Starting phenix.real_space_refine on Sun Feb 18 02:32:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egh_31117/02_2024/7egh_31117.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egh_31117/02_2024/7egh_31117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egh_31117/02_2024/7egh_31117.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egh_31117/02_2024/7egh_31117.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egh_31117/02_2024/7egh_31117.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egh_31117/02_2024/7egh_31117.pdb" } resolution = 3.04 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= 0.001 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 90 5.49 5 S 114 5.16 5 C 12790 2.51 5 N 3606 2.21 5 O 3943 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 333": "OD1" <-> "OD2" Residue "A GLU 400": "OE1" <-> "OE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "A GLU 682": "OE1" <-> "OE2" Residue "A ARG 706": "NH1" <-> "NH2" Residue "A GLU 721": "OE1" <-> "OE2" Residue "A GLU 828": "OE1" <-> "OE2" Residue "A GLU 895": "OE1" <-> "OE2" Residue "A ASP 992": "OD1" <-> "OD2" Residue "A ARG 996": "NH1" <-> "NH2" Residue "A ARG 1008": "NH1" <-> "NH2" Residue "A ARG 1030": "NH1" <-> "NH2" Residue "A GLU 1057": "OE1" <-> "OE2" Residue "A ARG 1181": "NH1" <-> "NH2" Residue "A GLU 1203": "OE1" <-> "OE2" Residue "A GLU 1218": "OE1" <-> "OE2" Residue "A GLU 1223": "OE1" <-> "OE2" Residue "A ARG 1224": "NH1" <-> "NH2" Residue "B GLU 21": "OE1" <-> "OE2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B ARG 230": "NH1" <-> "NH2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B GLU 398": "OE1" <-> "OE2" Residue "B ARG 539": "NH1" <-> "NH2" Residue "B ARG 541": "NH1" <-> "NH2" Residue "B GLU 547": "OE1" <-> "OE2" Residue "B GLU 582": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B ARG 597": "NH1" <-> "NH2" Residue "B ARG 598": "NH1" <-> "NH2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B ARG 629": "NH1" <-> "NH2" Residue "B PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 688": "OE1" <-> "OE2" Residue "B ARG 725": "NH1" <-> "NH2" Residue "B GLU 770": "OE1" <-> "OE2" Residue "B ARG 817": "NH1" <-> "NH2" Residue "B GLU 831": "OE1" <-> "OE2" Residue "B ARG 966": "NH1" <-> "NH2" Residue "B TYR 975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 229": "OE1" <-> "OE2" Residue "F ARG 239": "NH1" <-> "NH2" Residue "F GLU 265": "OE1" <-> "OE2" Residue "F ARG 284": "NH1" <-> "NH2" Residue "F GLU 303": "OE1" <-> "OE2" Residue "F ARG 315": "NH1" <-> "NH2" Residue "F ARG 320": "NH1" <-> "NH2" Residue "F ARG 330": "NH1" <-> "NH2" Residue "F ARG 335": "NH1" <-> "NH2" Residue "F ARG 373": "NH1" <-> "NH2" Residue "F ARG 395": "NH1" <-> "NH2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "H ARG 183": "NH1" <-> "NH2" Residue "H ARG 184": "NH1" <-> "NH2" Residue "f GLU 226": "OE1" <-> "OE2" Residue "f GLU 229": "OE1" <-> "OE2" Residue "f ARG 239": "NH1" <-> "NH2" Residue "f ARG 258": "NH1" <-> "NH2" Residue "f ARG 284": "NH1" <-> "NH2" Residue "f ARG 315": "NH1" <-> "NH2" Residue "f ARG 373": "NH1" <-> "NH2" Residue "f ARG 395": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20543 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 5199 Classifications: {'peptide': 630} Link IDs: {'PTRANS': 41, 'TRANS': 588} Chain breaks: 9 Chain: "B" Number of atoms: 7796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 7796 Classifications: {'peptide': 963} Link IDs: {'PTRANS': 45, 'TRANS': 917} Chain breaks: 1 Chain: "F" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2006 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 14, 'TRANS': 252} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 57 Chain: "G" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1171 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 2 Chain: "H" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 580 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 6, 'TRANS': 65} Chain: "X" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 918 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "Y" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 927 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "f" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1946 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 13, 'TRANS': 246} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 57 Time building chain proxies: 10.76, per 1000 atoms: 0.52 Number of scatterers: 20543 At special positions: 0 Unit cell: (141.37, 215.22, 142.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 90 15.00 O 3943 8.00 N 3606 7.00 C 12790 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 945 " - pdb=" SG CYS B 986 " distance=2.23 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: 8.23 Conformation dependent library (CDL) restraints added in 3.5 seconds 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4488 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 15 sheets defined 51.3% alpha, 14.6% beta 45 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 7.36 Creating SS restraints... Processing helix chain 'A' and resid 346 through 354 Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 472 through 478 Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'A' and resid 569 through 574 removed outlier: 3.637A pdb=" N TYR A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 608 through 614 Processing helix chain 'A' and resid 640 through 657 Processing helix chain 'A' and resid 667 through 672 removed outlier: 4.032A pdb=" N THR A 672 " --> pdb=" O GLN A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 817 Processing helix chain 'A' and resid 826 through 834 removed outlier: 3.980A pdb=" N ILE A 830 " --> pdb=" O ARG A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 848 removed outlier: 3.625A pdb=" N ILE A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU A 848 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 880 removed outlier: 3.857A pdb=" N VAL A 880 " --> pdb=" O ILE A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 901 Processing helix chain 'A' and resid 925 through 929 Processing helix chain 'A' and resid 930 through 944 Processing helix chain 'A' and resid 993 through 998 Processing helix chain 'A' and resid 998 through 1011 removed outlier: 3.862A pdb=" N ASN A1002 " --> pdb=" O LEU A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1019 removed outlier: 3.528A pdb=" N ILE A1017 " --> pdb=" O PRO A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1035 Processing helix chain 'A' and resid 1055 through 1079 Processing helix chain 'A' and resid 1187 through 1204 removed outlier: 3.599A pdb=" N ILE A1197 " --> pdb=" O ALA A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1242 