Starting phenix.real_space_refine on Mon Oct 14 18:15:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yf5_39211/10_2024/8yf5_39211.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yf5_39211/10_2024/8yf5_39211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yf5_39211/10_2024/8yf5_39211.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yf5_39211/10_2024/8yf5_39211.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yf5_39211/10_2024/8yf5_39211.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yf5_39211/10_2024/8yf5_39211.cif" } resolution = 3.78 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 11848 2.51 5 N 3142 2.21 5 O 3417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 18476 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5640 Classifications: {'peptide': 685} Link IDs: {'PTRANS': 45, 'TRANS': 639} Chain breaks: 4 Chain: "B" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3122 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain: "C" Number of atoms: 5536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5536 Classifications: {'peptide': 674} Link IDs: {'PTRANS': 43, 'TRANS': 630} Chain breaks: 5 Chain: "D" Number of atoms: 3114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3114 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 16, 'TRANS': 363} Chain: "E" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1064 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Time building chain proxies: 10.60, per 1000 atoms: 0.57 Number of scatterers: 18476 At special positions: 0 Unit cell: (152.388, 141.93, 125.496, 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 69 16.00 O 3417 8.00 N 3142 7.00 C 11848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.75 Conformation dependent library (CDL) restraints added in 2.4 seconds 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4298 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 14 sheets defined 50.2% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 removed outlier: 3.698A pdb=" N TRP A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.634A pdb=" N GLY A 31 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 72 through 92 removed outlier: 3.661A pdb=" N MET A 76 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 129 removed outlier: 3.624A pdb=" N MET A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN A 111 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N GLN A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 113 " --> pdb=" O LYS A 109 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER A 115 " --> pdb=" O ASN A 111 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 164 through 185 removed outlier: 3.670A pdb=" N HIS A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP A 172 " --> pdb=" O HIS A 168 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 189 removed outlier: 3.589A pdb=" N SER A 189 " --> pdb=" O PRO A 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 186 through 189' Processing helix chain 'A' and resid 203 through 217 removed outlier: 3.782A pdb=" N ILE A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 244 removed outlier: 3.801A pdb=" N THR A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N HIS A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 removed outlier: 4.121A pdb=" N ASP A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 302 Processing helix chain 'A' and resid 312 through 327 removed outlier: 3.887A pdb=" N ASP A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 356 Processing helix chain 'A' and resid 370 through 407 removed outlier: 3.565A pdb=" N ARG A 376 " --> pdb=" O PRO A 372 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 384 " --> pdb=" O GLU A 380 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASP A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TYR A 387 " --> pdb=" O LYS A 383 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A 391 " --> pdb=" O TYR A 387 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 392 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 removed outlier: 4.273A pdb=" N TYR A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU A 548 " --> pdb=" O LYS A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 581 Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 605 through 609 Processing helix chain 'A' and resid 620 through 629 Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.536A pdb=" N SER A 633 " --> pdb=" O PRO A 630 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER A 634 " --> pdb=" O ALA A 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 630 through 634' Processing helix chain 'A' and resid 641 through 647 removed outlier: 3.500A pdb=" N MET A 645 " --> pdb=" O PHE A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 656 Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 681 through 691 removed outlier: 3.613A pdb=" N LYS A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 691 " --> pdb=" O LYS A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 696 Processing helix chain 'A' and resid 697 through 704 Processing helix chain 'A' and resid 719 through 728 removed outlier: 3.810A pdb=" N LEU A 723 " --> pdb=" O HIS A 719 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 724 " --> pdb=" O TYR A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 819 Processing helix chain 'A' and resid 838 through 842 removed outlier: 3.540A pdb=" N TYR A 841 " --> pdb=" O PHE A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 864 Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.839A pdb=" N ILE B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'B' and resid 69 through 75 Processing helix chain 'B' and resid 76 through 