Starting phenix.real_space_refine on Sat Feb 17 07:31:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5t_26358/02_2024/7u5t_26358.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5t_26358/02_2024/7u5t_26358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5t_26358/02_2024/7u5t_26358.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5t_26358/02_2024/7u5t_26358.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5t_26358/02_2024/7u5t_26358.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5t_26358/02_2024/7u5t_26358.pdb" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8874 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5803 2.51 5 N 1534 2.21 5 O 1708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 47": "NH1" <-> "NH2" Residue "A ASP 57": "OD1" <-> "OD2" Residue "A ASP 143": "OD1" <-> "OD2" Residue "A ASP 173": "OD1" <-> "OD2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A ASP 224": "OD1" <-> "OD2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A ASP 324": "OD1" <-> "OD2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ASP 388": "OD1" <-> "OD2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A GLU 784": "OE1" <-> "OE2" Residue "A ASP 787": "OD1" <-> "OD2" Residue "A ASP 795": "OD1" <-> "OD2" Residue "A ASP 813": "OD1" <-> "OD2" Residue "A ASP 814": "OD1" <-> "OD2" Residue "A GLU 858": "OE1" <-> "OE2" Residue "A GLU 863": "OE1" <-> "OE2" Residue "B ARG 47": "NH1" <-> "NH2" Residue "B ASP 57": "OD1" <-> "OD2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 224": "OD1" <-> "OD2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B ARG 241": "NH1" <-> "NH2" Residue "B ARG 257": "NH1" <-> "NH2" Residue "B GLU 277": "OE1" <-> "OE2" Residue "B ASP 324": "OD1" <-> "OD2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B ASP 388": "OD1" <-> "OD2" Residue "B GLU 389": "OE1" <-> "OE2" Residue "B GLU 401": "OE1" <-> "OE2" Residue "B PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 677": "OD1" <-> "OD2" Residue "B GLU 712": "OE1" <-> "OE2" Residue "B ASP 716": "OD1" <-> "OD2" Residue "B GLU 746": "OE1" <-> "OE2" Residue "B GLU 751": "OE1" <-> "OE2" Residue "B GLU 756": "OE1" <-> "OE2" Residue "B PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 777": "OD1" <-> "OD2" Residue "B ASP 780": "OD1" <-> "OD2" Residue "B ASP 796": "OD1" <-> "OD2" Residue "B GLU 840": "OE1" <-> "OE2" Residue "B ASP 842": "OD1" <-> "OD2" Residue "B GLU 845": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9093 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4529 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 33, 'TRANS': 558} Chain breaks: 4 Chain: "B" Number of atoms: 4564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4564 Classifications: {'peptide': 598} Link IDs: {'PTRANS': 34, 'TRANS': 563} Chain breaks: 3 Time building chain proxies: 5.61, per 1000 atoms: 0.62 Number of scatterers: 9093 At special positions: 0 Unit cell: (91.2135, 134.946, 149.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1708 8.00 N 1534 7.00 C 5803 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 - 3.50 Amino acid : False - 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: 3.65 Conformation dependent library (CDL) restraints added in 2.0 seconds 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2212 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 14 sheets defined 50.1% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 removed outlier: 3.648A pdb=" N VAL A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 26 " --> pdb=" O ASP A 22 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 47 removed outlier: 3.634A pdb=" N ARG A 47 " --> pdb=" O ASN A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 44 through 47' Processing helix chain 'A' and resid 48 through 66 removed outlier: 5.544A pdb=" N GLU A 64 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 84 through 99 removed outlier: 3.537A pdb=" N LYS A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 removed outlier: 4.047A pdb=" N GLY A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 137 through 143 removed outlier: 3.589A pdb=" N VAL A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 179 removed outlier: 3.906A pdb=" N GLU A 178 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR A 179 " --> pdb=" O PHE A 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 175 through 179' Processing helix chain 'A' and resid 181 through 199 removed outlier: 3.506A pdb=" N ILE A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 210 removed outlier: 3.617A pdb=" N ARG A 206 " --> pdb=" O GLU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 219 removed outlier: 4.819A pdb=" N VAL A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 249 removed outlier: 3.593A pdb=" N VAL A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 261 Processing helix chain 'A' and resid 265 through 272 removed outlier: 3.655A pdb=" N ALA A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 298 removed