Processing helix chain 'B' and resid 102 through 117 removed outlier: 3.736A pdb=" N PHE B 106 " --> pdb=" O ASN B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 185 through 189 removed outlier: 3.547A pdb=" N PHE B 188 " --> pdb=" O SER B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 273 through 281 Processing helix chain 'B' and resid 283 through 295 removed outlier: 3.717A pdb=" N VAL B 287 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 295 " --> pdb=" O TYR B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'B' and resid 338 through 356 Processing helix chain 'B' and resid 366 through 409 removed outlier: 4.079A pdb=" N LEU B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL B 388 " --> pdb=" O LYS B 384 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N ASN B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 441 removed outlier: 3.559A pdb=" N LEU B 441 " --> pdb=" O PRO B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 464 Processing helix chain 'B' and resid 465 through 484 Processing helix chain 'B' and resid 492 through 495 removed outlier: 3.541A pdb=" N GLN B 495 " --> pdb=" O MET B 492 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 492 through 495' Processing helix chain 'B' and resid 499 through 512 Processing helix chain 'B' and resid 515 through 523 Processing helix chain 'B' and resid 595 through 600 removed outlier: 3.821A pdb=" N ASN B 599 " --> pdb=" O LYS B 595 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 600 " --> pdb=" O SER B 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 595 through 600' Processing helix chain 'B' and resid 645 through 656 removed outlier: 3.799A pdb=" N GLU B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 669 Processing helix chain 'B' and resid 670 through 672 No H-bonds generated for 'chain 'B' and resid 670 through 672' Processing helix chain 'B' and resid 674 through 686 Processing helix chain 'B' and resid 691 through 709 removed outlier: 3.542A pdb=" N ARG B 695 " --> pdb=" O PHE B 691 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE B 700 " --> pdb=" O MET B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 728 removed outlier: 3.722A pdb=" N CYS B 728 " --> pdb=" O THR B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 758 Proline residue: B 754 - end of helix Processing helix chain 'B' and resid 768 through 781 removed outlier: 3.533A pdb=" N THR B 773 " --> pdb=" O LYS B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 805 removed outlier: 3.508A pdb=" N SER B 805 " --> pdb=" O ALA B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 843 removed outlier: 4.204A pdb=" N LEU B 828 " --> pdb=" O PRO B 824 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 829 " --> pdb=" O ASP B 825 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 842 " --> pdb=" O ASN B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 864 Processing helix chain 'B' and resid 871 through 878 Processing helix chain 'B' and resid 883 through 901 Processing helix chain 'B' and resid 903 through 916 removed outlier: 3.521A pdb=" N LEU B 907 " --> pdb=" O SER B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 933 Processing helix chain 'B' and resid 946 through 959 removed outlier: 3.561A pdb=" N VAL B 950 " --> pdb=" O ASN B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 980 Processing helix chain 'F' and resid 217 through 231 Processing helix chain 'F' and resid 235 through 249 Processing helix chain 'F' and resid 250 through 253 removed outlier: 4.354A pdb=" N TYR F 253 " --> pdb=" O PRO F 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 250 through 253' Processing helix chain 'F' and resid 255 through 270 Processing helix chain 'F' and resid 275 through 291 Processing helix chain 'F' and resid 300 through 314 Proline residue: F 306 - end of helix Processing helix chain 'F' and resid 323 through 344 Processing helix chain 'F' and resid 351 through 364 Processing helix chain 'F' and resid 369 through 382 Processing helix chain 'F' and resid 384 through 391 removed outlier: 4.249A pdb=" N ILE F 388 " --> pdb=" O GLY F 384 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS F 389 " --> pdb=" O HIS F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 394 No H-bonds generated for 'chain 'F' and resid 392 through 394' Processing helix chain 'F' and resid 395 through 409 Processing helix chain 'F' and resid 415 through 438 Proline residue: F 433 - end of helix removed outlier: 3.540A pdb=" N LEU F 438 " --> pdb=" O VAL F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 452 removed outlier: 3.597A pdb=" N PHE F 452 " --> pdb=" O ARG F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 473 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 37 through 42 removed outlier: 3.678A pdb=" N ASP G 41 " --> pdb=" O VAL G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 176 Processing helix chain 'H' and resid 171 through 197 Processing helix chain 'H' and resid 221 through 228 removed outlier: 4.264A pdb=" N THR H 225 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'f' and resid 217 through 231 removed outlier: 3.543A pdb=" N CYS f 231 " --> pdb=" O ILE f 227 " (cutoff:3.500A) Processing helix chain 'f' and resid 235 through 248 removed outlier: 3.630A pdb=" N ARG f 239 " --> pdb=" O CYS f 235 " (cutoff:3.500A) Processing helix chain 'f' and resid 255 through 269 Processing helix chain 'f' and resid 275 through 291 removed outlier: 3.526A pdb=" N LEU f 279 " --> pdb=" O ASN f 275 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP f 291 " --> pdb=" O LYS f 287 " (cutoff:3.500A) Processing helix chain 'f' and resid 300 through 314 removed outlier: 3.633A pdb=" N LEU f 304 " --> pdb=" O TYR f 300 " (cutoff:3.500A) Proline residue: f 306 - end of helix Processing helix chain 'f' and resid 325 through 341 removed outlier: 4.120A pdb=" N LEU f 329 " --> pdb=" O ASN f 325 " (cutoff:3.500A) Processing helix chain 'f' and resid 350 through 364 Processing helix chain 'f' and resid 369 through 384 removed outlier: 4.055A pdb=" N GLY f 384 " --> pdb=" O LEU f 380 " (cutoff:3.500A) Processing helix chain 'f' and resid 384 through 391 removed outlier: 3.544A pdb=" N ILE f 388 " --> pdb=" O GLY f 384 " (cutoff:3.500A) Processing helix chain 'f' and resid 392 through 396 removed outlier: 3.689A pdb=" N LEU f 396 " --> pdb=" O LEU f 393 " (cutoff:3.500A) Processing helix chain 'f' and resid 397 through 404 removed outlier: 3.693A pdb=" N GLU f 401 " --> pdb=" O GLN f 397 " (cutoff:3.500A) Processing helix chain 'f' and resid 415 through 438 removed outlier: 3.825A pdb=" N GLY f 419 " --> pdb=" O ILE f 415 " (cutoff:3.500A) Proline residue: f 433 - end of helix Processing helix chain 'f' and