91 Processing helix chain 'B' and resid 102 through 110 Processing helix chain 'B' and resid 135 through 148 Processing helix chain 'B' and resid 151 through 167 removed outlier: 3.547A pdb=" N ALA B 167 " --> pdb=" O PHE B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 177 through 183 Processing helix chain 'B' and resid 184 through 187 Processing helix chain 'B' and resid 225 through 229 removed outlier: 4.259A pdb=" N ARG B 229 " --> pdb=" O ASP B 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 225 through 229' Processing helix chain 'B' and resid 241 through 261 Processing helix chain 'B' and resid 288 through 295 Processing helix chain 'B' and resid 306 through 326 removed outlier: 3.815A pdb=" N VAL B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 363 Processing helix chain 'B' and resid 364 through 380 Processing helix chain 'C' and resid 6 through 14 Processing helix chain 'C' and resid 54 through 59 Processing helix chain 'C' and resid 72 through 92 removed outlier: 3.625A pdb=" N MET C 76 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 78 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 128 removed outlier: 3.852A pdb=" N ASN C 111 " --> pdb=" O ARG C 107 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN C 112 " --> pdb=" O ALA C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 161 removed outlier: 4.024A pdb=" N ALA C 159 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE C 160 " --> pdb=" O SER C 157 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR C 161 " --> pdb=" O ASN C 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 156 through 161' Processing helix chain 'C' and resid 164 through 184 removed outlier: 3.506A pdb=" N ASP C 172 " --> pdb=" O HIS C 168 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 189 removed outlier: 3.708A pdb=" N SER C 189 " --> pdb=" O PRO C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 218 removed outlier: 3.533A pdb=" N ARG C 216 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 218 " --> pdb=" O SER C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 243 removed outlier: 4.483A pdb=" N PHE C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 302 Processing helix chain 'C' and resid 312 through 327 removed outlier: 3.781A pdb=" N PHE C 325 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE C 326 " --> pdb=" O PHE C 322 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 342 Processing helix chain 'C' and resid 343 through 356 Processing helix chain 'C' and resid 357 through 359 No H-bonds generated for 'chain 'C' and resid 357 through 359' Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 381 through 383 No H-bonds generated for 'chain 'C' and resid 381 through 383' Processing helix chain 'C' and resid 384 through 406 removed outlier: 3.642A pdb=" N LEU C 400 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 552 removed outlier: 3.929A pdb=" N ARG C 545 " --> pdb=" O GLY C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 581 Processing helix chain 'C' and resid 599 through 603 removed outlier: 3.597A pdb=" N PHE C 603 " --> pdb=" O ALA C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 629 Processing helix chain 'C' and resid 638 through 647 removed outlier: 4.207A pdb=" N SER C 643 " --> pdb=" O ASP C 639 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU C 644 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET C 645 " --> pdb=" O PHE C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 656 Processing helix chain 'C' and resid 681 through 690 removed outlier: 3.524A pdb=" N ALA C 688 " --> pdb=" O ARG C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 703 Processing helix chain 'C' and resid 718 through 728 removed outlier: 4.448A pdb=" N THR C 722 " --> pdb=" O SER C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 819 removed outlier: 3.751A pdb=" N ILE C 817 " --> pdb=" O ASP C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 867 removed outlier: 3.629A pdb=" N ASP C 866 " --> pdb=" O GLN C 862 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU C 867 " --> pdb=" O ILE C 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 54 removed outlier: 3.955A pdb=" N ILE D 52 " --> pdb=" O PRO D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 65 Processing helix chain 'D' and resid 69 through 75 removed outlier: 3.587A pdb=" N LYS D 75 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 91 Processing helix chain 'D' and resid 102 through 111 Processing helix chain 'D' and resid 135 through 149 Processing helix chain 'D' and resid 150 through 167 removed outlier: 4.040A pdb=" N LYS D 154 " --> pdb=" O THR D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 183 Processing helix chain 'D' and resid 225 through 229 removed outlier: 4.143A pdb=" N ARG D 229 " --> pdb=" O ASP D 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 225 through 229' Processing helix chain 'D' and resid 241 through 263 Processing helix chain 'D' and resid 287 through 295 removed outlier: 4.523A pdb=" N LEU D 291 " --> pdb=" O ASN D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 326 removed outlier: 3.817A pdb=" N SER D 310 " --> pdb=" O ASN D 306 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 363 Processing helix chain 'D' and resid 364 through 380 removed outlier: 3.886A pdb=" N GLY D 379 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN D 380 " --> pdb=" O ASN D 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 14 removed outlier: 3.501A pdb=" N VAL E 8 " --> pdb=" O SER E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 32 removed outlier: 3.563A pdb=" N ILE E 22 " --> pdb=" O THR E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 50 Processing