processing helix chain 'A' and resid 838 through 856 removed outlier: 4.231A pdb=" N ASP A 842 " --> pdb=" O ASN A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 905 removed outlier: 4.359A pdb=" N ILE A 905 " --> pdb=" O ILE A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 909 removed outlier: 3.749A pdb=" N LEU A 909 " --> pdb=" O GLU A 906 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 906 through 909' Processing helix chain 'A' and resid 917 through 921 Processing helix chain 'A' and resid 927 through 932 Processing helix chain 'A' and resid 940 through 962 removed outlier: 4.379A pdb=" N ARG A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 989 Processing helix chain 'A' and resid 1013 through 1027 Processing helix chain 'A' and resid 1030 through 1043 Processing helix chain 'A' and resid 1054 through 1066 Processing helix chain 'A' and resid 1067 through 1075 Processing helix chain 'A' and resid 1099 through 1101 No H-bonds generated for 'chain 'A' and resid 1099 through 1101' Processing helix chain 'A' and resid 1104 through 1113 removed outlier: 4.079A pdb=" N ARG A1108 " --> pdb=" O ALA A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1134 removed outlier: 3.778A pdb=" N ASP A1126 " --> pdb=" O GLN A1122 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG A1127 " --> pdb=" O ALA A1123 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A1128 " --> pdb=" O ASN A1124 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN A1129 " --> pdb=" O ILE A1125 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP A1130 " --> pdb=" O ASP A1126 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A1131 " --> pdb=" O ARG A1127 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A1133 " --> pdb=" O ASN A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1141 removed outlier: 3.969A pdb=" N THR A1141 " --> pdb=" O GLY A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1170 removed outlier: 3.631A pdb=" N ILE A1151 " --> pdb=" O ARG A1147 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS A1152 " --> pdb=" O ASP A1148 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A1155 " --> pdb=" O ILE A1151 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N MET A1170 " --> pdb=" O HIS A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1184 Processing helix chain 'A' and resid 1193 through 1199 removed outlier: 3.590A pdb=" N ILE A1197 " --> pdb=" O ASP A1193 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 309 through 311 removed outlier: 6.324A pdb=" N VAL B 309 " --> pdb=" O PHE B 351 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LEU B 353 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASP B 311 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N VAL B 388 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLY B 352 " --> pdb=" O VAL B 388 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 502 through 507 removed outlier: 6.980A pdb=" N TYR B 502 " --> pdb=" O LYS B 549 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ASN B 551 " --> pdb=" O TYR B 502 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA B 504 " --> pdb=" O ASN B 551 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N PHE B 553 " --> pdb=" O ALA B 504 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL B 506 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA B 555 " --> pdb=" O VAL B 506 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N THR B 602 " --> pdb=" O LEU B 587 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR B 583 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS B 608 " --> pdb=" O PHE B 581 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N PHE B 581 " --> pdb=" O LYS B 608 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 679 through 680 removed outlier: 3.678A pdb=" N ALA B 788 " --> pdb=" O VAL B 680 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 693 through 694 Processing sheet with id=AA5, first strand: chain 'B' and resid 1001 through 1003 Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 310 removed outlier: 3.551A pdb=" N VAL A 506 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL A 505 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL A 557 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ALA A 507 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 9.932A pdb=" N MET A 559 " --> pdb=" O ALA A 507 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA A 604 " --> pdb=" O HIS A 586 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N