resid 445 through 450 Processing helix chain 'f' and resid 454 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 786 through 787 removed outlier: 6.509A pdb=" N LEU A 680 " --> pdb=" O PHE A 780 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 782 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU A 682 " --> pdb=" O VAL A 782 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL G 73 " --> pdb=" O TYR A 683 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU G 43 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR A 771 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N GLN G 15 " --> pdb=" O GLN G 93 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N LEU G 95 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE G 17 " --> pdb=" O LEU G 95 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER G 97 " --> pdb=" O ILE G 17 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ARG G 19 " --> pdb=" O SER G 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 786 through 787 removed outlier: 6.509A pdb=" N LEU A 680 " --> pdb=" O PHE A 780 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 782 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU A 682 " --> pdb=" O VAL A 782 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL G 73 " --> pdb=" O TYR A 683 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N LYS G 66 " --> pdb=" O THR G 98 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N THR G 98 " --> pdb=" O LYS G 66 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL G 68 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL G 96 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU G 70 " --> pdb=" O MET G 94 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N MET G 94 " --> pdb=" O LEU G 70 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N CYS G 72 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N CYS G 92 " --> pdb=" O CYS G 72 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N MET G 74 " --> pdb=" O ASP G 90 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP G 90 " --> pdb=" O MET G 74 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER G 76 " --> pdb=" O THR G 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 786 through 787 removed outlier: 4.290A pdb=" N GLN A 741 " --> pdb=" O ILE A 752 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N LEU A 754 " --> pdb=" O LEU A 739 " (cutoff:3.500A) removed outlier: 12.853A pdb=" N LEU A 739 " --> pdb=" O LEU A 754 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 825 removed outlier: 3.732A pdb=" N TRP A 861 " --> pdb=" O LYS A 853 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 947 through 948 Processing sheet with id=AA6, first strand: chain 'A' and resid 1180 through 1185 removed outlier: 3.613A pdb=" N LYS A1166 " --> pdb=" O GLU G 182 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU G 182 " --> pdb=" O LYS A1166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 80 through 81 removed outlier: 5.552A pdb=" N ILE B 72 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N SER B 151 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 74 " --> pdb=" O ASN B 149 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL B 46 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASN B 37 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N PHE B 48 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE B 35 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLU B 50 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL B 33 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR B 52 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLN B 31 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N PHE B 54 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N THR B 29 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N THR B 201 " --> pdb=" O LYS B 27 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B 29 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N LYS B 203 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN B 31 " --> pdb=" O LYS B 203 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU B 205 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL B 33 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N THR B 207 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE B 35 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N ASP B 209 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 10.419A pdb=" N ASN B 37 " --> pdb=" O ASP B 209 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N CYS B 200 " --> pdb=" O ILE B 240 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE B 240 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B 222 " --> pdb=" O HIS B 235 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET B 237 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LEU B 220 " --> pdb=" O MET B 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 63 through 65 removed outlier: 4.055A pdb=" N ALA B 83 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 159 through 162 removed outlier: 5.758A pdb=" N LEU B 249 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 255 through 258 removed outlier: 6.354A pdb=" N LYS B 305 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N PHE B 325 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL B 307 " --> pdb=" O PHE B 325 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET B 322 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 360 through 361 removed outlier: 6.559A pdb=" N SER B 360 " --> pdb=" O VAL B 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 587 through 591 removed outlier: 4.570A pdb=" N PHE B 535 " --> pdb=" O GLU B 643 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 573 through 580 removed outlier: 7.404A pdb=" N LYS B 565 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ILE B 630 " --> pdb=" O LYS B 565 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR B 567 " --> pdb=" O ILE B 628 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ILE B 628 " --> pdb=" O THR B 567 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN B 569 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 604 through 605 Processing sheet with id=AB6, first strand: chain 'H' and resid 200 through 201 954 hydrogen bonds defined for protein. 2727 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 117 hydrogen bonds 234 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 10.16 Time building geometry restraints manager: 8.