helix chain 'E' and resid 53 through 71 Processing helix chain 'E' and resid 73 through 82 removed outlier: 4.010A pdb=" N LEU E 77 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP E 78 " --> pdb=" O THR E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 92 Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 96 through 113 Processing helix chain 'E' and resid 117 through 128 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 6.551A pdb=" N ILE A 229 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N GLU A 253 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TYR A 51 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A 709 " --> pdb=" O PHE A 786 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA3, first strand: chain 'A' and resid 662 through 663 Processing sheet with id=AA4, first strand: chain 'A' and resid 759 through 760 Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 8 removed outlier: 3.844A pdb=" N VAL B 345 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 335 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE B 119 " --> pdb=" O TYR B 336 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE B 99 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N PHE B 134 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N TRP B 101 " --> pdb=" O PHE B 134 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE B 98 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N GLY B 211 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR B 100 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N ALA B 213 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR B 195 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN B 194 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ARG B 200 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLN B 23 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA7, first strand: chain 'B' and resid 216 through 217 removed outlier: 4.452A pdb=" N LYS B 266 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU B 232 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE B 267 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU B 283 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR B 269 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL B 281 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N PHE B 271 " --> pdb=" O ARG B 279 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 18 through 20 removed outlier: 6.513A pdb=" N HIS C 227 " --> pdb=" O LYS C 249 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LEU C 251 " --> pdb=" O HIS C 227 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE C 229 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N GLU C 253 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ASP C 48 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 193 " --> pdb=" O VAL C 712 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 364 through 365 Processing sheet with id=AB1, first strand: chain 'C' and resid 662 through 663 Processing sheet with id=AB2, first strand: chain 'C' and resid 759 through 760 Processing sheet with id=AB3, first strand: chain 'D' and resid 5 through 8 removed outlier: 3.732A pdb=" N VAL D 123 " --> pdb=" O TRP D 332 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE D 119 " --> pdb=" O TYR D 336 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE D 99 " --> pdb=" O ILE D 132 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N PHE D 134 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 10.446A pdb=" N TRP D 101 " --> pdb=" O PHE D 134 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE D 98 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLY D 211 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR D 100 " --> pdb=" O GLY D 211 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N ALA D 213 " --> pdb=" O THR D 100 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR D 195 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ARG D 200 " --> pdb=" O GLN D 23 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLN D 23 " --> pdb=" O ARG D 200 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 44 through 45 Processing sheet with id=AB5, first strand: chain 'D' and resid 216 through 217 removed outlier: 3.586A pdb=" N CYS D 216 " --> pdb=" O ILE D 231 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYR D 230 " --> pdb=" O LYS D 266 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ILE D 268 " --> pdb=" O TYR D 230 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLU D 232 " --> pdb=" O ILE D 268 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N GLY D 270 " --> pdb=" O GLU D 232 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS D 234 " --> pdb=" O GLY D 270 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ARG D 272 " --> pdb=" O LYS D 234 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N THR D 236 " --> pdb=" O ARG D 272 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE D 267 " --> pdb=" O GLU D 283 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLU D 283 " --> pdb=" O ILE D 267 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR D 269 " --> pdb=" O VAL D 281 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL D 281 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE D 271 " --> pdb=" O ARG D 279 " (cutoff:3.500A) 824 hydrogen bonds defined for protein. 2328 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: 6.09 Time building geometry restraints manager: 5.