outlier: 4.492A pdb=" N ILE A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 removed outlier: 3.730A pdb=" N VAL A 306 " --> pdb=" O PRO A 302 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N CYS A 312 " --> pdb=" O ARG A 308 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.614A pdb=" N LYS A 329 " --> pdb=" O LYS A 325 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 338 removed outlier: 4.126A pdb=" N HIS A 336 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR A 337 " --> pdb=" O LYS A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 removed outlier: 3.712A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 381 through 386 removed outlier: 3.895A pdb=" N VAL A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 381 through 386' Processing helix chain 'A' and resid 662 through 671 Processing helix chain 'A' and resid 688 through 690 No H-bonds generated for 'chain 'A' and resid 688 through 690' Processing helix chain 'A' and resid 691 through 696 removed outlier: 3.647A pdb=" N ASP A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 696 " --> pdb=" O PHE A 692 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 691 through 696' Processing helix chain 'A' and resid 735 through 745 removed outlier: 3.597A pdb=" N VAL A 742 " --> pdb=" O THR A 738 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 745 " --> pdb=" O VAL A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 776 removed outlier: 3.554A pdb=" N ALA A 770 " --> pdb=" O ASN A 766 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 779 No H-bonds generated for 'chain 'A' and resid 777 through 779' Processing helix chain 'A' and resid 814 through 825 removed outlier: 3.809A pdb=" N ALA A 818 " --> pdb=" O ASP A 814 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 822 " --> pdb=" O ALA A 818 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 823 " --> pdb=" O MET A 819 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 824 " --> pdb=" O SER A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 828 No H-bonds generated for 'chain 'A' and resid 826 through 828' Processing helix chain 'A' and resid 836 through 841 removed outlier: 3.897A pdb=" N THR A 840 " --> pdb=" O ARG A 837 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 841 " --> pdb=" O SER A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 853 removed outlier: 3.526A pdb=" N LEU A 851 " --> pdb=" O TRP A 847 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS A 852 " --> pdb=" O TRP A 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 32 removed outlier: 3.728A pdb=" N VAL B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG B 26 " --> pdb=" O ASP B 22 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 29 " --> pdb=" O VAL B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 47 removed outlier: 3.555A pdb=" N ARG B 47 " --> pdb=" O ASN B 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 44 through 47' Processing helix chain 'B' and resid 48 through 66 removed outlier: 5.556A pdb=" N GLU B 64 " --> pdb=" O THR B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.591A pdb=" N ASN B 82 " --> pdb=" O GLY B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 95 removed outlier: 3.567A pdb=" N LYS B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 removed outlier: 3.532A pdb=" N MET B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 137 through 143 Processing helix chain 'B' and resid 175 through 179 removed outlier: 3.917A pdb=" N GLU B 178 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR B 179 " --> pdb=" O PHE B 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 175 through 179' Processing helix chain 'B' and resid 182 through 199 removed outlier: 3.910A pdb=" N GLY B 188 " --> pdb=" O GLN B 184 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 210 removed outlier: 3.611A pdb=" N ARG B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN B 209 " --> pdb=" O THR B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 removed outlier: 4.583A pdb=" N VAL B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.539A pdb=" N VAL B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 249 removed outlier: 3.584A pdb=" N SER B 239 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 245 " --> pdb=" O ARG B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 261 removed outlier: 3.701A pdb=" N LEU B 260 " --> pdb=" O ARG B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 280 through 298 removed outlier: 4.516A pdb=" N ILE B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU B 293 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 315 removed outlier: 3.688A pdb=" N VAL B 306 " --> pdb=" O PRO B 302 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS B 312 " --> pdb=" O ARG B 308 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 332 Processing helix chain 'B' and resid 333 through 338 removed outlier: 4.278A pdb=" N HIS B 336 " --> pdb=" O PRO B 333 