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3176 1.31 - 1.43: 6045 1.43 - 1.56: 11603 1.56 - 1.69: 180 1.69 - 1.81: 178 Bond restraints: 21182 Sorted by residual: bond pdb=" C ASN B 61 " pdb=" O ASN B 61 " ideal model delta sigma weight residual 1.239 1.181 0.058 9.60e-03 1.09e+04 3.63e+01 bond pdb=" C ARG F 395 " pdb=" O ARG F 395 " ideal model delta sigma weight residual 1.237 1.315 -0.078 1.39e-02 5.18e+03 3.15e+01 bond pdb=" CA SER B 903 " pdb=" CB SER B 903 " ideal model delta sigma weight residual 1.528 1.456 0.073 1.49e-02 4.50e+03 2.39e+01 bond pdb=" CA SER f 217 " pdb=" CB SER f 217 " ideal model delta sigma weight residual 1.528 1.453 0.075 1.54e-02 4.22e+03 2.38e+01 bond pdb=" N ARG F 395 " pdb=" CA ARG F 395 " ideal model delta sigma weight residual 1.458 1.516 -0.058 1.22e-02 6.72e+03 2.28e+01 ... (remaining 21177 not shown) Histogram of bond angle deviations from ideal: 95.70 - 103.49: 484 103.49 - 111.27: 8678 111.27 - 119.05: 9284 119.05 - 126.83: 10111 126.83 - 134.61: 504 Bond angle restraints: 29061 Sorted by residual: angle pdb=" N HIS B 491 " pdb=" CA HIS B 491 " pdb=" C HIS B 491 " ideal model delta sigma weight residual 111.28 100.96 10.32 1.09e+00 8.42e-01 8.97e+01 angle pdb=" N VAL F 271 " pdb=" CA VAL F 271 " pdb=" C VAL F 271 " ideal model delta sigma weight residual 112.90 106.03 6.87 9.60e-01 1.09e+00 5.13e+01 angle pdb=" N PRO A 715 " pdb=" CA PRO A 715 " pdb=" C PRO A 715 " ideal model delta sigma weight residual 111.03 100.08 10.95 1.54e+00 4.22e-01 5.06e+01 angle pdb=" N GLN B 495 " pdb=" CA GLN B 495 " pdb=" C GLN B 495 " ideal model delta sigma weight residual 113.28 104.69 8.59 1.22e+00 6.72e-01 4.96e+01 angle pdb=" N LEU A 396 " pdb=" CA LEU A 396 " pdb=" C LEU A 396 " ideal model delta sigma weight residual 113.16 104.83 8.33 1.24e+00 6.50e-01 4.51e+01 ... (remaining 29056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.02: 11625 30.02 - 60.03: 948 60.03 - 90.05: 27 90.05 - 120.07: 1 120.07 - 150.09: 1 Dihedral angle restraints: 12602 sinusoidal: 5714 harmonic: 6888 Sorted by residual: dihedral pdb=" C THR F 310 " pdb=" N THR F 310 " pdb=" CA THR F 310 " pdb=" CB THR F 310 " ideal model delta harmonic sigma weight residual -122.00 -140.15 18.15 0 2.50e+00 1.60e-01 5.27e+01 dihedral pdb=" C GLN A1067 " pdb=" N GLN A1067 " pdb=" CA GLN A1067 " pdb=" CB GLN A1067 " ideal model delta harmonic sigma weight residual -122.60 -140.12 17.52 0 2.50e+00 1.60e-01 4.91e+01 dihedral pdb=" N GLN A1067 " pdb=" C GLN A1067 " pdb=" CA GLN A1067 " pdb=" CB GLN A1067 " ideal model delta harmonic sigma weight residual 122.80 138.94 -16.14 0 2.50e+00 1.60e-01 4.17e+01 ... (remaining 12599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2888 0.132 - 0.263: 313 0.263 - 0.395: 33 0.395 - 0.527: 4 0.527 - 0.659: 3 Chirality restraints: 3241 Sorted by residual: chirality pdb=" CA GLN A1067 " pdb=" N GLN A1067 " pdb=" C GLN A1067 " pdb=" CB GLN A1067 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA THR F 310 " pdb=" N THR F 310 " pdb=" C THR F 310 " pdb=" CB THR F 310 " both_signs ideal model delta sigma weight residual False 2.53 1.90 0.62 2.00e-01 2.50e+01 9.74e+00 chirality pdb=" CA ARG F 268 " pdb=" N ARG F 268 " pdb=" C ARG F 268 " pdb=" CB ARG F 268 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.31e+00 ... (remaining 3238 not shown) Planarity restraints: 3397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 969 " -0.028 2.00e-02 2.50e+03 5.75e-02 3.30e+01 pdb=" C PRO A 969 " 0.099 2.00e-02 2.50e+03 pdb=" O PRO A 969 " -0.039 2.00e-02 2.50e+03 pdb=" N ASN A 970 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 263 " -0.025 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C ILE F 263 " 0.085 2.00e-02 2.50e+03 pdb=" O ILE F 263 " -0.032 2.00e-02 2.50e+03 pdb=" N SER F 264 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 260 " 0.022 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C PRO B 260 " -0.076 2.00e-02 2.50e+03 pdb=" O PRO B 260 " 0.028 2.00e-02 2.50e+03 pdb=" N TYR B 261 " 0.026 2.00e-02 2.50e+03 ... (remaining 3394 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2242 2.74 - 3.28: 18838 3.28 - 3.82: 35103 3.82 - 4.36: 42782 4.36 - 4.90: 69789 Nonbonded interactions: 168754 Sorted by model distance: nonbonded pdb=" N ASN A 970 " pdb=" OD1 ASN A 970 " model vdw 2.206 2.520 nonbonded pdb=" O CYS A 725 " pdb=" SG CYS A 725 " model vdw 2.219 3.400 nonbonded pdb=" O LYS G 129 " pdb=" NZ LYS G 129 " model vdw 2.228 2.520 nonbonded pdb=" O GLN f 352 " pdb=" OG1 THR f 356 " model vdw 2.247 2.440 nonbonded pdb=" O PRO A 931 " pdb=" OG1 THR A 935 " model vdw 2.255 2.440 ... (remaining 168749 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'F' and resid 214 through 473) selection = chain 'f' } 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: 5.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 27.410 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 61.440 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 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 : 0.009 0.107 21182 Z= 0.582 Angle : 1.210 11.384 29061 Z= 0.806 Chirality : 0.086 0.659 3241 Planarity : 0.008 0.075 3397 Dihedral : 18.684 150.086 8111 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.26 % Favored : 95.61 % Rotamer: Outliers : 5.07 % Allowed : 9.54 % Favored : 85.39 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.16), residues: 2300 helix: -1.12 (0.14), residues: 1110 sheet: -1.14 (0.30), residues: 271 loop : -1.78 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 416 HIS 0.014 0.002 HIS F 385 PHE 0.035 0.003 PHE B 190 TYR 0.019 0.002 TYR H 223 ARG 0.033 0.001 ARG F 335 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 373 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8280 (mt-10) REVERT: A 653 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6925 (mt-10) REVERT: A 691 MET cc_start: 0.8230 (tpp) cc_final: 0.7785 (tpp) REVERT: A 744 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6918 (tp30) REVERT: A 786 CYS cc_start: 0.7758 (m) cc_final: 0.7359 (m) REVERT: A 821 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.5584 (tpp-160) REVERT: A 943 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8316 (mtmm) REVERT: A 1058 HIS cc_start: 0.6787 (OUTLIER) cc_final: 0.6524 (t-170) REVERT: A 1071 ASP cc_start: 0.7620 (t0) cc_final: 0.7193 (m-30) REVERT: B 41 GLN cc_start: 0.7660 (mp10) cc_final: 0.7429 (mp10) REVERT: B 71 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6798 (ttt-90) REVERT: B 80 LEU cc_start: 0.7970 (mt) cc_final: 0.7713 (mt) REVERT: B 120 ASP cc_start: 0.7287 (m-30) cc_final: 0.6675 (m-30) REVERT: B 137 HIS cc_start: 0.7448 (t70) cc_final: 0.7083 (t70) REVERT: B 145 LYS cc_start: 0.8296 (mttt) cc_final: 0.7684 (mtpp) REVERT: B 156 LYS cc_start: 0.8370 (mttm) cc_final: 0.8141 (mttm) REVERT: B 205 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7643 (mp0) REVERT: B 212 MET cc_start: 0.8399 (mtt) cc_final: 0.8140 (mtt) REVERT: B 262 