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3786 1.33 - 1.45: 4473 1.45 - 1.57: 10559 1.57 - 1.69: 0 1.69 - 1.81: 115 Bond restraints: 18933 Sorted by residual: bond pdb=" CA CYS C 324 " pdb=" C CYS C 324 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.80e-02 3.09e+03 2.08e+00 bond pdb=" CD GLN E 67 " pdb=" OE1 GLN E 67 " ideal model delta sigma weight residual 1.231 1.206 0.025 1.90e-02 2.77e+03 1.73e+00 bond pdb=" CA ILE C 22 " pdb=" CB ILE C 22 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.33e+00 bond pdb=" C LEU E 84 " pdb=" N PRO E 85 " ideal model delta sigma weight residual 1.335 1.351 -0.015 1.36e-02 5.41e+03 1.29e+00 bond pdb=" C TYR A 14 " pdb=" N PRO A 15 " ideal model delta sigma weight residual 1.336 1.323 0.013 1.20e-02 6.94e+03 1.15e+00 ... (remaining 18928 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 25061 1.50 - 3.01: 412 3.01 - 4.51: 87 4.51 - 6.01: 33 6.01 - 7.52: 6 Bond angle restraints: 25599 Sorted by residual: angle pdb=" N VAL A 628 " pdb=" CA VAL A 628 " pdb=" C VAL A 628 " ideal model delta sigma weight residual 113.53 109.46 4.07 9.80e-01 1.04e+00 1.72e+01 angle pdb=" CA ARG D 341 " pdb=" CB ARG D 341 " pdb=" CG ARG D 341 " ideal model delta sigma weight residual 114.10 121.62 -7.52 2.00e+00 2.50e-01 1.41e+01 angle pdb=" N GLN E 67 " pdb=" CA GLN E 67 " pdb=" CB GLN E 67 " ideal model delta sigma weight residual 110.40 116.28 -5.88 1.63e+00 3.76e-01 1.30e+01 angle pdb=" C GLN E 66 " pdb=" N GLN E 67 " pdb=" CA GLN E 67 " ideal model delta sigma weight residual 121.14 115.23 5.91 1.75e+00 3.27e-01 1.14e+01 angle pdb=" C TYR E 125 " pdb=" N GLN E 126 " pdb=" CA GLN E 126 " ideal model delta sigma weight residual 120.72 115.55 5.17 1.67e+00 3.59e-01 9.59e+00 ... (remaining 25594 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 10275 17.41 - 34.81: 977 34.81 - 52.22: 191 52.22 - 69.63: 31 69.63 - 87.04: 12 Dihedral angle restraints: 11486 sinusoidal: 4837 harmonic: 6649 Sorted by residual: dihedral pdb=" CA VAL C 669 " pdb=" C VAL C 669 " pdb=" N ILE C 670 " pdb=" CA ILE C 670 " ideal model delta harmonic sigma weight residual -180.00 -162.12 -17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA MET E 95 " pdb=" C MET E 95 " pdb=" N ILE E 96 " pdb=" CA ILE E 96 " ideal model delta harmonic sigma weight residual -180.00 -162.29 -17.71 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ASP C 30 " pdb=" CB ASP C 30 " pdb=" CG ASP C 30 " pdb=" OD1 ASP C 30 " ideal model delta sinusoidal sigma weight residual -30.00 -89.28 59.28 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 11483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2005 0.042 - 0.084: 535 0.084 - 0.126: 175 0.126 - 0.168: 8 0.168 - 0.210: 2 Chirality restraints: 2725 Sorted by residual: chirality pdb=" CB ILE E 115 " pdb=" CA ILE E 115 " pdb=" CG1 ILE E 115 " pdb=" CG2 ILE E 115 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA TYR E 125 " pdb=" N TYR E 125 " pdb=" C TYR E 125 " pdb=" CB TYR E 125 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" CA ARG D 341 " pdb=" N ARG D 341 " pdb=" C ARG D 341 " pdb=" CB ARG D 341 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.64e-01 ... (remaining 2722 not shown) Planarity restraints: 3289 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 110 " 0.031 2.00e-02 2.50e+03 2.98e-02 2.21e+01 pdb=" CG TRP E 110 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 TRP E 110 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP E 110 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 110 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 110 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 110 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 110 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 110 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E 110 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 637 " -0.030 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO A 638 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 638 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 638 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 67 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO A 68 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " 0.020 5.00e-02 4.00e+02 ... (remaining 3286 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 335 2.66 - 3.22: 18288 3.22 - 3.78: 29637 3.78 - 4.34: 39142 4.34 - 4.90: 62432 Nonbonded interactions: 149834 Sorted by model distance: nonbonded pdb=" O MET C 626 " pdb=" OH TYR C 656 " model vdw 2.098 3.040 nonbonded pdb=" OH TYR A 850 " pdb=" OH TYR B 45 " model vdw 2.156 3.040 nonbonded pdb=" OH TYR C 850 " pdb=" OH TYR D 45 " model vdw 2.169 3.040 nonbonded pdb=" OH TYR C 596 " pdb=" OD2 ASP C 663 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR A 596 " pdb=" OD2 ASP A 663 " model vdw 2.209 3.040 ... (remaining 149829 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' and (resid 5 through 63 or resid 69 through 129 or resid 156 through \ 257 or resid 283 through 407 or resid 532 through 824 or resid 834 through 864)) \ selection = (chain 'C' and resid 5 through 864) } ncs_group { reference = (chain 'B' and resid 1 through 380) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 40.750 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18933 Z= 0.211 Angle : 0.530 7.517 25599 Z= 0.269 Chirality : 0.041 0.210 2725 Planarity : 0.003 0.050 3289 Dihedral : 13.978 87.035 7188 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: 1.15 (0.19), residues: 2222 helix: 1.49 (0.18), residues: 937 sheet: 0.08 (0.32), residues: 270 loop : 0.41 (0.21), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.001 TRP E 110 HIS 0.003 0.001 HIS C 717 PHE 0.013 0.001 PHE B 152 TYR 0.018 0.001 TYR B 269 ARG 0.007 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 2.