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR B 337 " --> pdb=" O LYS B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 347 removed outlier: 3.680A pdb=" N LYS B 345 " --> pdb=" O ASP B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 381 through 386 removed outlier: 3.744A pdb=" N VAL B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 381 through 386' Processing helix chain 'B' and resid 644 through 654 Processing helix chain 'B' and resid 669 through 672 removed outlier: 3.618A pdb=" N ALA B 672 " --> pdb=" O GLN B 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 669 through 672' Processing helix chain 'B' and resid 673 through 679 removed outlier: 3.610A pdb=" N ASP B 677 " --> pdb=" O LYS B 673 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 673 through 679' Processing helix chain 'B' and resid 718 through 724 removed outlier: 3.698A pdb=" N VAL B 724 " --> pdb=" O THR B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 757 Processing helix chain 'B' and resid 758 through 760 No H-bonds generated for 'chain 'B' and resid 758 through 760' Processing helix chain 'B' and resid 785 through 790 removed outlier: 3.547A pdb=" N GLY B 790 " --> pdb=" O ILE B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 807 removed outlier: 3.549A pdb=" N SER B 804 " --> pdb=" O ALA B 800 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 805 " --> pdb=" O MET B 801 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 806 " --> pdb=" O SER B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 810 No H-bonds generated for 'chain 'B' and resid 808 through 810' Processing helix chain 'B' and resid 818 through 823 removed outlier: 3.751A pdb=" N THR B 821 " --> pdb=" O GLU B 818 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR B 822 " --> pdb=" O ARG B 819 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY B 823 " --> pdb=" O SER B 820 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 818 through 823' Processing helix chain 'B' and resid 828 through 835 removed outlier: 3.514A pdb=" N LEU B 833 " --> pdb=" O TRP B 829 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS B 834 " --> pdb=" O TRP B 830 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.163A pdb=" N GLU A 4 " --> pdb=" O HIS A 15 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS A 15 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 6 " --> pdb=" O THR A 13 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A 13 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N VAL A 170 " --> pdb=" O LYS A 11 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR A 13 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N CYS A 172 " --> pdb=" O THR A 13 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS A 15 " --> pdb=" O CYS A 172 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A 131 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N PHE A 171 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLN A 133 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP A 173 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE A 106 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL A 134 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA A 108 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR A 36 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU A 107 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 38 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 109 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N VAL A 40 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR A 37 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N TYR A 74 " --> pdb=" O TYR A 37 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE A 39 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL A 76 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR A 41 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 360 Processing sheet with id=AA4, first strand: chain 'A' and resid 363 through 365 removed outlier: 7.144A pdb=" N LYS A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 809 through 810 removed outlier: 7.195A pdb=" N VAL A 809 " --> pdb=" O LEU A 835 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 402 removed outlier: 3.600A pdb=" N VAL A 713 " --> pdb=" O CYS A 676 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 752 through 755 removed outlier: 3.508A pdb=" N ILE A 789 " --> pdb=" O ILE A 754 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.485A pdb=" N GLU B 4 " --> pdb=" O HIS B 15 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N HIS B 15 " --> pdb=" O GLU B 4 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL B 6 " --> pdb=" O THR B 13 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N VAL B 170 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR B 13 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N CYS B 172 " --> pdb=" O THR B 13 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N HIS B 15 " --> pdb=" O CYS B 172 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL B 131 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N PHE B 171 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN B 133 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASP B 173 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE B 106 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL B 134 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA B 108 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR B 36 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU B 107 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL B 38 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 109 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL B 40 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N TYR B 37 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N TYR B 74 " --> pdb=" O TYR B 37 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE B 39 " --> pdb=" O TYR B 74 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL B 76 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR B 41 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 149 through 151 Processing sheet with id=AB1, first strand: chain 'B' and resid 359 through 360 Processing sheet with id=AB2, first strand: chain 'B' and resid 363 through 365 removed outlier: 7.150A pdb=" N LYS B 368 " --> pdb=" O GLU B 364 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 814 through 816 removed outlier: 3.542A pdb=" N VAL B 390 " --> pdb=" O ILE B 816 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 401 through 403 removed outlier: 3.501A pdb=" N CYS B 658 " --> pdb=" O VAL B 695 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 695 " --> pdb=" O CYS B 658 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 708 through 710 removed outlier: 6.643A pdb=" N VAL B 709 " --> pdb=" O THR B 737 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 771 " --> pdb=" O ILE B 736 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN B 765 " --> pdb=" O GLU B 772 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 825 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: 2.95 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1522 1.31 - 1.44: 2191 1.44 - 1.56: 5476 1.56 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 9263 Sorted by residual: bond pdb=" N GLU A 730 " pdb=" CA GLU A 730 " ideal model delta sigma weight residual 1.463 1.491 -0.027 6.90e-03 2.10e+04 1.59e+01 bond pdb=" N TYR B 646 " pdb=" CA TYR B 646 " ideal model delta sigma weight residual 1.463 1.489 -0.026 6.90e-03 2.10e+04 1.42e+01 bond pdb=" C LYS B 680 " pdb=" N PRO B 681 " ideal model delta sigma weight residual 1.335 1.381 -0.046 1.28e-02 6.10e+03 1.30e+01 bond pdb=" N ILE A 794 " pdb=" CA ILE A 794 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.15e-02 7.56e+03 1.09e+01 bond pdb=" N ILE B 776 " pdb=" CA ILE B 776 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.11e-02 8.12e+03 1.06e+01 ... (remaining 9258 not shown) Histogram of bond angle deviations from ideal: 98.78 - 105.81: 256 105.81 - 112.85: 5035 112.85 - 119.89: 3256 119.89 - 126.92: 3912 126.92 - 133.96: 103 Bond angle restraints: 12562 Sorted by residual: angle pdb=" N ASN A 61 " pdb=" CA ASN A 61 " pdb=" C ASN A 61 " ideal model delta sigma weight residual 113.18 105.08 8.10 1.33e+00 5.65e-01 3.71e+01 angle pdb=" C ILE A 757 " pdb=" N ALA A 758 " pdb=" CA ALA A 758 " ideal model delta sigma weight residual 122.11 113.10 9.01 1.64e+00 3.72e-01 3.02e+01 angle pdb=" N PRO B 705 " pdb=" CA PRO B 705 " pdb=" C PRO B 705 " ideal model delta sigma weight residual 110.50 118.93 -8.43 1.57e+00 4.06e-01 2.88e+01 angle pdb=" CA ILE A 757 " pdb=" C ILE A 757 " pdb=" O ILE A 757 " ideal model delta sigma weight residual 122.63 117.99 4.64 8.70e-01 1.32e+00 2.84e+01 angle pdb=" C GLU A 830 " pdb=" N PRO A 831 " pdb=" CA PRO A 831 " ideal model delta sigma weight residual 119.93 125.20 -5.27 1.07e+00 8.73e-01 2.42e+01 ... (remaining 12557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.81: 5091 15.81 - 31.62: 433 31.62 - 47.43: 88 47.43 - 63.24: 23 63.24 - 79.05: 9 Dihedral angle restraints: 5644 sinusoidal: 2227 harmonic: 3417 Sorted by residual: dihedral pdb=" CA LEU A 274 " pdb=" C LEU A 274 " pdb=" N THR A 275 " pdb=" CA THR A 275 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA LEU B 274 " pdb=" C LEU B 274 " pdb=" N THR B 275 " pdb=" CA THR B 275 " ideal model delta harmonic sigma weight residual 180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PRO A 717 " pdb=" C PRO A 717 " pdb=" N ARG A 718 " pdb=" CA ARG A 718 " ideal model delta harmonic sigma weight residual -180.00 -157.91 -22.09 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 5641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1183 0.077 - 0.153: 274 0.153 - 0.230: 34 0.230 - 0.306: 7 0.306 - 0.383: 1 Chirality restraints: 1499 Sorted by residual: chirality pdb=" CB ILE B 403 " pdb=" CA ILE B 403 " pdb=" CG1 ILE B 403 " pdb=" CG2 ILE B 403 