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.8012 (mtm) REVERT: B 264 GLU cc_start: 0.7282 (pm20) cc_final: 0.6950 (pm20) REVERT: B 337 ASP cc_start: 0.7706 (t0) cc_final: 0.7496 (t0) REVERT: B 437 HIS cc_start: 0.7543 (t-90) cc_final: 0.6740 (m90) REVERT: B 448 MET cc_start: 0.8851 (mmt) cc_final: 0.8500 (mmt) REVERT: B 520 LYS cc_start: 0.8396 (tttt) cc_final: 0.8092 (ttmm) REVERT: B 582 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7242 (mt-10) REVERT: B 615 ASP cc_start: 0.7793 (t0) cc_final: 0.7502 (t0) REVERT: B 639 LYS cc_start: 0.8334 (tttm) cc_final: 0.7976 (tttt) REVERT: B 640 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8809 (t) REVERT: B 641 GLU cc_start: 0.7600 (mp0) cc_final: 0.7315 (mp0) REVERT: B 648 MET cc_start: 0.8580 (mtt) cc_final: 0.8368 (mtp) REVERT: B 683 ASP cc_start: 0.7976 (m-30) cc_final: 0.7387 (m-30) REVERT: B 765 ASN cc_start: 0.7867 (m110) cc_final: 0.7363 (m-40) REVERT: B 785 ARG cc_start: 0.8571 (mtm180) cc_final: 0.8303 (mtm-85) REVERT: B 798 MET cc_start: 0.7476 (mmm) cc_final: 0.7215 (mtp) REVERT: B 892 GLU cc_start: 0.8178 (tt0) cc_final: 0.7917 (tt0) REVERT: F 236 GLU cc_start: 0.6902 (tm-30) cc_final: 0.6512 (tm-30) REVERT: F 254 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7580 (tm-30) REVERT: F 295 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7776 (pp) REVERT: F 296 TYR cc_start: 0.7358 (t80) cc_final: 0.7150 (t80) REVERT: F 298 GLU cc_start: 0.7418 (pm20) cc_final: 0.7165 (pt0) REVERT: F 352 GLN cc_start: 0.8290 (tt0) cc_final: 0.8074 (mp10) REVERT: F 391 LEU cc_start: 0.8083 (tp) cc_final: 0.7857 (tt) REVERT: F 398 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8332 (tp-100) REVERT: G 14 SER cc_start: 0.7748 (t) cc_final: 0.7260 (p) REVERT: G 46 GLU cc_start: 0.6887 (tt0) cc_final: 0.6266 (tt0) REVERT: G 66 LYS cc_start: 0.5673 (mtmt) cc_final: 0.5473 (mttm) REVERT: G 69 ASP cc_start: 0.6914 (m-30) cc_final: 0.6671 (m-30) REVERT: G 75 GLU cc_start: 0.8284 (pt0) cc_final: 0.7818 (pt0) REVERT: G 98 THR cc_start: 0.7775 (m) cc_final: 0.7542 (p) REVERT: G 153 LYS cc_start: 0.3636 (OUTLIER) cc_final: 0.3035 (tptt) REVERT: H 177 GLU cc_start: 0.7660 (tp30) cc_final: 0.7387 (tp30) REVERT: H 178 LYS cc_start: 0.7285 (mmtp) cc_final: 0.7030 (mmmm) REVERT: f 215 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: f 238 LYS cc_start: 0.8293 (mtpt) cc_final: 0.7732 (mttt) REVERT: f 389 LYS cc_start: 0.8218 (mtpt) cc_final: 0.7930 (mtpp) outliers start: 103 outliers final: 21 residues processed: 451 average time/residue: 0.4144 time to fit residues: 270.1760 Evaluate side-chains 292 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 261 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 416 TRP Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 821 ARG Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 1023 TRP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1073 GLN Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain A residue 1237 ASN Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 182 GLU Chi-restraints excluded: chain f residue 215 GLU Chi-restraints excluded: chain f residue 253 TYR Chi-restraints excluded: chain f residue 326 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.0470 chunk 181 optimal weight: 3.9990 chunk 100 optimal weight: 0.3980 chunk 62 optimal weight: 3.9990 chunk 122 optimal weight: 0.2980 chunk 97 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 114 optimal weight: 0.4980 chunk 140 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN A 505 ASN A 508 ASN A 590 GLN A 860 ASN A 896 GLN A1238 GLN B 30 HIS B 137 HIS B 176 HIS B 183 GLN B 235 HIS B 348 GLN B 415 HIS B 432 HIS B 439 HIS B 450 GLN B 509 ASN B 521 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 GLN B 813 ASN B 882 HIS B 908 GLN B 916 ASN B 952 GLN F 221 GLN F 270 ASN F 422 HIS G 33 GLN G 48 HIS f 343 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6097 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21182 Z= 0.211 Angle : 0.611 10.101 29061 Z= 0.325 Chirality : 0.041 0.220 3241 Planarity : 0.005 0.052 3397 Dihedral : 18.417 150.443 3582 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.66 % Allowed : 13.08 % Favored : 84.26 % 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: -0.76 (0.17), residues: 2300 helix: 0.33 (0.15), residues: 1117 sheet: -0.73 (0.30), residues: 275 loop : -1.42 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 932 HIS 0.008 0.001 HIS G 36 PHE 0.021 0.001 PHE B 190 TYR 0.012 0.001 TYR A 683 ARG 0.012 0.001 ARG A1233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 293 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6782 (tp30) REVERT: A 404 MET cc_start: 0.7786 (mmm) cc_final: 0.7383 (mmm) REVERT: A 481 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8170 (mp0) REVERT: A 625 PHE cc_start: 0.7879 (p90) cc_final: 0.7663 (p90) REVERT: A 691 MET cc_start: 0.8145 (tpp) cc_final: 0.7789 (tpp) REVERT: A 692 MET cc_start: 0.8194 (mtp) cc_final: 0.7819 (mtm) REVERT: A 744 GLU cc_start: 0.7299 (tm-30) cc_final: 0.6888 (tp30) REVERT: A 786 CYS cc_start: 0.7813 (m) cc_final: 0.7415 (m) REVERT: A 945 LYS cc_start: 0.6543 (OUTLIER) cc_final: 0.6338 (mtpp) REVERT: A 1058 HIS cc_start: 0.6579 (OUTLIER) cc_final: 0.6045 (t-170) REVERT: A 1061 ARG cc_start: 0.8113 (ttp-110) cc_final: 0.7693 (mtm110) REVERT: A 1071 ASP cc_start: 0.7525 (t0) cc_final: 0.7232 (m-30) REVERT: B 41 GLN cc_start: 0.7641 (mp10) cc_final: 0.7424 (mp10) REVERT: B 80 LEU cc_start: 0.8016 (mt) cc_final: 0.7747 (mt) REVERT: B 120 ASP cc_start: 0.7153 (m-30) cc_final: 0.6463 (m-30) REVERT: B 145 LYS cc_start: 0.8186 (mttt) cc_final: 0.7485 (mtpp) REVERT: B 156 LYS cc_start: 0.8450 (mttm) cc_final: 0.8210 (mttm) REVERT: B 205 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7687 (mp0) REVERT: B 212 MET cc_start: 0.8430 (mtt) cc_final: 0.8151 (mtt) REVERT: B 262 MET cc_start: 0.7994 (ttm) cc_final: 0.7600 (mtm) REVERT: B 264 GLU cc_start: 0.7131 (pm20) cc_final: 0.6844 (pm20) REVERT: B 295 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7294 (mt) REVERT: B 352 GLN cc_start: 0.7867 (mt0) cc_final: 0.7654 (mt0) REVERT: B 437 HIS cc_start: 0.7238 (t-90) cc_final: 0.6621 (m90) REVERT: B 448 MET cc_start: 0.8863 (mmt) cc_final: 0.8384 (mmt) REVERT: B 492 MET cc_start: 0.7402 (mmm) cc_final: 0.7157 (mmt) REVERT: B 520 LYS cc_start: 0.8352 (tttt) cc_final: 0.8011 (ttmm) REVERT: B 582 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7321 (mt-10) REVERT: B 615 ASP cc_start: 0.7774 (t0) cc_final: 0.7438 (t0) REVERT: B 639 LYS cc_start: 0.8346 (tttm) cc_final: 0.7989 (tttt) REVERT: B 640 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8841 (t) REVERT: B 641 GLU cc_start: 0.7497 (mp0) cc_final: 0.7281 (mp0) REVERT: B 683 ASP