Starting phenix.real_space_refine on Tue Aug 6 11:20:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5t_26358/08_2024/7u5t_26358.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5t_26358/08_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_26358/08_2024/7u5t_26358.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5t_26358/08_2024/7u5t_26358.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5t_26358/08_2024/7u5t_26358.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5t_26358/08_2024/7u5t_26358.cif" } 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 6.43, per 1000 atoms: 0.71 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: 3.61 Conformation dependent library (CDL) restraints added in 1.7 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: 1.27 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: 3.13 Time building geometry restraints manager: 3.92 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 3.040 nonbonded pdb=" O SER A 838 " pdb=" OG SER A 838 " model vdw 2.291 3.040 nonbonded pdb=" O MET B 45 " pdb=" OG1 THR B 48 " model vdw 2.309 3.040 nonbonded pdb=" OD1 ASP B 710 " pdb=" OG1 THR B 737 " model vdw 2.316 3.040 nonbonded pdb=" O SER B 2 " pdb=" OG SER B 2 " model vdw 2.324 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 5.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.620 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.750 ------------------------------------------------------------------------------- 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 : 1.063 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: 0.2500 time to fit residues: 98.4101 Evaluate side-chains 137 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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: 0.0980 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 35 optimal weight: 0.0270 chunk 56 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 393 HIS A 706 GLN ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 98 GLN B 376 GLN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9263 Z= 0.243 Angle : 0.680 7.048 12562 Z= 0.352 Chirality : 0.046 0.189 1499 Planarity : 0.006 0.057 1590 Dihedral : 5.400 38.494 1252 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.85 % Allowed : 13.39 % Favored : 83.76 % 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: -4.07 (0.21), residues: 1172 helix: -3.15 (0.16), residues: 541 sheet: -2.04 (0.42), residues: 110 loop : -2.16 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 829 HIS 0.003 0.001 HIS B 280 PHE 0.020 0.002 PHE B 327 TYR 0.021 0.002 TYR A 370 ARG 0.006 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 193 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 164 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ASP cc_start: 0.7402 (m-30) cc_final: 0.7041 (m-30) REVERT: A 232 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7241 (mt) REVERT: A 381 ASP cc_start: 0.5975 (p0) cc_final: 0.5735 (p0) REVERT: A 707 THR cc_start: 0.3513 (OUTLIER) cc_final: 0.3285 (m) REVERT: A 771 MET cc_start: 0.6481 (mmm) cc_final: 0.6274 (mmm) REVERT: A 774 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.5835 (mp0) REVERT: B 173 ASP cc_start: 0.6853 (t0) cc_final: 0.6651 (t0) REVERT: B 189 MET cc_start: 0.7573 (tpp) cc_final: 0.7359 (tpp) REVERT: B 210 PHE cc_start: 0.6935 (t80) cc_final: 0.6713 (t80) REVERT: B 366 ILE cc_start: 0.8684 (mt) cc_final: 0.8338 (mm) REVERT: B 736 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6645 (mt) outliers start: 29 outliers final: 12 residues processed: 181 average time/residue: 0.1942 time to fit residues: 49.5869 Evaluate side-chains 140 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 72 LEU 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 388 ASP Chi-restraints excluded: chain A residue 707 THR 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 774 GLU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 736 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.6989 > 50: distance: 14 - 190: 21.661 distance: 24 - 178: 23.285 distance: 27 - 175: 10.485 distance: 134 - 136: 7.761 distance: 136 - 137: 15.689 distance: 137 - 138: 4.135 distance: 137 - 140: 24.862 distance: 138 - 139: 5.733 distance: 138 - 144: 11.048 distance: 140 - 141: 23.303 distance: 141 - 142: 20.359 distance: 141 - 143: 16.482 distance: 144 - 145: 13.411 distance: 145 - 146: 6.026 distance: 145 - 148: 10.765 distance: 146 - 147: 36.149 distance: 146 - 150: 9.605 distance: 148 - 149: 10.624 distance: 150 - 151: 20.573 distance: 151 - 152: 37.605 distance: 151 - 154: 18.004 distance: 152 - 153: 5.679 distance: 152 - 159: 57.927 distance: 154 - 155: 21.407 distance: 155 - 156: 53.052 distance: 156 - 157: 24.429 distance: 157 - 158: 56.286 distance: 159 - 160: 33.719 distance: 160 - 161: 15.432 distance: 160 - 163: 20.694 distance: 161 - 162: 37.258 distance: 161 - 168: 16.815 distance: 163 - 164: 34.080 distance: 164 - 165: 7.674 distance: 165 - 166: 19.009 distance: 165 - 167: 24.250 distance: 168 - 169: 34.579 distance: 168 - 174: 31.951 distance: 169 - 170: 15.055 distance: 169 - 172: 33.764 distance: 170 - 171: 17.154 distance: 170 - 175: 13.371 distance: 172 - 173: 19.599 distance: 173 - 174: 20.940 distance: 175 - 176: 18.444 distance: 176 - 177: 22.244 distance: 176 - 179: 20.543 distance: 177 - 178: 31.080 distance: 177 - 182: 9.811 distance: 179 - 180: 23.063 distance: 179 - 181: 20.057 distance: 182 - 183: 22.881 distance: 183 - 184: 13.957 distance: 183 - 186: 18.234 distance: 184 - 185: 7.781 distance: 184 - 190: 24.336 distance: 186 - 187: 14.468 distance: 187 - 189: 24.372 distance: 190 - 191: 22.945 distance: 191 - 192: 33.685 distance: 191 - 194: 27.131 distance: 192 - 193: 15.793 distance: 192 - 198: 25.224 distance: 194 - 195: 54.548 distance: 194 - 196: 37.241 distance: 195 - 197: 28.853 distance: 199 - 200: 5.160 distance: 199 - 202: 29.554 distance: 200 - 201: 3.299 distance: 200 - 206: 3.806 distance: 202 - 203: 14.747 distance: 203 - 204: 26.216 distance: 203 - 205: 33.690 distance: 207 - 208: 50.749 distance: 207 - 210: 36.006 distance: 208 - 209: 8.681 distance: 208 - 215: 31.177 distance: 210 - 211: 12.920 distance: 211 - 212: 15.949 distance: 212 - 214: 19.321