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 MET cc_start: 0.8822 (tmm) cc_final: 0.8552 (tmm) REVERT: A 626 MET cc_start: 0.8757 (ptt) cc_final: 0.8008 (ppp) REVERT: A 838 PHE cc_start: 0.7323 (m-80) cc_final: 0.7049 (m-80) REVERT: B 189 CYS cc_start: 0.9363 (m) cc_final: 0.9106 (m) REVERT: C 76 MET cc_start: 0.9090 (ptt) cc_final: 0.8452 (ppp) REVERT: C 167 MET cc_start: 0.8213 (mmp) cc_final: 0.7651 (mmm) REVERT: C 360 LYS cc_start: 0.8573 (ptmt) cc_final: 0.8178 (tppt) REVERT: C 645 MET cc_start: 0.8399 (tmm) cc_final: 0.7239 (tmm) REVERT: C 783 MET cc_start: 0.7987 (mtp) cc_final: 0.7556 (mtm) REVERT: D 1 MET cc_start: 0.6673 (ppp) cc_final: 0.5640 (ppp) REVERT: D 17 MET cc_start: 0.7757 (tmm) cc_final: 0.7386 (tmm) REVERT: D 53 ASP cc_start: 0.8889 (m-30) cc_final: 0.8586 (m-30) REVERT: E 72 ARG cc_start: 0.7671 (mtp85) cc_final: 0.6627 (ptt-90) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.3083 time to fit residues: 69.6419 Evaluate side-chains 119 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 130 optimal weight: 0.0050 chunk 203 optimal weight: 8.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 GLN C 402 ASN C 565 ASN D 191 ASN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18933 Z= 0.210 Angle : 0.565 7.267 25599 Z= 0.291 Chirality : 0.043 0.208 2725 Planarity : 0.004 0.050 3289 Dihedral : 3.830 18.214 2479 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.49 % Allowed : 7.37 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.05 (0.18), residues: 2222 helix: 1.46 (0.17), residues: 978 sheet: 0.05 (0.32), residues: 269 loop : 0.24 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP E 110 HIS 0.005 0.001 HIS E 122 PHE 0.020 0.001 PHE C 7 TYR 0.013 0.001 TYR B 269 ARG 0.006 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 138 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8809 (pmm) cc_final: 0.8267 (pmm) REVERT: A 566 MET cc_start: 0.8087 (tmm) cc_final: 0.7699 (tmm) REVERT: A 838 PHE cc_start: 0.7266 (m-80) cc_final: 0.6959 (m-80) REVERT: B 53 ASP cc_start: 0.8059 (m-30) cc_final: 0.7855 (m-30) REVERT: B 179 LYS cc_start: 0.9246 (mmmm) cc_final: 0.9041 (mmmm) REVERT: B 189 CYS cc_start: 0.9409 (m) cc_final: 0.9145 (m) REVERT: C 76 MET cc_start: 0.8968 (ptt) cc_final: 0.8339 (ppp) REVERT: C 167 MET cc_start: 0.8123 (mmp) cc_final: 0.7851 (mmm) REVERT: C 360 LYS cc_start: 0.8621 (ptmt) cc_final: 0.8209 (tppt) REVERT: C 645 MET cc_start: 0.7807 (tmm) cc_final: 0.6872 (tmm) REVERT: C 783 MET cc_start: 0.7848 (mtp) cc_final: 0.7494 (mtm) REVERT: D 17 MET cc_start: 0.7760 (tmm) cc_final: 0.7388 (tmm) REVERT: D 53 ASP cc_start: 0.8865 (m-30) cc_final: 0.8526 (m-30) REVERT: E 69 ARG cc_start: 0.8081 (ttm-80) cc_final: 0.7530 (mmm-85) REVERT: E 72 ARG cc_start: 0.7654 (mtp85) cc_final: 0.6691 (ptt-90) REVERT: E 80 PHE cc_start: 0.9080 (m-80) cc_final: 0.8737 (m-80) outliers start: 10 outliers final: 7 residues processed: 143 average time/residue: 0.2916 time to fit residues: 66.7132 Evaluate side-chains 128 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 672 GLN Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 67 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 169 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 chunk 56 optimal weight: 0.0170 chunk 203 optimal weight: 9.9990 chunk 220 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 overall best weight: 3.5224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 636 ASN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN D 356 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 18933 Z= 0.323 Angle : 0.586 7.262 25599 Z= 0.301 Chirality : 0.044 0.216 2725 Planarity : 0.004 0.048 3289 Dihedral : 3.993 18.470 2479 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.98 % Allowed : 10.47 % Favored : 88.55 % 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: 1.01 (0.18), residues: 2222 helix: 1.51 (0.17), residues: 974 sheet: -0.15 (0.32), residues: 279 loop : 0.18 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 110 HIS 0.005 0.001 HIS C 334 PHE 0.017 0.001 PHE A 248 TYR 0.014 0.001 TYR C 841 ARG 0.005 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8902 (pmm) cc_final: 0.8384 (pmm) REVERT: A 113 GLN cc_start: 0.9283 (OUTLIER) cc_final: 0.8899 (pm20) REVERT: A 205 GLU cc_start: 0.7929 (pm20) cc_final: 0.7710 (pm20) REVERT: A 838 PHE cc_start: 0.7316 (m-80) cc_final: 0.6951 (m-80) REVERT: B 53 ASP cc_start: 0.8171 (m-30) cc_final: 0.7931 (m-30) REVERT: B 189 CYS cc_start: 0.9397 (m) cc_final: 0.9178 (m) REVERT: C 76 MET cc_start: 0.8985 (ptt) cc_final: 0.8349 (ppp) REVERT: C 167 MET cc_start: 0.8043 (mmp) cc_final: 0.7737 (mmm) REVERT: C 354 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8658 (tm-30) REVERT: C 360 LYS cc_start: 0.8634 (ptmt) cc_final: 0.8177 (tppt) REVERT: C 783 MET cc_start: 0.7888 (mtp) cc_final: 0.7597 (mtm) REVERT: C 797 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8608 (ptp) REVERT: D 17 MET cc_start: 0.7812 (tmm) cc_final: 0.7557 (tmm) REVERT: D 53 ASP cc_start: 0.8832 (m-30) cc_final: 0.8477 (m-30) REVERT: E 69 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7718 (ttm-80) REVERT: E 72 ARG cc_start: 0.7539 (mtp85) cc_final: 0.6539 (ptt-90) REVERT: E 80 PHE cc_start: 0.9115 (m-80) cc_final: 0.8764 (m-80) outliers start: 20 outliers final: 13 residues processed: 137 average time/residue: 0.2963 time to fit residues: 65.4528 Evaluate side-chains 135 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 797 MET Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 100 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 0.5980 chunk 153 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 204 optimal weight: 8.9990 chunk 216 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 18933 Z= 0.384 Angle : 0.619 8.312 25599 Z= 0.315 Chirality : 0.044 