HIS A 586 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL A 606 " --> pdb=" O MET A 584 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N MET A 584 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LYS A 608 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE A 582 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 618 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A 619 " --> pdb=" O PHE A 641 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 679 through 680 Processing sheet with id=AA8, first strand: chain 'A' and resid 733 through 735 Processing sheet with id=AA9, first strand: chain 'A' and resid 1001 through 1003 941 hydrogen bonds defined for protein. 2703 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6973 1.34 - 1.46: 4300 1.46 - 1.58: 10077 1.58 - 1.69: 0 1.69 - 1.81: 163 Bond restraints: 21513 Sorted by residual: bond pdb=" C2 SAM B1302 " pdb=" N3 SAM B1302 " ideal model delta sigma weight residual 1.322 1.378 -0.056 2.00e-02 2.50e+03 7.93e+00 bond pdb=" C8 SAM B1302 " pdb=" N7 SAM B1302 " ideal model delta sigma weight residual 1.298 1.351 -0.053 2.00e-02 2.50e+03 6.93e+00 bond pdb=" C2 SAM B1302 " pdb=" N1 SAM B1302 " ideal model delta sigma weight residual 1.329 1.378 -0.049 2.00e-02 2.50e+03 6.03e+00 bond pdb=" C6 SAM B1302 " pdb=" N1 SAM B1302 " ideal model delta sigma weight residual 1.337 1.377 -0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" C SAM B1302 " pdb=" OXT SAM B1302 " ideal model delta sigma weight residual 1.256 1.230 0.026 2.00e-02 2.50e+03 1.71e+00 ... (remaining 21508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 28803 1.75 - 3.49: 246 3.49 - 5.24: 35 5.24 - 6.98: 14 6.98 - 8.73: 4 Bond angle restraints: 29102 Sorted by residual: angle pdb=" C LYS B 725 " pdb=" N TRP B 726 " pdb=" CA TRP B 726 " ideal model delta sigma weight residual 121.54 130.27 -8.73 1.91e+00 2.74e-01 2.09e+01 angle pdb=" CA TYR B 86 " pdb=" CB TYR B 86 " pdb=" CG TYR B 86 " ideal model delta sigma weight residual 113.90 119.33 -5.43 1.80e+00 3.09e-01 9.11e+00 angle pdb=" O SAM B1302 " pdb=" C SAM B1302 " pdb=" OXT SAM B1302 " ideal model delta sigma weight residual 126.77 118.07 8.70 3.00e+00 1.11e-01 8.41e+00 angle pdb=" N VAL B 260 " pdb=" CA VAL B 260 " pdb=" C VAL B 260 " ideal model delta sigma weight residual 111.67 109.06 2.61 9.50e-01 1.11e+00 7.56e+00 angle pdb=" N1 SAM B1302 " pdb=" C2 SAM B1302 " pdb=" N3 SAM B1302 " ideal model delta sigma weight residual 128.51 120.28 8.23 3.00e+00 1.11e-01 7.53e+00 ... (remaining 29097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 12297 17.77 - 35.53: 560 35.53 - 53.30: 75 53.30 - 71.06: 5 71.06 - 88.83: 3 Dihedral angle restraints: 12940 sinusoidal: 5316 harmonic: 7624 Sorted by residual: dihedral pdb=" CB LYS B1144 " pdb=" CG LYS B1144 " pdb=" CD LYS B1144 " pdb=" CE LYS B1144 " ideal model delta sinusoidal sigma weight residual 180.00 121.72 58.28 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA ARG B 71 " pdb=" CB ARG B 71 " pdb=" CG ARG B 71 " pdb=" CD ARG B 71 " ideal model delta sinusoidal sigma weight residual -180.00 -126.69 -53.31 3 1.50e+01 4.44e-03 9.19e+00 dihedral pdb=" N MET D 40 " pdb=" CA MET D 40 " pdb=" CB MET D 40 " pdb=" CG MET D 40 " ideal model delta sinusoidal sigma weight residual -60.00 -112.92 52.92 3 1.50e+01 4.44e-03 9.16e+00 ... (remaining 12937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2057 0.031 - 0.063: 780 0.063 - 0.094: 187 0.094 - 0.125: 95 0.125 - 0.157: 10 Chirality restraints: 3129 Sorted by residual: chirality pdb=" C2' SAM B1302 " pdb=" C1' SAM B1302 " pdb=" C3' SAM B1302 " pdb=" O2' SAM B1302 " both_signs ideal model delta sigma weight residual False -2.76 -2.60 -0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" CA TYR B 86 " pdb=" N TYR B 86 " pdb=" C TYR B 86 " pdb=" CB TYR B 86 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" C1' SAM B1302 " pdb=" C2' SAM B1302 " pdb=" N9 SAM B1302 " pdb=" O4' SAM B1302 " both_signs ideal model delta sigma weight residual False 2.30 2.44 -0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 3126 not shown) Planarity restraints: 3789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 203 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.45e+00 pdb=" N PRO B 204 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 204 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 204 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A1144 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C LYS A1144 