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CA ILE A 757 " pdb=" N ILE A 757 " pdb=" C ILE A 757 " pdb=" CB ILE A 757 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA VAL A 832 " pdb=" N VAL A 832 " pdb=" C VAL A 832 " pdb=" CB VAL A 832 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 1496 not shown) Planarity restraints: 1590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 704 " -0.019 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C LYS B 704 " 0.063 2.00e-02 2.50e+03 pdb=" O LYS B 704 " -0.023 2.00e-02 2.50e+03 pdb=" N PRO B 705 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 727 " -0.016 2.00e-02 2.50e+03 3.14e-02 9.83e+00 pdb=" C VAL A 727 " 0.054 2.00e-02 2.50e+03 pdb=" O VAL A 727 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP A 728 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 154 " 0.045 5.00e-02 4.00e+02 6.86e-02 7.54e+00 pdb=" N PRO B 155 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 155 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 155 " 0.038 5.00e-02 4.00e+02 ... (remaining 1587 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2387 2.80 - 3.33: 8350 3.33 - 3.85: 15283 3.85 - 4.38: 18731 4.38 - 4.90: 30689 Nonbonded interactions: 75440 Sorted by model distance: nonbonded pdb=" O MET A 45 " pdb=" OG1 THR A 48 " model vdw 2.280 2.440 nonbonded pdb=" O SER A 838 " pdb=" OG SER A 838 " model vdw 2.291 2.440 nonbonded pdb=" O MET B 45 " pdb=" OG1 THR B 48 " model vdw 2.309 2.440 nonbonded pdb=" OD1 ASP B 710 " pdb=" OG1 THR B 737 " model vdw 2.316 2.440 nonbonded pdb=" O SER B 2 " pdb=" OG SER B 2 " model vdw 2.324 2.440 ... (remaining 75435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 2 through 249 or resid 256 through 662 or resid 667 throug \ h 846)) } 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: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 13.890 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 28.980 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 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 : 0.008 0.059 9263 Z= 0.551 Angle : 1.089 9.158 12562 Z= 0.695 Chirality : 0.065 0.383 1499 Planarity : 0.007 0.069 1590 Dihedral : 13.049 79.052 3432 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.10 % Allowed : 5.22 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.95 (0.17), residues: 1172 helix: -4.59 (0.10), residues: 552 sheet: -2.99 (0.36), residues: 130 loop : -3.20 (0.22), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 848 HIS 0.005 0.001 HIS B 774 PHE 0.023 0.003 PHE B 327 TYR 0.020 0.002 TYR B 646 ARG 0.007 0.001 ARG B 749 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 296 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ILE cc_start: 0.7795 (mm) cc_final: 0.7251 (mm) REVERT: A 161 ILE cc_start: 0.8730 (mm) cc_final: 0.8502 (mm) REVERT: A 794 ILE cc_start: 0.7026 (mm) cc_final: 0.6644 (tt) outliers start: 1 outliers final: 1 residues processed: 296 average time/residue: 0.2453 time to fit residues: 95.8676 Evaluate side-chains 137 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 729 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 82 ASN A 393 HIS A 706 GLN ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 376 GLN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 688 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 9263 Z= 0.299 Angle : 0.705 8.150 12562 Z= 0.366 Chirality : 0.047 0.163 1499 Planarity : 0.006 0.060 1590 Dihedral : 5.435 36.110 1252 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.05 % Allowed : 13.88 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.21), residues: 1172 helix: -3.17 (0.16), residues: 541 sheet: -2.17 (0.43), residues: 112 loop : -2.00 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 829 HIS 0.003 0.001 HIS B 280 PHE 0.021 0.002 PHE B 327 TYR 0.022 0.002 TYR A 370 ARG 0.007 0.001 ARG B 743 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 175 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ASP cc_start: 0.7626 (m-30) cc_final: 0.7250 (m-30) REVERT: A 189 MET cc_start: 0.7013 (tpt) cc_final: 0.6783 (mmm) REVERT: A 232 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7349 (mt) REVERT: A 381 ASP cc_start: 0.6201 (p0) cc_final: 0.5987 (p0) REVERT: A 771 MET cc_start: 0.6184 (mmm) cc_final: 0.5936 (mmm) REVERT: B 173 ASP cc_start: 0.7124 (t0) cc_final: 0.6884 (t0) REVERT: B 366 ILE cc_start: 0.8837 (mt) cc_final: 0.8588 (mm) outliers start: 31 outliers final: 16 residues processed: 196 average time/residue: 0.2011 time to fit residues: 56.0632 Evaluate side-chains 142 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 860 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 703 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 0.0980 chunk 89 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 107 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 95 optimal weight: 0.1980 chunk 106 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 HIS B 31 