0.161 2725 Planarity : 0.004 0.047 3289 Dihedral : 4.167 18.239 2479 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.52 % Allowed : 11.74 % Favored : 86.73 % 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: 0.85 (0.18), residues: 2222 helix: 1.45 (0.17), residues: 978 sheet: -0.36 (0.31), residues: 277 loop : 0.04 (0.21), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 110 HIS 0.006 0.001 HIS C 334 PHE 0.018 0.001 PHE A 248 TYR 0.017 0.002 TYR C 841 ARG 0.004 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8962 (pmm) cc_final: 0.8574 (pmm) REVERT: A 113 GLN cc_start: 0.9288 (OUTLIER) cc_final: 0.8885 (pm20) REVERT: A 205 GLU cc_start: 0.7949 (pm20) cc_final: 0.7747 (pm20) REVERT: A 566 MET cc_start: 0.7999 (tmm) cc_final: 0.7490 (tmm) REVERT: A 838 PHE cc_start: 0.7341 (m-80) cc_final: 0.6921 (m-80) REVERT: B 53 ASP cc_start: 0.8252 (m-30) cc_final: 0.7947 (m-30) REVERT: C 110 MET cc_start: 0.8463 (mmp) cc_final: 0.8004 (mmp) REVERT: C 167 MET cc_start: 0.8189 (mmp) cc_final: 0.7671 (mmm) REVERT: C 354 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8727 (tm-30) REVERT: C 360 LYS cc_start: 0.8581 (ptmt) cc_final: 0.8101 (tppt) REVERT: C 783 MET cc_start: 0.7969 (mtp) cc_final: 0.7713 (mtm) REVERT: D 17 MET cc_start: 0.8044 (tmm) cc_final: 0.7812 (tmm) REVERT: D 53 ASP cc_start: 0.8857 (m-30) cc_final: 0.8499 (m-30) REVERT: E 69 ARG cc_start: 0.7836 (ttm-80) cc_final: 0.7560 (ttm-80) REVERT: E 72 ARG cc_start: 0.7655 (mtp85) cc_final: 0.6681 (ptt-90) REVERT: E 80 PHE cc_start: 0.9126 (m-80) cc_final: 0.8769 (m-80) outliers start: 31 outliers final: 17 residues processed: 153 average time/residue: 0.2854 time to fit residues: 71.8107 Evaluate side-chains 135 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain E residue 20 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 184 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 GLN ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18933 Z= 0.221 Angle : 0.546 8.978 25599 Z= 0.276 Chirality : 0.043 0.279 2725 Planarity : 0.004 0.047 3289 Dihedral : 3.972 19.270 2479 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.43 % Allowed : 13.22 % Favored : 85.36 % 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: 1.03 (0.18), residues: 2222 helix: 1.60 (0.17), residues: 980 sheet: -0.26 (0.31), residues: 276 loop : 0.14 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 110 HIS 0.004 0.001 HIS A 247 PHE 0.012 0.001 PHE D 158 TYR 0.018 0.001 TYR C 841 ARG 0.004 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 2.053 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.8924 (pmm) cc_final: 0.8549 (pmm) REVERT: A 113 GLN cc_start: 0.9271 (OUTLIER) cc_final: 0.8945 (pm20) REVERT: A 205 GLU cc_start: 0.7976 (pm20) cc_final: 0.7728 (pm20) REVERT: A 624 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8355 (tm-30) REVERT: A 838 PHE cc_start: 0.7266 (m-80) cc_final: 0.6846 (m-80) REVERT: B 53 ASP cc_start: 0.8197 (m-30) cc_final: 0.7859 (m-30) REVERT: B 252 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9287 (mm) REVERT: C 76 MET cc_start: 0.9102 (ptt) cc_final: 0.8303 (ppp) REVERT: C 167 MET cc_start: 0.8117 (mmp) cc_final: 0.7557 (mmm) REVERT: C 354 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8672 (tm-30) REVERT: C 356 LEU cc_start: 0.9719 (OUTLIER) cc_final: 0.9460 (mt) REVERT: C 360 LYS cc_start: 0.8585 (ptmt) cc_final: 0.8111 (tppt) REVERT: D 17 MET cc_start: 0.7915 (tmm) cc_final: 0.7691 (tmm) REVERT: D 53 ASP cc_start: 0.8788 (m-30) cc_final: 0.8514 (m-30) REVERT: E 69 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7559 (ttm-80) REVERT: E 72 ARG cc_start: 0.7658 (mtp85) cc_final: 0.6691 (ptt-90) REVERT: E 80 PHE cc_start: 0.9098 (m-80) cc_final: 0.8856 (m-80) outliers start: 29 outliers final: 15 residues processed: 156 average time/residue: 0.2828 time to fit residues: 71.4517 Evaluate side-chains 145 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain E residue 20 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 0.4980 chunk 194 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 216 optimal weight: 40.0000 chunk 179 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18933 Z= 0.148 Angle : 0.532 9.418 25599 Z= 0.266 Chirality : 0.042 0.282 2725 Planarity : 0.004 0.046 3289 Dihedral : 3.774 18.914 2479 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.28 % Allowed : 13.96 % Favored : 84.77 % 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: 1.21 (0.19), residues: 2222 helix: 1.71 (0.17), residues: 982 sheet: -0.02 (0.31), residues: 280 loop : 0.23 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 9 HIS 0.004 0.001 HIS A 221 PHE 0.011 0.001 PHE B 158 TYR 0.019 0.001 TYR C 841 ARG 0.004 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 2.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8846 (pmm) cc_final: 0.8617 (pmm) REVERT: A 113 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.8932 (pm20) REVERT: A 318 ASP cc_start: 0.8508 (m-30) cc_final: 0.8280 (m-30) REVERT: A 566 MET cc_start: 0.7831 (tmm) cc_final: 0.7357 (tmm) REVERT: A 645 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.6781 (tmm) REVERT: A 838 PHE cc_start: 0.7170 (m-80) cc_final: 0.6749 (m-80) REVERT: B 53 ASP cc_start: 0.8258 (m-30) cc_final: 0.7957 (m-30) REVERT: B 252 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9303 (mm) REVERT: C 76 MET cc_start: 0.9076 (ptt) cc_final: 0.8370 (ppp) REVERT: C 110 MET cc_start: 0.8468 (mmp) cc_final: 0.8208 (mmp) REVERT: C 167 MET cc_start: 0.8237 (mmp) cc_final: 0.7643 (mmp) REVERT: C 360 LYS cc_start: 0.8667 (ptmt) cc_final: 0.8191 (tppt) REVERT: C 645 MET cc_start: 0.7406 (tmm) cc_final: 0.6341 (tmm) REVERT: C 797 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8538 (ptp) REVERT: D 17 MET cc_start: 0.7895 (tmm) cc_final: 0.7659 (tmm) REVERT: D 53 ASP cc_start: 0.8739 (m-30) cc_final: 0.8481 (m-30) REVERT: D 164 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8574 (pp20) REVERT: E 72 ARG cc_start: 0.7550 (mtp85) cc_final: 0.6551 (ptt-90) REVERT: E 80 PHE cc_start: 0.9097 (m-80) cc_final: 0.8871 (m-80) outliers start: 26 outliers final: 15 residues processed: 159 average time/residue: 0.2913 time to fit residues: 75.0964 Evaluate side-chains 144 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 2.