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS A1144 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG A1145 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 57 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO B 58 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 58 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 58 " -0.020 5.00e-02 4.00e+02 ... (remaining 3786 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 126 2.54 - 3.13: 16202 3.13 - 3.72: 31365 3.72 - 4.31: 41703 4.31 - 4.90: 71540 Nonbonded interactions: 160936 Sorted by model distance: nonbonded pdb=" OD2 ASP A 999 " pdb="MG MG A1301 " model vdw 1.950 2.170 nonbonded pdb=" OD2 ASP B 999 " pdb="MG MG B1301 " model vdw 1.968 2.170 nonbonded pdb=" OD1 ASP A 999 " pdb="MG MG A1301 " model vdw 1.985 2.170 nonbonded pdb=" OD1 ASP B 999 " pdb="MG MG B1301 " model vdw 2.017 2.170 nonbonded pdb=" OD2 ASP A 997 " pdb="MG MG A1301 " model vdw 2.055 2.170 ... (remaining 160931 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 1 through 1124 or (resid 1125 and (name N or name CA or na \ me C or name O or name CB )) or resid 1126 through 1204 or (resid 1205 and (name \ N or name CA or name C or name O or name CB or name CG1 or name CG2 or name CD1 \ )) or resid 1301)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.490 Find NCS groups from input model: 0.220 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:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.003 0.056 21513 Z= 0.125 Angle : 0.471 8.726 29102 Z= 0.249 Chirality : 0.038 0.157 3129 Planarity : 0.003 0.046 3789 Dihedral : 9.799 88.831 8026 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.71 % Allowed : 5.12 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.17), residues: 2584 helix: 1.85 (0.15), residues: 1249 sheet: 0.03 (0.47), residues: 139 loop : -1.43 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 931 TYR 0.025 0.001 TYR B 86 PHE 0.013 0.001 PHE B1021 TRP 0.014 0.001 TRP B 862 HIS 0.003 0.001 HIS B 945 Details of bonding type rmsd covalent geometry : bond 0.00273 (21513) covalent geometry : angle 0.47135 (29102) hydrogen bonds : bond 0.16298 ( 941) hydrogen bonds : angle 5.26103 ( 2703) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 MET cc_start: 0.8440 (mpp) cc_final: 0.8210 (mtt) REVERT: B 337 ARG cc_start: 0.7784 (mmm160) cc_final: 0.7525 (ttt-90) REVERT: A 766 VAL cc_start: 0.7678 (OUTLIER) cc_final: 0.7408 (m) REVERT: A 904 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7651 (mm) outliers start: 16 outliers final: 7 residues processed: 163 average time/residue: 0.7201 time to fit residues: 130.4839 Evaluate side-chains 110 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 904 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 918 ASN D 44 ASN A 457 GLN A 554 ASN A 556 GLN A 633 ASN A1183 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.083854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.056298 restraints weight = 84332.986| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.96 r_work: 0.2942 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21513 Z= 0.181 Angle : 0.553 7.908 29102 Z= 0.290 Chirality : 0.040 0.153 3129 Planarity : 0.004 0.092 3789 Dihedral : 5.054 53.366 2889 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.51 % Allowed : 8.14 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.17), residues: 2584 helix: 1.82 (0.15), residues: 1287 sheet: -0.20 (0.47), residues: 132 loop : -1.55 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 339 TYR 0.024 0.001 TYR B 86 PHE 0.016 0.001 PHE B 864 TRP 0.015 0.001 TRP B 862 HIS 0.004 0.001 HIS B 125 Details of bonding type rmsd covalent geometry : bond 0.00434 (21513) covalent geometry : angle 0.55284 (29102) hydrogen bonds : bond 0.05565 ( 941) hydrogen bonds : angle 4.20260 ( 2703) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 401 TRP cc_start: 0.7234 (p90) cc_final: 0.6616 (p-90) REVERT: B 517 MET cc_start: 0.8077 (mtt) cc_final: 0.7849 (mtt) REVERT: B 1005 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7455 (mtm) REVERT: C 18 MET cc_start: 0.8379 (mtt) cc_final: 0.8075 (mtt) REVERT: C 22 ASN cc_start: 0.8626 (m-40) cc_final: 0.8277 (m110) REVERT: D 24 ARG cc_start: 0.7255 (tpp80) cc_final: 0.6559 (tpt-90) REVERT: A 638 MET cc_start: 0.5530 (ptp) cc_final: 0.5067 (pmm) REVERT: A 659 TYR cc_start: 0.7140 (OUTLIER) cc_final: 0.6259 (p90) REVERT: A 666 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.8951 (tp) REVERT: A 755 MET cc_start: 0.8217 (mmm) cc_final: 