cc_start: 0.7903 (m-30) cc_final: 0.7344 (m-30) REVERT: B 785 ARG cc_start: 0.8502 (mtm180) cc_final: 0.8273 (mtm-85) REVERT: B 798 MET cc_start: 0.7472 (mmm) cc_final: 0.7002 (mtp) REVERT: B 892 GLU cc_start: 0.8153 (tt0) cc_final: 0.7780 (mt-10) REVERT: B 937 THR cc_start: 0.8727 (t) cc_final: 0.8388 (p) REVERT: F 259 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.7457 (t80) REVERT: F 295 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7661 (pp) REVERT: F 327 TRP cc_start: 0.4642 (OUTLIER) cc_final: 0.4304 (t-100) REVERT: F 391 LEU cc_start: 0.8167 (tp) cc_final: 0.7837 (tt) REVERT: F 398 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8484 (tp-100) REVERT: G 34 SER cc_start: 0.7085 (t) cc_final: 0.6864 (p) REVERT: G 69 ASP cc_start: 0.6943 (m-30) cc_final: 0.6610 (m-30) REVERT: H 177 GLU cc_start: 0.7796 (tp30) cc_final: 0.7456 (tp30) REVERT: H 178 LYS cc_start: 0.7291 (mmtp) cc_final: 0.6977 (mmmm) REVERT: f 238 LYS cc_start: 0.8306 (mtpt) cc_final: 0.7945 (mtmt) REVERT: f 249 ASP cc_start: 0.7380 (m-30) cc_final: 0.7092 (m-30) REVERT: f 270 ASN cc_start: 0.4591 (OUTLIER) cc_final: 0.3514 (t0) REVERT: f 389 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7869 (mtpp) REVERT: f 402 ARG cc_start: 0.7263 (tmm-80) cc_final: 0.6325 (tmm-80) REVERT: f 424 GLN cc_start: 0.7908 (tt0) cc_final: 0.7702 (tt0) outliers start: 54 outliers final: 27 residues processed: 337 average time/residue: 0.3586 time to fit residues: 179.1560 Evaluate side-chains 301 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 264 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 945 LYS Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 1023 TRP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain A residue 1237 ASN Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 259 PHE Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain F residue 327 TRP Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain f residue 253 TYR Chi-restraints excluded: chain f residue 270 ASN Chi-restraints excluded: chain f residue 326 HIS Chi-restraints excluded: chain f residue 347 THR Chi-restraints excluded: chain f residue 391 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 181 optimal weight: 8.9990 chunk 148 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 0.9990 chunk 235 optimal weight: 0.4980 chunk 194 optimal weight: 3.9990 chunk 216 optimal weight: 0.6980 chunk 74 optimal weight: 0.0470 chunk 175 optimal weight: 4.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 ASN A1058 HIS B 59 ASN B 137 HIS B 576 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 915 GLN B 916 ASN F 343 HIS ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 GLN f 214 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6117 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21182 Z= 0.251 Angle : 0.581 7.634 29061 Z= 0.311 Chirality : 0.041 0.178 3241 Planarity : 0.004 0.040 3397 Dihedral : 18.113 150.189 3542 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.64 % Allowed : 14.61 % Favored : 81.75 % 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: -0.22 (0.17), residues: 2300 helix: 0.85 (0.15), residues: 1121 sheet: -0.54 (0.29), residues: 274 loop : -1.24 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 932 HIS 0.020 0.001 HIS f 214 PHE 0.021 0.001 PHE B 190 TYR 0.031 0.001 TYR F 281 ARG 0.006 0.000 ARG F 207 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 283 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6883 (tp30) REVERT: A 404 MET cc_start: 0.7862 (mmm) cc_final: 0.7333 (mmm) REVERT: A 639 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7287 (pp) REVERT: A 692 MET cc_start: 0.8128 (mtp) cc_final: 0.7659 (mtm) REVERT: A 744 GLU cc_start: 0.7206 (tm-30) cc_final: 0.6787 (tp30) REVERT: A 945 LYS cc_start: 0.6663 (OUTLIER) cc_final: 0.6321 (mtpp) REVERT: A 1058 HIS cc_start: 0.6400 (OUTLIER) cc_final: 0.5665 (t70) REVERT: A 1165 LEU cc_start: -0.3270 (OUTLIER) cc_final: -0.3516 (tt) REVERT: B 41 GLN cc_start: 0.7585 (mp10) cc_final: 0.7375 (mp10) REVERT: B 71 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6614 (ttt90) REVERT: B 120 ASP cc_start: 0.7240 (m-30) cc_final: 0.6557 (m-30) REVERT: B 145 LYS cc_start: 0.8170 (mttt) cc_final: 0.7529 (mtpp) REVERT: B 156 LYS cc_start: 0.8467 (mttm) cc_final: 0.8202 (mttm) REVERT: B 212 MET cc_start: 0.8448 (mtt) cc_final: 0.8166 (mtt) REVERT: B 262 MET cc_start: 0.7993 (ttm) cc_final: 0.7683 (mtm) REVERT: B 264 GLU cc_start: 0.7147 (pm20) cc_final: 0.6887 (pm20) REVERT: B 295 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7399 (mt) REVERT: B 437 HIS cc_start: 0.7470 (t-90) cc_final: 0.6688 (m90) REVERT: B 492 MET cc_start: 0.7458 (mmm) cc_final: 0.7210 (mmt) REVERT: B 520 LYS cc_start: 0.8399 (tttt) cc_final: 0.8040 (ttmm) REVERT: B 581 ILE cc_start: 0.7860 (mt) cc_final: 0.7538 (mm) REVERT: B 639 LYS cc_start: 0.8422 (tttm) cc_final: 0.8157 (tttt) REVERT: B 683 ASP cc_start: 0.7871 (m-30) cc_final: 0.7312 (m-30) REVERT: B 785 ARG cc_start: 0.8520 (mtm180) cc_final: 0.8266 (mtm-85) REVERT: B 797 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7680 (mm-30) REVERT: B 798 MET cc_start: 0.7409 (mmm) cc_final: 0.6978 (mtp) REVERT: B 892 GLU cc_start: 0.8204 (tt0) cc_final: 0.7806 (mt-10) REVERT: B 916 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.8202 (p0) REVERT: F 252 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7462 (tt) REVERT: F 259 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7391 (t80) REVERT: F 281 TYR cc_start: 0.7175 (m-80) cc_final: 0.6899 (m-80) REVERT: F 287 LYS cc_start: 0.8709 (tptp) cc_final: 0.8215 (ttmt) REVERT: F 295 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7658 (pp) REVERT: F 327 TRP cc_start: 0.4687 (OUTLIER) cc_final: 0.4319 (t-100) REVERT: F 347 THR cc_start: 0.6228 (OUTLIER) cc_final: 0.5664 (m) REVERT: F 391 LEU cc_start: 0.8187 (tp) cc_final: 0.7855 (tt) REVERT: F 398 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8358 (tp-100) REVERT: G 46 GLU cc_start: 0.7099 (tt0) cc_final: 0.6298 (tt0) REVERT: G 55 ILE cc_start: 0.8185 (mt) cc_final: 0.7833 (tp) REVERT: H 177 GLU cc_start: 0.7837 (tp30) cc_final: 0.7512 (tp30) REVERT: H 178 LYS cc_start: 0.7281 (mmtp) cc_final: 0.6932 (mtpt) REVERT: H 184 ARG cc_start: 0.7467 (mmm-85) cc_final: 0.7103 (mtp85) REVERT: f 238 LYS cc_start: 0.8306 (mtpt) cc_final: 0.7916 (mtmt) REVERT: f 249 ASP cc_start: 0.7644 (m-30) cc_final: 0.7280 (m-30) REVERT: f 389 LYS cc_start: 0.8222 (mtpt) cc_final: 0.7890 (mtpp) REVERT: f 402 ARG cc_start: 0.7333 (tmm-80) cc_final: 0.6764 (tmm-80) REVERT: f 424 GLN cc_start: 0.7904 (tt0) cc_final: 0.7619 (tt0) outliers start: 74 outliers final: 41 residues processed: 339 average time/residue: 0.3652 time to fit residues: 