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 797 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain E residue 20 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 135 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18933 Z= 0.251 Angle : 0.573 11.255 25599 Z= 0.285 Chirality : 0.043 0.275 2725 Planarity : 0.004 0.044 3289 Dihedral : 3.850 18.870 2479 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.38 % Allowed : 14.30 % Favored : 84.32 % 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: 1.17 (0.19), residues: 2222 helix: 1.69 (0.17), residues: 981 sheet: -0.10 (0.31), residues: 282 loop : 0.21 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 110 HIS 0.003 0.001 HIS A 805 PHE 0.011 0.001 PHE D 158 TYR 0.018 0.001 TYR C 841 ARG 0.005 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 2.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8631 (pmm) REVERT: A 113 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.8876 (pm20) REVERT: A 318 ASP cc_start: 0.8533 (m-30) cc_final: 0.8292 (m-30) REVERT: A 566 MET cc_start: 0.7739 (tmm) cc_final: 0.7220 (tmm) REVERT: A 626 MET cc_start: 0.9011 (ttp) cc_final: 0.8062 (tmm) REVERT: A 645 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.6760 (tmm) REVERT: A 838 PHE cc_start: 0.7223 (m-80) cc_final: 0.6793 (m-80) REVERT: B 53 ASP cc_start: 0.8311 (m-30) cc_final: 0.7996 (m-30) REVERT: B 252 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9330 (mm) REVERT: C 76 MET cc_start: 0.9105 (ptt) cc_final: 0.8406 (ppp) REVERT: C 167 MET cc_start: 0.8411 (mmp) cc_final: 0.8064 (mmm) REVERT: C 360 LYS cc_start: 0.8612 (ptmt) cc_final: 0.8136 (tppt) REVERT: C 645 MET cc_start: 0.7370 (tmm) cc_final: 0.6282 (tmm) REVERT: D 17 MET cc_start: 0.7783 (tmm) cc_final: 0.7571 (tmm) REVERT: D 53 ASP cc_start: 0.8789 (m-30) cc_final: 0.8517 (m-30) REVERT: E 69 ARG cc_start: 0.7680 (ttm-80) cc_final: 0.7471 (ttm-80) REVERT: E 72 ARG cc_start: 0.7553 (mtp85) cc_final: 0.6550 (ptt-90) REVERT: E 80 PHE cc_start: 0.9107 (m-80) cc_final: 0.8837 (m-80) REVERT: E 110 TRP cc_start: 0.8770 (m-10) cc_final: 0.8483 (m-10) outliers start: 28 outliers final: 18 residues processed: 146 average time/residue: 0.2645 time to fit residues: 63.3754 Evaluate side-chains 145 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 797 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain E residue 20 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 128 optimal weight: 0.0070 chunk 65 optimal weight: 6.9990 chunk 42 optimal weight: 0.0470 chunk 41 optimal weight: 5.9990 chunk 137 optimal weight: 0.0980 chunk 147 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 169 optimal weight: 7.9990 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18933 Z= 0.136 Angle : 0.555 11.126 25599 Z= 0.273 Chirality : 0.043 0.289 2725 Planarity : 0.004 0.043 3289 Dihedral : 3.658 18.548 2479 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.23 % Allowed : 14.89 % Favored : 83.88 % 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: 1.26 (0.19), residues: 2222 helix: 1.73 (0.17), residues: 986 sheet: 0.09 (0.31), residues: 288 loop : 0.24 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 352 HIS 0.004 0.001 HIS A 221 PHE 0.012 0.001 PHE B 158 TYR 0.019 0.001 TYR C 841 ARG 0.003 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 2.341 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8650 (pmm) REVERT: A 113 GLN cc_start: 0.9217 (OUTLIER) cc_final: 0.8867 (pm20) REVERT: A 318 ASP cc_start: 0.8533 (m-30) cc_final: 0.8296 (m-30) REVERT: A 566 MET cc_start: 0.7552 (tmm) cc_final: 0.7065 (tmm) REVERT: A 626 MET cc_start: 0.8953 (ttp) cc_final: 0.8147 (tmm) REVERT: A 645 MET cc_start: 0.8184 (tmm) cc_final: 0.7302 (tmm) REVERT: A 838 PHE cc_start: 0.7082 (m-80) cc_final: 0.6684 (m-80) REVERT: B 53 ASP cc_start: 0.8218 (m-30) cc_final: 0.7901 (m-30) REVERT: B 252 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9247 (mm) REVERT: C 76 MET cc_start: 0.9056 (ptt) cc_final: 0.8360 (ppp) REVERT: C 110 MET cc_start: 0.8427 (mmp) cc_final: 0.8189 (mmp) REVERT: C 360 LYS cc_start: 0.8668 (ptmt) cc_final: 0.8235 (tppt) REVERT: C 645 MET cc_start: 0.7338 (tmm) cc_final: 0.6329 (tmm) REVERT: C 797 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8616 (ptp) REVERT: D 17 MET cc_start: 0.7881 (tmm) cc_final: 0.7638 (tmm) REVERT: D 53 ASP cc_start: 0.8706 (m-30) cc_final: 0.8460 (m-30) REVERT: E 72 ARG cc_start: 0.7552 (mtp85) cc_final: 0.6551 (ptt-90) REVERT: E 80 PHE cc_start: 0.9092 (m-80) cc_final: 0.8842 (m-80) outliers start: 25 outliers final: 15 residues processed: 158 average time/residue: 0.2794 time to fit residues: 71.7017 Evaluate side-chains 146 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 797 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain E residue 20 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 5.9990 chunk 206 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18933 Z= 0.184 Angle : 0.569 11.560 25599 Z= 0.279 Chirality : 0.043 0.281 2725 Planarity : 0.003 0.042 3289 Dihedral : 3.668 20.333 2479 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.18 % Allowed : 15.43 % Favored : 83.39 % 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: 1.30 (0.19), residues: 2222 helix: 1.80 (0.17), residues: 978 sheet: 0.06 (0.31), residues: 289 loop : 0.25 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 352 HIS 0.003 0.001 HIS A 247 PHE 0.010 0.001 PHE C 166 TYR 0.020 0.001 TYR C 841 ARG 0.004 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 2.193 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8636 (pmm) REVERT: A 113 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.8894 (pm20) REVERT: A 318 ASP cc_start: 0.8412 (m-30) cc_final: 0.8168 (m-30) REVERT: A 626 MET cc_start: 0.8956 (ttp) cc_final: 0.8085 (tmm) REVERT: A 645 MET cc_start: 0.8235 (tmm) cc_final: 0.7360 (tmm) REVERT: A 664 MET cc_start: 0.7987 (tpt) cc_final: 0.7675 (tpt) REVERT: A 838 PHE cc_start: 0.7107 (m-80) cc_final: 0.6714 (m-80) REVERT: B 53 ASP cc_start: 0.8268 (m-30) cc_final: 0.7942 (m-30) REVERT: B 252 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9222 (mm) REVERT: C 76 MET cc_start: 0.9088 (ptt) cc_final: 0.8398 (ppp) REVERT: C 110 MET cc_start: 0.8467 (mmp) cc_final: 0.8220 (mmp) REVERT: C 167 MET cc_start: 0.8297 (mmp) cc_final: 0.7313 (mmm) REVERT: C 360 LYS cc_start: 0.8692 (ptmt) cc_final: 0.8215 (tppt) REVERT: C 625 LEU cc_start: 0.8909 (mt) cc_final: 0.8483 (mt) REVERT: C 645 MET cc_start: 0.7288 (tmm) cc_final: 0.6277 (tmm) REVERT: D 1 MET cc_start: 0.6651 (tmm) cc_final: 0.5977 (tpt) REVERT: D 17 MET cc_start: 0.7895 (tmm) cc_final: 0.7655 (tmm) REVERT: D 53 ASP cc_start: 0.8743 (m-30) cc_final: 0.8493 (m-30) REVERT: D 164 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8609 (pp20) REVERT: E 72 ARG cc_start: 0.7550 (mtp85) cc_final: 0.6548 (ptt-90) REVERT: E 80 PHE cc_start: 0.9100 (m-80) cc_final: 0.8849 (m-80) outliers start: 24 outliers final: 15 residues processed: 145 average time/residue: 0.2712 time to fit residues: 64.3615 Evaluate side-chains 144 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 797 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 95 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 100 optimal weight: 0.4980 chunk 147 optimal weight: 0.4980 chunk 223 optimal weight: 0.9990 chunk 205 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 108 optimal weight: 30.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18933 Z= 0.165 Angle : 0.568 10.908 25599 Z= 0.278 Chirality : 0.042 0.281 2725 Planarity : 0.003 0.043 3289 Dihedral : 3.637 20.107 2479 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.98 % Allowed : 15.72 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.30 (0.18), residues: 2222 helix: 1.78 (0.17), residues: 980 sheet: 0.15 (0.31), residues: 287 loop : 0.24 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 352 HIS 0.004 0.001 HIS A 59 PHE 0.010 0.001 PHE B 158 TYR 0.021 0.001 TYR C 841 ARG 0.004 0.000 ARG E 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 2.207 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8639 (pmm) REVERT: A 113 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8885 (pm20) REVERT: A 318 ASP cc_start: 0.8217 (m-30) cc_final: 0.7911 (m-30) REVERT: A 626 MET cc_start: 0.8944 (ttp) cc_final: 0.8074 (tmm) REVERT: A 645 MET cc_start: 0.8243 (tmm) cc_final: 0.7351 (tmm) REVERT: A 838 PHE cc_start: 0.7083 (m-80) cc_final: 0.6695 (m-80) REVERT: B 53 ASP cc_start: 0.8248 (m-30) cc_final: 0.7932 (m-30) REVERT: B 252 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9197 (mm) REVERT: C 76 MET cc_start: 0.9087 (ptt) cc_final: 0.8394 (ppp) REVERT: C 110 MET cc_start: 0.8470 (mmp) cc_final: 0.8222 (mmp) REVERT: C 167 MET cc_start: 0.8214 (mmp) cc_final: 0.7437 (mmm) REVERT: C 360 LYS cc_start: 0.8692 (ptmt) cc_final: 0.8218 (tppt) REVERT: C 625 LEU cc_start: 0.8915 (mt) cc_final: 0.8453 (mt) REVERT: C 645 MET cc_start: 0.7275 (tmm) cc_final: 0.6270 (tmm) REVERT: D 1 MET cc_start: 0.6723 (tmm) cc_final: 0.6225 (ppp) REVERT: D 17 MET cc_start: 0.8093 (tmm) cc_final: 0.7850 (tmm) REVERT: D 53 ASP cc_start: 0.8729 (m-30) cc_final: 0.8485 (m-30) REVERT: D 164 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8600 (pp20) REVERT: E 69 ARG cc_start: 0.7777 (ttm170) cc_final: 0.7475 (ttm170) REVERT: E 72 ARG cc_start: 0.7492 (mtp85) cc_final: 0.6465 (ptt-90) REVERT: E 80 PHE cc_start: 0.9110 (m-80) cc_final: 0.8856 (m-80) outliers start: 20 outliers final: 14 residues processed: 144 average time/residue: 0.2835 time to fit residues: 66.0649 Evaluate side-chains 144 residues out of total 2035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 797 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 95 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 ASN ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.077851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.052698 restraints weight = 74325.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.054478 restraints weight = 40076.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.055512 restraints weight = 28864.590| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 18933 Z= 0.364 Angle : 0.652 11.461 25599 Z= 0.325 Chirality : 0.044 0.261 2725 Planarity : 0.004 0.042 3289 Dihedral : 3.982 21.680 2479 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.03 % Allowed : 15.92 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.08 (0.19), residues: 2222 helix: 1.62 (0.17), residues: 989 sheet: -0.20 (0.31), residues: 291 loop : 0.17 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 332 HIS 0.005 0.001 HIS C 719 PHE 0.011 0.001 PHE A 248 TYR 0.027 0.001 TYR C 841 ARG 0.003 0.000 ARG E 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2831.81 seconds wall clock time: 53 minutes 38.16 seconds (3218.16 seconds total)