0.7974 (mmm) REVERT: A 773 MET cc_start: 0.8855 (ttt) cc_final: 0.8525 (ttm) REVERT: A 904 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7273 (mp) outliers start: 34 outliers final: 11 residues processed: 130 average time/residue: 0.6134 time to fit residues: 90.4936 Evaluate side-chains 114 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain B residue 1072 MET Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 904 ILE Chi-restraints excluded: chain A residue 1072 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 252 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 173 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.083393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.056088 restraints weight = 84489.050| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 4.14 r_work: 0.2908 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21513 Z= 0.182 Angle : 0.535 7.425 29102 Z= 0.283 Chirality : 0.040 0.153 3129 Planarity : 0.004 0.050 3789 Dihedral : 5.062 53.194 2886 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.56 % Allowed : 9.70 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.17), residues: 2584 helix: 1.79 (0.15), residues: 1285 sheet: -0.51 (0.46), residues: 132 loop : -1.65 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1127 TYR 0.023 0.001 TYR B 86 PHE 0.015 0.001 PHE B 864 TRP 0.015 0.001 TRP B 862 HIS 0.004 0.001 HIS A 945 Details of bonding type rmsd covalent geometry : bond 0.00438 (21513) covalent geometry : angle 0.53476 (29102) hydrogen bonds : bond 0.05613 ( 941) hydrogen bonds : angle 4.05662 ( 2703) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 401 TRP cc_start: 0.7387 (p90) cc_final: 0.6658 (p-90) REVERT: B 517 MET cc_start: 0.8088 (mtt) cc_final: 0.7859 (mtt) REVERT: B 934 GLN cc_start: 0.8924 (tt0) cc_final: 0.8703 (tp-100) REVERT: C 18 MET cc_start: 0.8486 (mtt) cc_final: 0.8139 (mtt) REVERT: C 22 ASN cc_start: 0.8724 (m-40) cc_final: 0.8342 (m110) REVERT: A 110 MET cc_start: 0.0762 (tpt) cc_final: 0.0544 (tpp) REVERT: A 638 MET cc_start: 0.5409 (ptp) cc_final: 0.5131 (pmm) REVERT: A 659 TYR cc_start: 0.7227 (OUTLIER) cc_final: 0.6269 (p90) REVERT: A 666 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.8953 (tp) REVERT: A 755 MET cc_start: 0.8260 (mmm) cc_final: 0.7990 (mmm) REVERT: A 773 MET cc_start: 0.8899 (ttt) cc_final: 0.8474 (ttm) outliers start: 35 outliers final: 13 residues processed: 127 average time/residue: 0.7861 time to fit residues: 112.7264 Evaluate side-chains 112 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 999 ASP Chi-restraints excluded: chain B residue 1072 MET Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 666 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 227 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 154 optimal weight: 30.0000 chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 156 optimal weight: 30.0000 chunk 106 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 217 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.082948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.055509 restraints weight = 84752.617| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 4.17 r_work: 0.2890 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 21513 Z= 0.210 Angle : 0.554 7.899 29102 Z= 0.293 Chirality : 0.041 0.157 3129 Planarity : 0.004 0.086 3789 Dihedral : 5.148 51.409 2882 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.51 % Allowed : 10.46 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.17), residues: 2584 helix: 1.75 (0.15), residues: 1285 sheet: -0.59 (0.45), residues: 128 loop : -1.72 (0.17), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 339 TYR 0.023 0.002 TYR B 86 PHE 0.017 0.001 PHE B 864 TRP 0.032 0.001 TRP A 216 HIS 0.005 0.001 HIS A 945 Details of bonding type rmsd covalent geometry : bond 0.00507 (21513) covalent geometry : angle 0.55432 (29102) hydrogen bonds : bond 0.05855 ( 941) hydrogen bonds : angle 4.05702 ( 2703) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 934 GLN cc_start: 0.8910 (tt0) cc_final: 0.8710 (tp-100) REVERT: B 1005 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7342 (mtm) REVERT: C 18 MET cc_start: 0.8464 (mtt) cc_final: 0.8157 (mtt) REVERT: C 22 ASN cc_start: 0.8719 (m-40) cc_final: 0.8366 (m110) REVERT: A 110 MET cc_start: 0.0836 (tpt) cc_final: 0.0575 (tpp) REVERT: A 638 MET cc_start: 0.5412 (ptp) cc_final: 0.4972 (pmm) REVERT: A 659 TYR cc_start: 0.7202 (OUTLIER) cc_final: 0.6305 (p90) REVERT: A 666 