182.3094 Evaluate side-chains 325 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 271 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 851 ASP Chi-restraints excluded: chain A residue 945 LYS Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 1023 TRP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain A residue 1237 ASN Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 764 HIS Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 915 GLN Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 259 PHE Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain F residue 327 TRP Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain f residue 253 TYR Chi-restraints excluded: chain f residue 270 ASN Chi-restraints excluded: chain f residue 326 HIS Chi-restraints excluded: chain f residue 347 THR Chi-restraints excluded: chain f residue 391 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 104 optimal weight: 0.3980 chunk 146 optimal weight: 0.9980 chunk 219 optimal weight: 0.9980 chunk 231 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN B 69 GLN B 137 HIS B 426 ASN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 915 GLN B 916 ASN ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 21182 Z= 0.350 Angle : 0.606 8.130 29061 Z= 0.323 Chirality : 0.043 0.187 3241 Planarity : 0.005 0.057 3397 Dihedral : 18.030 150.724 3538 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.89 % Allowed : 16.13 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.17), residues: 2300 helix: 0.98 (0.15), residues: 1121 sheet: -0.38 (0.30), residues: 274 loop : -1.20 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 932 HIS 0.008 0.001 HIS B 137 PHE 0.023 0.002 PHE B 190 TYR 0.026 0.001 TYR F 281 ARG 0.009 0.001 ARG A1233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 268 time to evaluate : 2.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6836 (tp30) REVERT: A 404 MET cc_start: 0.7910 (mmm) cc_final: 0.7359 (mmm) REVERT: A 639 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7193 (pp) REVERT: A 692 MET cc_start: 0.8080 (mtp) cc_final: 0.7501 (mtm) REVERT: A 744 GLU cc_start: 0.7197 (tm-30) cc_final: 0.6793 (tp30) REVERT: A 945 LYS cc_start: 0.6666 (OUTLIER) cc_final: 0.6353 (mtpp) REVERT: A 1058 HIS cc_start: 0.6232 (OUTLIER) cc_final: 0.5465 (t70) REVERT: B 41 GLN cc_start: 0.7594 (mp10) cc_final: 0.7375 (mp10) REVERT: B 71 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6650 (ttt90) REVERT: B 120 ASP cc_start: 0.7307 (m-30) cc_final: 0.6592 (m-30) REVERT: B 145 LYS cc_start: 0.8188 (mttt) cc_final: 0.7533 (mtpp) REVERT: B 156 LYS cc_start: 0.8508 (mttm) cc_final: 0.8211 (mttm) REVERT: B 212 MET cc_start: 0.8458 (mtt) cc_final: 0.8196 (mtt) REVERT: B 262 MET cc_start: 0.8089 (ttm) cc_final: 0.7879 (mtm) REVERT: B 263 HIS cc_start: 0.8101 (m90) cc_final: 0.7871 (m-70) REVERT: B 264 GLU cc_start: 0.7192 (pm20) cc_final: 0.6865 (pm20) REVERT: B 295 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7499 (mt) REVERT: B 298 ARG cc_start: 0.7943 (mmm-85) cc_final: 0.7562 (mmt-90) REVERT: B 437 HIS cc_start: 0.7565 (t-90) cc_final: 0.6787 (m90) REVERT: B 520 LYS cc_start: 0.8432 (tttt) cc_final: 0.8080 (ttmm) REVERT: B 683 ASP cc_start: 0.7833 (m-30) cc_final: 0.7284 (m-30) REVERT: B 785 ARG cc_start: 0.8546 (mtm180) cc_final: 0.8261 (mtm-85) REVERT: B 798 MET cc_start: 0.7465 (mmm) cc_final: 0.6955 (mtp) REVERT: B 892 GLU cc_start: 0.8198 (tt0) cc_final: 0.7797 (mt-10) REVERT: B 915 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7389 (mm-40) REVERT: F 219 GLU cc_start: 0.5576 (OUTLIER) cc_final: 0.4611 (pp20) REVERT: F 252 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7453 (tt) REVERT: F 281 TYR cc_start: 0.7249 (m-80) cc_final: 0.6899 (m-80) REVERT: F 287 LYS cc_start: 0.8752 (tptp) cc_final: 0.8206 (ttmt) REVERT: F 295 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7679 (pp) REVERT: F 327 TRP cc_start: 0.4579 (OUTLIER) cc_final: 0.4359 (t-100) REVERT: F 335 ARG cc_start: 0.6965 (ttp-170) cc_final: 0.6639 (ttp-170) REVERT: F 347 THR cc_start: 0.6696 (OUTLIER) cc_final: 0.6247 (m) REVERT: F 389 LYS cc_start: 0.7790 (ptmm) cc_final: 0.7365 (mmmt) REVERT: F 391 LEU cc_start: 0.8197 (tp) cc_final: 0.7774 (tt) REVERT: F 398 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8553 (tp40) REVERT: G 55 ILE cc_start: 0.8216 (mt) cc_final: 0.7908 (tp) REVERT: H 178 LYS cc_start: 0.7291 (mmtp) cc_final: 0.6925 (mtpt) REVERT: H 184 ARG cc_start: 0.7426 (mmm-85) cc_final: 0.7092 (mtp85) REVERT: f 238 LYS cc_start: 0.8278 (mtpt) cc_final: 0.7852 (mtmt) REVERT: f 249 ASP cc_start: 0.7824 (m-30) cc_final: 0.7506 (m-30) REVERT: f 389 LYS cc_start: 0.8272 (mtpt) cc_final: 0.7687 (ttmt) outliers start: 79 outliers final: 54 residues processed: 327 average time/residue: 0.3597 time to fit residues: 175.2847 Evaluate side-chains 325 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 259 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 851 ASP Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 945 LYS Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1023 TRP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain A residue 1237 ASN Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 426 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 764 HIS Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 915 GLN Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain F residue 327 TRP Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain f residue 253 TYR Chi-restraints excluded: chain f residue 270 ASN Chi-restraints excluded: chain f residue 326 HIS Chi-restraints excluded: chain f residue 347 THR Chi-restraints excluded: chain f residue 391 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.7980 chunk 131 optimal weight: 0.1980 chunk 3 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 197 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN B 137 HIS B 426 ASN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 915 GLN B 916 ASN ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 21182 Z= 0.315 Angle : 0.588 7.897 29061 Z= 0.313 Chirality : 0.042 0.183 3241 Planarity : 0.004 0.042 3397 Dihedral : 17.985 150.759 3536 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.28 % Allowed : 16.58 % Favored : 79.14 % 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: 0.07 (0.17), residues: 2300 helix: 1.10 (0.15), residues: 1121 sheet: -0.28 (0.30), residues: 272 loop : -1.16 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 932 HIS 0.008 0.001 HIS B 137 PHE 0.023 0.002 PHE B 190 TYR 0.021 0.001 TYR F 281 ARG 0.006 0.000 ARG f 320 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 265 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6888 (tp30) REVERT: A 404 