ASN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9263 Z= 0.186 Angle : 0.594 10.362 12562 Z= 0.301 Chirality : 0.044 0.169 1499 Planarity : 0.005 0.051 1590 Dihedral : 4.831 38.271 1252 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.15 % Allowed : 16.73 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.23), residues: 1172 helix: -2.17 (0.19), residues: 542 sheet: -1.63 (0.42), residues: 127 loop : -1.73 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 847 HIS 0.003 0.001 HIS A 815 PHE 0.019 0.002 PHE B 327 TYR 0.018 0.002 TYR A 337 ARG 0.002 0.000 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ASP cc_start: 0.7581 (m-30) cc_final: 0.7219 (m-30) REVERT: A 232 LEU cc_start: 0.7814 (mm) cc_final: 0.7360 (mt) REVERT: A 381 ASP cc_start: 0.6057 (p0) cc_final: 0.5682 (p0) REVERT: A 707 THR cc_start: 0.3359 (OUTLIER) cc_final: 0.3138 (m) REVERT: A 767 ARG cc_start: 0.7377 (mmt90) cc_final: 0.6909 (mpt-90) outliers start: 32 outliers final: 24 residues processed: 161 average time/residue: 0.1668 time to fit residues: 40.1940 Evaluate side-chains 145 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 653 MET Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 831 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 114 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.5738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 9263 Z= 0.274 Angle : 0.635 10.873 12562 Z= 0.322 Chirality : 0.046 0.181 1499 Planarity : 0.005 0.053 1590 Dihedral : 4.851 34.280 1252 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.63 % Allowed : 16.73 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.24), residues: 1172 helix: -1.78 (0.20), residues: 549 sheet: -1.58 (0.40), residues: 153 loop : -1.53 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 830 HIS 0.005 0.001 HIS B 797 PHE 0.016 0.002 PHE A 692 TYR 0.014 0.002 TYR A 370 ARG 0.004 0.001 ARG B 749 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 148 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8176 (mm) cc_final: 0.7690 (mt) REVERT: A 259 LEU cc_start: 0.9000 (mp) cc_final: 0.8581 (tt) REVERT: A 344 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7419 (tt) REVERT: A 707 THR cc_start: 0.3487 (OUTLIER) cc_final: 0.3276 (m) REVERT: A 767 ARG cc_start: 0.7542 (mmt90) cc_final: 0.7158 (mmt180) REVERT: B 18 TYR cc_start: 0.6019 (t80) cc_final: 0.5663 (t80) REVERT: B 189 MET cc_start: 0.8029 (tpp) cc_final: 0.7741 (tpp) REVERT: B 328 LEU cc_start: 0.5931 (OUTLIER) cc_final: 0.5697 (mm) REVERT: B 344 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8004 (mp) outliers start: 47 outliers final: 31 residues processed: 181 average time/residue: 0.1695 time to fit residues: 45.6388 Evaluate side-chains 151 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 116 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 849 ASP Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 820 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.6263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9263 Z= 0.240 Angle : 0.606 9.665 12562 Z= 0.306 Chirality : 0.045 0.178 1499 Planarity : 0.005 0.054 1590 Dihedral : 4.692 34.964 1252 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.13 % Allowed : 19.39 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.24), residues: 1172 helix: -1.42 (0.21), residues: 541 sheet: -1.17 (0.44), residues: 143 loop : -1.49 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 829 HIS 0.004 0.001 HIS A 15 PHE 0.014 0.001 PHE B 327 TYR 0.014 0.002 TYR B 51 ARG 0.002 0.000 ARG B 798 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 136 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7865 (mt) REVERT: A 259 LEU cc_start: 0.9010 (mp) cc_final: 0.8516 (tt) REVERT: A 344 LEU cc_start: 0.7637 (mp) cc_final: 0.7378 (tt) REVERT: A 707 THR cc_start: 0.3277 (OUTLIER) cc_final: 0.3062 (m) REVERT: B 95 LEU cc_start: 0.8938 (mt) cc_final: 0.8506 (mt) REVERT: B 116 ASP cc_start: 0.7739 (t0) cc_final: 0.7110 (t0) REVERT: B 189 MET cc_start: 0.8009 (tpp) cc_final: 0.7637 (tpp) REVERT: B 291 GLU cc_start: 0.8249 (mm-30) cc_final: 0.8026 (mm-30) REVERT: B 328 LEU cc_start: 0.5798 (OUTLIER) cc_final: 0.5491 (mm) outliers start: 42 outliers final: 27 residues processed: 163 average time/residue: 0.1703 time to fit residues: 41.1379 Evaluate side-chains 147 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 858 GLU Chi-restraints excluded: chain A residue 860 ASP Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain B residue 820 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.0570 chunk 102 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 59 optimal weight: 4.