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.8960 (tp) REVERT: A 755 MET cc_start: 0.8346 (mmm) cc_final: 0.8050 (mmm) REVERT: A 766 VAL cc_start: 0.7160 (OUTLIER) cc_final: 0.6883 (m) REVERT: A 773 MET cc_start: 0.8895 (ttt) cc_final: 0.8588 (ttm) outliers start: 34 outliers final: 13 residues processed: 125 average time/residue: 0.7428 time to fit residues: 104.9049 Evaluate side-chains 115 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 999 ASP Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain B residue 1072 MET Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 1072 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 183 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 chunk 72 optimal weight: 0.2980 chunk 78 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 23 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 173 optimal weight: 30.0000 chunk 186 optimal weight: 20.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.083798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.056627 restraints weight = 84404.252| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 4.13 r_work: 0.2929 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21513 Z= 0.114 Angle : 0.506 9.310 29102 Z= 0.264 Chirality : 0.038 0.160 3129 Planarity : 0.003 0.050 3789 Dihedral : 4.951 52.760 2882 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.42 % Allowed : 10.64 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.17), residues: 2584 helix: 1.85 (0.15), residues: 1288 sheet: -0.37 (0.49), residues: 113 loop : -1.67 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1127 TYR 0.026 0.001 TYR C 112 PHE 0.012 0.001 PHE B 77 TRP 0.013 0.001 TRP B 862 HIS 0.003 0.000 HIS B1166 Details of bonding type rmsd covalent geometry : bond 0.00256 (21513) covalent geometry : angle 0.50644 (29102) hydrogen bonds : bond 0.04595 ( 941) hydrogen bonds : angle 3.88335 ( 2703) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 401 TRP cc_start: 0.7358 (p90) cc_final: 0.6823 (p-90) REVERT: B 517 MET cc_start: 0.8112 (mtt) cc_final: 0.7864 (mtt) REVERT: B 934 GLN cc_start: 0.8903 (tt0) cc_final: 0.8685 (tp-100) REVERT: B 1005 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7367 (mtm) REVERT: C 18 MET cc_start: 0.8460 (mtt) cc_final: 0.8127 (mtt) REVERT: C 22 ASN cc_start: 0.8681 (m-40) cc_final: 0.8267 (m110) REVERT: D 40 MET cc_start: 0.7995 (tpt) cc_final: 0.7525 (ttm) REVERT: A 1 MET cc_start: 0.7412 (tpt) cc_final: 0.7183 (tpt) REVERT: A 110 MET cc_start: 0.0858 (tpt) cc_final: 0.0628 (tpp) REVERT: A 232 LYS cc_start: 0.8633 (tptt) cc_final: 0.8396 (pptt) REVERT: A 277 MET cc_start: 0.4619 (mmt) cc_final: 0.4183 (mmm) REVERT: A 638 MET cc_start: 0.5343 (ptp) cc_final: 0.4928 (pmm) REVERT: A 659 TYR cc_start: 0.7133 (OUTLIER) cc_final: 0.6234 (p90) REVERT: A 666 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.8940 (tp) REVERT: A 755 MET cc_start: 0.8313 (mmm) cc_final: 0.8002 (mmm) REVERT: A 773 MET cc_start: 0.8859 (ttt) cc_final: 0.8552 (ttm) REVERT: A 829 VAL cc_start: 0.7565 (OUTLIER) cc_final: 0.7034 (m) REVERT: A 999 ASP cc_start: 0.7136 (OUTLIER) cc_final: 0.5973 (p0) outliers start: 32 outliers final: 12 residues processed: 122 average time/residue: 0.6240 time to fit residues: 87.0147 Evaluate side-chains 113 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 999 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 117 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 243 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 169 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 208 optimal weight: 0.5980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.083775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.056609 restraints weight = 84252.132| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 4.11 r_work: 0.2933 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21513 Z= 0.115 Angle : 0.504 11.620 29102 Z= 0.261 Chirality : 0.038 0.136 3129 Planarity : 0.003 0.042 3789 Dihedral : 4.805 54.167 2882 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.56 % Allowed : 10.73 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.17), residues: 2584 helix: 1.88 (0.15), residues: 1288 sheet: -0.44 (0.47), residues: 124 loop : -1.62 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 24 TYR 0.022 0.001 TYR B 86 PHE 0.015 0.001 PHE A 77 TRP 0.012 0.001 TRP B 862 HIS 0.003 0.001 HIS A 945 Details of bonding type rmsd covalent geometry : bond 0.00264 (21513) covalent geometry : angle 0.50408 (29102) hydrogen bonds : bond 0.04394 ( 941) hydrogen bonds : angle 3.79025 ( 2703) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 401 TRP cc_start: 0.7311 (p90) cc_final: 0.6732 (p-90) REVERT: B 517 MET cc_start: 0.8061 (mtt) cc_final: 0.7857 (mtp) REVERT: B 934 GLN cc_start: 0.8895 (tt0) cc_final: 0.8654 (tp-100) REVERT: B 1005 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7362 (mtm) REVERT: C 18 MET cc_start: 0.8514 (mtt) cc_final: 0.8170 (mtt) REVERT: C 22 ASN cc_start: 0.8685 (m-40) cc_final: 0.8279 (m110) REVERT: D 40 MET cc_start: 0.7835 (tpt) cc_final: 0.7609 (tmm) REVERT: A 1 MET cc_start: 0.7410 (tpt) cc_final: 0.7172 (tpt) REVERT: A 277 MET cc_start: 0.5024 (mmt) cc_final: 0.4620 (mmm) REVERT: A 587 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7182 (tm) REVERT: A 638 MET cc_start: 0.5301 (ptp) cc_final: 0.5055 (pmm) REVERT: A 659 TYR cc_start: 0.7022 (OUTLIER) cc_final: 0.6194 (p90) REVERT: A 666 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.8957 (tp) REVERT: A 755 MET cc_start: 0.8323 (mmm) cc_final: 0.8003 (mmm) REVERT: A 766 VAL cc_start: 0.7200 (OUTLIER) cc_final: 0.6935 (m) REVERT: A 773 MET cc_start: 0.8846 (ttt) cc_final: 0.8390 (ttm) REVERT: A 829 VAL cc_start: 0.7563 (OUTLIER) cc_final: 0.7035 (m) outliers start: 35 outliers final: 14 residues processed: 124 average time/residue: 0.7091 time to fit residues: 99.2204 Evaluate side-chains 116 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain B residue 1174 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 829 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 66 optimal weight: 1.9990 chunk 218 optimal weight: 10.0000 chunk 257 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 184 optimal weight: 20.0000 chunk 135 optimal weight: 6.9990 chunk 154 optimal weight: 30.0000 chunk 49 optimal weight: 6.9990 chunk 30 optimal weight: 0.0040 chunk 11 optimal weight: 2.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.083106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.055674 restraints weight = 84439.027| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 4.06 r_work: 0.2918 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21513 Z= 0.158 Angle : 0.524 10.529 29102 Z= 0.273 Chirality : 0.039 0.147 3129 Planarity : 0.003 0.045 3789 Dihedral : 4.929 52.668 2882 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.42 % Allowed : 11.30 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.17), residues: 2584 helix: 1.83 (0.15), residues: 1288 sheet: -0.52 (0.46), residues: 128 loop : -1.65 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B1127 TYR 0.023 0.001 TYR B 86 PHE 0.015 0.001 PHE B 864 TRP 0.013 0.001 TRP B 862 HIS 0.004 0.001 HIS A 945 Details of bonding type rmsd covalent geometry : bond 0.00379 (21513) covalent geometry : angle 0.52448 (29102) hydrogen bonds : bond 0.05056 ( 941) hydrogen bonds : angle 3.85446 ( 2703) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 401 TRP cc_start: 0.7305 (p90) cc_final: 0.6623 (p-90) REVERT: B 1005 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7364 (mtm) REVERT: C 18 MET cc_start: 0.8494 (mtt) cc_final: 0.8194 (mtt) REVERT: C 22 ASN cc_start: 0.8697 (m-40) cc_final: 0.8314 (m110) REVERT: D 40 MET cc_start: 0.7747 (tpt) cc_final: 0.7387 (tmm) REVERT: A 1 MET cc_start: 0.7432 (tpt) cc_final: 0.7193 (tpt) REVERT: A 110 MET cc_start: 0.0893 (tpt) cc_final: 0.0674 (tpp) REVERT: A 277 MET cc_start: 0.5079 (mmt) cc_final: 0.4765 (mmm) REVERT: A 512 MET cc_start: 0.7101 (ptm) cc_final: 0.5539 (tmm) REVERT: A 587 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7118 (tm) REVERT: A 638 MET cc_start: 0.5361 (ptp) cc_final: 0.5112 (pmm) REVERT: A 659 TYR cc_start: 0.7015 (OUTLIER) cc_final: 0.6218 (p90) REVERT: A 666 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.8956 (tp) REVERT: A 755 MET cc_start: 0.8362 (mmm) cc_final: 0.8046 (mmm) REVERT: A 766 VAL cc_start: 0.7227 (OUTLIER) cc_final: 0.6969 (m) REVERT: A 773 MET cc_start: 0.8842 (ttt) cc_final: 0.8523 (ttm) REVERT: A 829 VAL cc_start: 0.7585 (OUTLIER) cc_final: 0.7058 (m) outliers start: 32 outliers final: 15 residues processed: 121 average time/residue: 0.6224 time to fit residues: 85.9237 Evaluate side-chains 116 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 829 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 228 optimal weight: 6.9990 chunk 23 optimal weight: 0.0970 chunk 188 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 226 optimal weight: 2.9990 chunk 230 optimal weight: 0.6980 chunk 165 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 199 optimal weight: 0.8980 overall best weight: 1.