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.7146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 9263 Z= 0.351 Angle : 0.691 10.528 12562 Z= 0.351 Chirality : 0.048 0.216 1499 Planarity : 0.005 0.060 1590 Dihedral : 5.056 30.567 1252 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.82 % Allowed : 19.19 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.24), residues: 1172 helix: -1.44 (0.22), residues: 540 sheet: -1.27 (0.44), residues: 140 loop : -1.65 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 844 HIS 0.005 0.001 HIS A 23 PHE 0.027 0.002 PHE A 692 TYR 0.017 0.002 TYR B 51 ARG 0.003 0.001 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 133 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6190 (tp30) cc_final: 0.5917 (tm-30) REVERT: A 259 LEU cc_start: 0.9012 (mp) cc_final: 0.8532 (tt) REVERT: A 344 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7215 (tt) REVERT: A 707 THR cc_start: 0.3559 (OUTLIER) cc_final: 0.3350 (m) REVERT: A 745 VAL cc_start: 0.7991 (m) cc_final: 0.7711 (p) REVERT: A 767 ARG cc_start: 0.7756 (mmt90) cc_final: 0.7109 (mpt-90) REVERT: B 18 TYR cc_start: 0.6269 (t80) cc_final: 0.5954 (t80) REVERT: B 116 ASP cc_start: 0.7935 (t0) cc_final: 0.7243 (t0) REVERT: B 189 MET cc_start: 0.8170 (tpp) cc_final: 0.7687 (tpp) REVERT: B 328 LEU cc_start: 0.5614 (OUTLIER) cc_final: 0.5190 (mm) REVERT: B 344 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7992 (mt) REVERT: B 403 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7456 (mp) outliers start: 49 outliers final: 29 residues processed: 167 average time/residue: 0.1663 time to fit residues: 42.3683 Evaluate side-chains 155 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 121 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 849 ASP Chi-restraints excluded: chain A residue 860 ASP Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 718 PHE Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 818 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 63 optimal weight: 0.0040 chunk 113 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 HIS B 23 HIS ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.7351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9263 Z= 0.206 Angle : 0.584 9.038 12562 Z= 0.291 Chirality : 0.044 0.192 1499 Planarity : 0.005 0.059 1590 Dihedral : 4.469 18.370 1249 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.74 % Allowed : 20.28 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.25), residues: 1172 helix: -1.11 (0.22), residues: 537 sheet: -1.07 (0.43), residues: 153 loop : -1.42 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 830 HIS 0.003 0.001 HIS B 23 PHE 0.014 0.002 PHE A 384 TYR 0.022 0.002 TYR A 297 ARG 0.002 0.000 ARG B 798 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8100 (mt) REVERT: A 259 LEU cc_start: 0.8980 (mp) cc_final: 0.8548 (tt) REVERT: A 344 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7082 (tt) REVERT: A 697 LEU cc_start: 0.8106 (mt) cc_final: 0.7788 (tt) REVERT: A 707 THR cc_start: 0.3468 (OUTLIER) cc_final: 0.3266 (m) REVERT: A 745 VAL cc_start: 0.7988 (m) cc_final: 0.7782 (p) REVERT: B 18 TYR cc_start: 0.6314 (t80) cc_final: 0.6111 (t80) REVERT: B 116 ASP cc_start: 0.7851 (t0) cc_final: 0.7124 (t0) REVERT: B 189 MET cc_start: 0.7957 (tpp) cc_final: 0.7571 (tpp) REVERT: B 328 LEU cc_start: 0.5518 (OUTLIER) cc_final: 0.5161 (mm) REVERT: B 344 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7833 (mp) outliers start: 38 outliers final: 24 residues processed: 163 average time/residue: 0.1656 time to fit residues: 40.9030 Evaluate side-chains 150 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 121 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 860 ASP Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 818 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 72 optimal weight: 0.0870 chunk 77 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.7558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9263 Z= 0.210 Angle : 0.600 8.922 12562 Z= 0.298 Chirality : 0.044 0.200 1499 Planarity : 0.005 0.053 1590 Dihedral : 4.376 18.671 1249 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.25 % Allowed : 21.56 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.25), residues: 1172 helix: -0.92 (0.23), residues: 534 sheet: -0.81 (0.44), residues: 143 loop : -1.33 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 830 HIS 0.004 0.000 HIS B 23 PHE 0.028 0.002 PHE A 692 TYR 0.031 0.002 TYR B 844 ARG 0.002 0.000 ARG A 761 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 128 time to evaluate : 1.077 Fit side-chains revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7956 (mt) REVERT: A 259 LEU cc_start: 0.8967 (mp) cc_final: 0.8587 (tt) REVERT: A 344 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7002 (tt) REVERT: A 697 LEU cc_start: 0.8294 (mt) cc_final: 0.7988 (mt) REVERT: B 95 LEU cc_start: 0.8845 (mt) cc_final: 0.8435 (mt) REVERT: B 116 ASP cc_start: 0.7888 (t0) cc_final: 0.7187 (t0) REVERT: B 185 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.7173 (t80) REVERT: B 189 MET cc_start: 0.7886 (tpp) cc_final: 0.7498 (tpp) REVERT: B 328 LEU cc_start: 0.5721 (OUTLIER) cc_final: 0.5365 (mm) REVERT: B 344 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7835 (mp) REVERT: B 403 