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 934 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.083868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.056729 restraints weight = 84228.033| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 4.09 r_work: 0.2951 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 21513 Z= 0.106 Angle : 0.499 11.295 29102 Z= 0.257 Chirality : 0.038 0.136 3129 Planarity : 0.003 0.041 3789 Dihedral : 4.767 53.977 2882 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.11 % Allowed : 11.75 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.17), residues: 2584 helix: 1.89 (0.15), residues: 1290 sheet: -0.42 (0.47), residues: 124 loop : -1.59 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 24 TYR 0.021 0.001 TYR B 86 PHE 0.013 0.001 PHE A 77 TRP 0.012 0.001 TRP B 862 HIS 0.003 0.001 HIS B1166 Details of bonding type rmsd covalent geometry : bond 0.00238 (21513) covalent geometry : angle 0.49891 (29102) hydrogen bonds : bond 0.04128 ( 941) hydrogen bonds : angle 3.72938 ( 2703) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1005 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7352 (mtm) REVERT: C 18 MET cc_start: 0.8491 (mtt) cc_final: 0.8167 (mtt) REVERT: C 22 ASN cc_start: 0.8677 (m-40) cc_final: 0.8262 (m110) REVERT: D 40 MET cc_start: 0.7664 (tpt) cc_final: 0.7314 (tmm) REVERT: A 1 MET cc_start: 0.7419 (tpt) cc_final: 0.7171 (tpt) REVERT: A 110 MET cc_start: 0.0942 (tpt) cc_final: 0.0726 (tpp) REVERT: A 277 MET cc_start: 0.5169 (mmt) cc_final: 0.4832 (mmm) REVERT: A 512 MET cc_start: 0.6868 (ptm) cc_final: 0.5775 (tmm) REVERT: A 587 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7077 (tm) REVERT: A 659 TYR cc_start: 0.6978 (OUTLIER) cc_final: 0.6186 (p90) REVERT: A 666 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.8954 (tp) REVERT: A 755 MET cc_start: 0.8342 (mmm) cc_final: 0.8031 (mmm) REVERT: A 766 VAL cc_start: 0.7192 (OUTLIER) cc_final: 0.6929 (m) REVERT: A 773 MET cc_start: 0.8838 (ttt) cc_final: 0.8532 (ttm) REVERT: A 829 VAL cc_start: 0.7535 (OUTLIER) cc_final: 0.7005 (m) outliers start: 25 outliers final: 11 residues processed: 120 average time/residue: 0.6328 time to fit residues: 86.0165 Evaluate side-chains 115 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 1005 MET Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 829 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 123 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 13 optimal weight: 0.0770 chunk 159 optimal weight: 10.0000 chunk 11 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 235 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 934 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.084293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.057289 restraints weight = 84226.089| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 4.12 r_work: 0.2961 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 21513 Z= 0.096 Angle : 0.493 12.022 29102 Z= 0.252 Chirality : 0.037 0.130 3129 Planarity : 0.003 0.069 3789 Dihedral : 4.614 56.001 2882 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.07 % Allowed : 12.06 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.17), residues: 2584 helix: 1.96 (0.15), residues: 1282 sheet: -0.37 (0.48), residues: 124 loop : -1.53 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B1127 TYR 0.022 0.001 TYR B 86 PHE 0.011 0.001 PHE B 77 TRP 0.015 0.001 TRP B 401 HIS 0.003 0.000 HIS B1166 Details of bonding type rmsd covalent geometry : bond 0.00211 (21513) covalent geometry : angle 0.49334 (29102) hydrogen bonds : bond 0.03739 ( 941) hydrogen bonds : angle 3.67479 ( 2703) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 MET cc_start: 0.8467 (mtt) cc_final: 0.8130 (mtt) REVERT: C 22 ASN cc_start: 0.8672 (m-40) cc_final: 0.8257 (m110) REVERT: D 40 MET cc_start: 0.7677 (tpt) cc_final: 0.7365 (ttm) REVERT: A 1 MET cc_start: 0.7423 (tpt) cc_final: 0.7171 (tpt) REVERT: A 110 MET cc_start: 0.0937 (tpt) cc_final: 0.0670 (tpp) REVERT: A 277 MET cc_start: 0.5249 (mmt) cc_final: 0.4908 (mmm) REVERT: A 512 MET cc_start: 0.6761 (ptm) cc_final: 0.5800 (tmm) REVERT: A 587 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7044 (tm) REVERT: A 638 MET cc_start: 0.5701 (pmm) cc_final: 0.5236 (pmm) REVERT: A 659 TYR cc_start: 0.6935 (OUTLIER) cc_final: 0.6125 (p90) REVERT: A 755 MET cc_start: 0.8325 (mmm) cc_final: 0.8015 (mmm) REVERT: A 766 VAL