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7372 (mp) outliers start: 33 outliers final: 23 residues processed: 153 average time/residue: 0.1557 time to fit residues: 36.6729 Evaluate side-chains 148 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 860 ASP Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 818 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.1980 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 63 optimal weight: 0.0040 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 100 optimal weight: 0.0050 chunk 69 optimal weight: 0.9990 chunk 112 optimal weight: 0.2980 overall best weight: 0.2406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.7686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 9263 Z= 0.173 Angle : 0.602 9.621 12562 Z= 0.297 Chirality : 0.044 0.196 1499 Planarity : 0.005 0.052 1590 Dihedral : 4.171 17.950 1249 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.85 % Allowed : 21.95 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.25), residues: 1172 helix: -0.78 (0.23), residues: 529 sheet: -0.60 (0.45), residues: 143 loop : -1.14 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 847 HIS 0.003 0.000 HIS B 23 PHE 0.018 0.001 PHE B 803 TYR 0.023 0.001 TYR B 51 ARG 0.004 0.000 ARG A 767 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 135 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 SER cc_start: 0.8298 (OUTLIER) cc_final: 0.7993 (m) REVERT: A 232 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7805 (mt) REVERT: A 259 LEU cc_start: 0.8979 (mp) cc_final: 0.8546 (tt) REVERT: A 344 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6917 (tt) REVERT: A 697 LEU cc_start: 0.8194 (mt) cc_final: 0.7794 (mt) REVERT: B 95 LEU cc_start: 0.8774 (mt) cc_final: 0.8359 (mt) REVERT: B 116 ASP cc_start: 0.7778 (t0) cc_final: 0.7071 (t0) REVERT: B 189 MET cc_start: 0.7746 (tpp) cc_final: 0.7409 (tpp) REVERT: B 208 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7152 (mm-30) REVERT: B 328 LEU cc_start: 0.5768 (OUTLIER) cc_final: 0.5486 (mm) REVERT: B 344 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7782 (mp) outliers start: 29 outliers final: 18 residues processed: 158 average time/residue: 0.1619 time to fit residues: 40.1890 Evaluate side-chains 146 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 860 ASP Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 720 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.7932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 9263 Z= 0.258 Angle : 0.649 10.392 12562 Z= 0.318 Chirality : 0.046 0.183 1499 Planarity : 0.005 0.051 1590 Dihedral : 4.387 26.307 1249 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.56 % Allowed : 22.44 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.25), residues: 1172 helix: -0.79 (0.23), residues: 522 sheet: -0.56 (0.46), residues: 133 loop : -1.10 (0.29), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 830 HIS 0.005 0.001 HIS B 23 PHE 0.025 0.002 PHE A 692 TYR 0.026 0.002 TYR B 51 ARG 0.003 0.000 ARG A 767 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: A 211 SER cc_start: 0.8416 (OUTLIER) cc_final: 0.8055 (m) REVERT: A 232 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7983 (mt) REVERT: A 259 LEU cc_start: 0.9002 (mp) cc_final: 0.8559 (tt) REVERT: B 95 LEU cc_start: 0.8888 (mt) cc_final: 0.8485 (mt) REVERT: B 116 ASP cc_start: 0.8054 (t0) cc_final: 0.7311 (t0) REVERT: B 328 LEU cc_start: 0.5700 (OUTLIER) cc_final: 0.5352 (mm) REVERT: B 344 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7909 (mp) REVERT: B 403 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7310 (mp) outliers start: 26 outliers final: 19 residues processed: 145 average time/residue: 0.1525 time to fit residues: 34.6266 Evaluate side-chains 143 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 860 ASP Chi-restraints excluded: chain B residue 185 PHE Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 720 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 82 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.144976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.121345 restraints weight = 16391.476| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.61 r_work: 0.3698 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.8085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 9263 Z= 0.222 Angle : 0.641 13.355 12562 Z= 0.314 Chirality : 0.045 0.205 1499 Planarity : 0.005 0.053 1590 Dihedral : 4.340 30.179 1249 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.36 % Allowed : 23.13 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.25), residues: 1172 helix: -0.73 (0.23), residues: 521 sheet: -0.53 (0.47), residues: 133 loop : -1.09 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 830 HIS 0.004 0.001 HIS B 23 PHE 0.012 0.001 PHE B 327 TYR 0.031 0.002 TYR B 51 ARG 0.003 0.000 ARG A 767 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2164.99 seconds wall clock time: 40 minutes 10.08 seconds (2410.08 seconds total)