cc_start: 0.7223 (OUTLIER) cc_final: 0.6966 (m) REVERT: A 773 MET cc_start: 0.8839 (ttt) cc_final: 0.8389 (ttm) REVERT: A 829 VAL cc_start: 0.7565 (OUTLIER) cc_final: 0.7033 (m) outliers start: 24 outliers final: 13 residues processed: 122 average time/residue: 0.5762 time to fit residues: 79.8695 Evaluate side-chains 115 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 829 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 112 optimal weight: 2.9990 chunk 19 optimal weight: 0.0170 chunk 80 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 239 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 223 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 934 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.084224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.057208 restraints weight = 84534.858| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 4.13 r_work: 0.2956 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 21513 Z= 0.103 Angle : 0.509 12.445 29102 Z= 0.259 Chirality : 0.038 0.162 3129 Planarity : 0.003 0.063 3789 Dihedral : 4.573 56.636 2882 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.89 % Allowed : 12.51 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.17), residues: 2584 helix: 1.98 (0.15), residues: 1281 sheet: -0.32 (0.49), residues: 124 loop : -1.53 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 339 TYR 0.022 0.001 TYR B 86 PHE 0.012 0.001 PHE A 17 TRP 0.011 0.001 TRP B 862 HIS 0.003 0.000 HIS B1166 Details of bonding type rmsd covalent geometry : bond 0.00235 (21513) covalent geometry : angle 0.50877 (29102) hydrogen bonds : bond 0.03831 ( 941) hydrogen bonds : angle 3.69078 ( 2703) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 401 TRP cc_start: 0.7273 (p90) cc_final: 0.6763 (p-90) REVERT: B 517 MET cc_start: 0.7593 (mtp) cc_final: 0.7360 (ttt) REVERT: C 18 MET cc_start: 0.8471 (mtt) cc_final: 0.8148 (mtt) REVERT: C 22 ASN cc_start: 0.8667 (m-40) cc_final: 0.8260 (m110) REVERT: A 1 MET cc_start: 0.7448 (tpt) cc_final: 0.7206 (tpt) REVERT: A 110 MET cc_start: 0.0961 (tpt) cc_final: 0.0699 (tpp) REVERT: A 277 MET cc_start: 0.5219 (mmt) cc_final: 0.4913 (mmm) REVERT: A 512 MET cc_start: 0.6942 (ptm) cc_final: 0.6050 (tmm) REVERT: A 559 MET cc_start: 0.4341 (pmm) cc_final: 0.4055 (pmm) REVERT: A 587 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7013 (tm) REVERT: A 638 MET cc_start: 0.5833 (pmm) cc_final: 0.5450 (ptp) REVERT: A 659 TYR cc_start: 0.6882 (OUTLIER) cc_final: 0.6056 (p90) REVERT: A 755 MET cc_start: 0.8336 (mmm) cc_final: 0.8003 (mmm) REVERT: A 766 VAL cc_start: 0.7266 (OUTLIER) cc_final: 0.7009 (m) REVERT: A 773 MET cc_start: 0.8830 (ttt) cc_final: 0.8538 (ttm) REVERT: A 829 VAL cc_start: 0.7571 (OUTLIER) cc_final: 0.7041 (m) outliers start: 20 outliers final: 12 residues processed: 115 average time/residue: 0.6044 time to fit residues: 79.0223 Evaluate side-chains 114 residues out of total 2248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 659 TYR Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 829 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 206 optimal weight: 7.9990 chunk 166 optimal weight: 10.0000 chunk 63 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 178 optimal weight: 20.0000 chunk 242 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 157 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 934 GLN B1131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.083968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.056926 restraints weight = 84652.126| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 4.10 r_work: 0.2946 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21513 Z= 0.116 Angle : 0.524 13.889 29102 Z= 0.266 Chirality : 0.038 0.153 3129 Planarity : 0.003 0.074 3789 Dihedral : 4.603 56.695 2882 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.89 % Allowed : 12.82 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.17), residues: 2584 helix: 1.96 (0.15), residues: 1281 sheet: -0.33 (0.48), residues: 124 loop : -1.55 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG B1127 TYR 0.022 0.001 TYR B 86 PHE 0.012 0.001 PHE A 17 TRP 0.011 0.001 TRP B 862 HIS 0.003 0.000 HIS A 945 Details of bonding type rmsd covalent geometry : bond 0.00270 (21513) covalent geometry : angle 0.52425 (29102) hydrogen bonds : bond 0.04094 ( 941) hydrogen bonds : angle 3.71622 ( 2703) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7883.87 seconds wall clock time: 134 minutes 37.14 seconds (8077.14 seconds total)