MET cc_start: 0.7897 (mmm) cc_final: 0.7315 (mmm) REVERT: A 639 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7268 (pp) REVERT: A 692 MET cc_start: 0.8004 (mtp) cc_final: 0.7392 (mtm) REVERT: A 744 GLU cc_start: 0.7165 (tm-30) cc_final: 0.6773 (tp30) REVERT: A 945 LYS cc_start: 0.6685 (OUTLIER) cc_final: 0.6354 (mtpp) REVERT: A 1058 HIS cc_start: 0.6183 (OUTLIER) cc_final: 0.5488 (t70) REVERT: A 1165 LEU cc_start: -0.3434 (OUTLIER) cc_final: -0.3668 (tt) REVERT: B 41 GLN cc_start: 0.7591 (mp10) cc_final: 0.7366 (mp10) REVERT: B 71 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6651 (ttt90) REVERT: B 120 ASP cc_start: 0.7265 (m-30) cc_final: 0.6546 (m-30) REVERT: B 145 LYS cc_start: 0.8172 (mttt) cc_final: 0.7517 (mtpp) REVERT: B 212 MET cc_start: 0.8452 (mtt) cc_final: 0.8196 (mtt) REVERT: B 262 MET cc_start: 0.8052 (ttm) cc_final: 0.7812 (mtm) REVERT: B 295 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7539 (mt) REVERT: B 437 HIS cc_start: 0.7490 (t-90) cc_final: 0.6674 (m90) REVERT: B 520 LYS cc_start: 0.8446 (tttt) cc_final: 0.8087 (ttmm) REVERT: B 683 ASP cc_start: 0.7781 (m-30) cc_final: 0.7251 (m-30) REVERT: B 785 ARG cc_start: 0.8547 (mtm180) cc_final: 0.8245 (mtm-85) REVERT: B 798 MET cc_start: 0.7474 (mmm) cc_final: 0.6942 (mtp) REVERT: B 892 GLU cc_start: 0.8239 (tt0) cc_final: 0.7842 (mt-10) REVERT: F 219 GLU cc_start: 0.5599 (OUTLIER) cc_final: 0.4634 (pp20) REVERT: F 252 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7443 (tt) REVERT: F 281 TYR cc_start: 0.7290 (m-80) cc_final: 0.6941 (m-80) REVERT: F 287 LYS cc_start: 0.8772 (tptp) cc_final: 0.8192 (ttmt) REVERT: F 295 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7642 (pp) REVERT: F 335 ARG cc_start: 0.6933 (ttp-170) cc_final: 0.6641 (ttp-170) REVERT: F 347 THR cc_start: 0.6854 (OUTLIER) cc_final: 0.6528 (m) REVERT: F 391 LEU cc_start: 0.8233 (tp) cc_final: 0.7825 (tt) REVERT: F 398 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8581 (tp40) REVERT: G 46 GLU cc_start: 0.7353 (tt0) cc_final: 0.6547 (tt0) REVERT: G 55 ILE cc_start: 0.8245 (mt) cc_final: 0.7873 (tp) REVERT: G 74 MET cc_start: 0.7571 (mtm) cc_final: 0.7336 (mtp) REVERT: G 153 LYS cc_start: 0.4161 (OUTLIER) cc_final: 0.3448 (tptt) REVERT: H 178 LYS cc_start: 0.7296 (mmtp) cc_final: 0.6885 (mtpt) REVERT: H 184 ARG cc_start: 0.7398 (mmm-85) cc_final: 0.7059 (mtp85) REVERT: f 238 LYS cc_start: 0.8258 (mtpt) cc_final: 0.7858 (mtmt) REVERT: f 249 ASP cc_start: 0.7922 (m-30) cc_final: 0.7573 (m-30) REVERT: f 340 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7833 (tt) REVERT: f 389 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7694 (ttmt) outliers start: 87 outliers final: 59 residues processed: 333 average time/residue: 0.3602 time to fit residues: 179.8062 Evaluate side-chains 329 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 257 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 416 TRP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 851 ASP Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 945 LYS Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1019 LYS Chi-restraints excluded: chain A residue 1023 TRP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain A residue 1237 ASN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain F residue 327 TRP Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain f residue 253 TYR Chi-restraints excluded: chain f residue 270 ASN Chi-restraints excluded: chain f residue 326 HIS Chi-restraints excluded: chain f residue 337 VAL Chi-restraints excluded: chain f residue 340 ILE Chi-restraints excluded: chain f residue 347 THR Chi-restraints excluded: chain f residue 391 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.4980 chunk 208 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 232 optimal weight: 0.0970 chunk 192 optimal weight: 0.9980 chunk 107 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 chunk 121 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 HIS ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 916 ASN ** F 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 201 GLN ** f 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21182 Z= 0.227 Angle : 0.556 7.986 29061 Z= 0.297 Chirality : 0.040 0.174 3241 Planarity : 0.004 0.039 3397 Dihedral : 17.905 150.664 3536 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.98 % Allowed : 16.82 % Favored : 79.19 % 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: 0.28 (0.17), residues: 2300 helix: 1.30 (0.16), residues: 1123 sheet: -0.18 (0.30), residues: 272 loop : -1.09 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 932 HIS 0.008 0.001 HIS B 137 PHE 0.023 0.001 PHE G 130 TYR 0.018 0.001 TYR F 281 ARG 0.007 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 270 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6841 (tp30) REVERT: A 639 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7293 (pp) REVERT: A 692 MET cc_start: 0.7910 (mtp) cc_final: 0.7353 (mtm) REVERT: A 744 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6557 (tp30) REVERT: A 745 ASN cc_start: 0.7942 (OUTLIER) cc_final: 0.7321 (p0) REVERT: A 1058 HIS cc_start: 0.6162 (OUTLIER) cc_final: 0.5470 (t70) REVERT: A 1165 LEU cc_start: -0.3429 (OUTLIER) cc_final: -0.3680 (tt) REVERT: B 41 GLN cc_start: 0.7588 (mp10) cc_final: 0.7365 (mp10) REVERT: B 71 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6655 (ttt90) REVERT: B 120 ASP cc_start: 0.7272 (m-30) cc_final: 0.6544 (m-30) REVERT: B 145 LYS cc_start: 0.8137 (mttt) cc_final: 0.7491 (mtpp) REVERT: B 212 MET cc_start: 0.8441 (mtt) cc_final: 0.8176 (mtt) REVERT: B 262 MET cc_start: 0.8008 (ttm) cc_final: 0.7795 (mtm) REVERT: B 295 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7530 (mt) REVERT: B 298 ARG cc_start: 0.7952 (mmm-85) cc_final: 0.7538 (mmt-90) REVERT: B 437 HIS cc_start: 0.7466 (t-90) cc_final: 0.6656 (m90) REVERT: B 520 LYS cc_start: 0.8418 (tttt) cc_final: 0.8037 (ttmm) REVERT: B 582 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7440 (mm-30) REVERT: B 683 ASP cc_start: 0.7762 (m-30) cc_final: 0.7211 (m-30) REVERT: B 785 ARG cc_start: 0.8541 (mtm180) cc_final: 0.8236 (mtm-85) REVERT: B 798 MET cc_start: 0.7441 (mmm) cc_final: 0.6953 (mtp) REVERT: B 892 GLU cc_start: 0.8239 (tt0) cc_final: 0.7739 (mt-10) REVERT: B 916 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.8177 (p0) REVERT: F 219 GLU cc_start: 0.5577 (OUTLIER) cc_final: 0.4630 (pp20) REVERT: F 252 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7513 (tt) REVERT: F 281 TYR cc_start: 0.7263 (m-80) cc_final: 0.7015 (m-80) REVERT: F 287 LYS cc_start: 0.8700 (tptp) cc_final: 0.8194 (ttmt) REVERT: F 295 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7618 (pp) REVERT: F 335 ARG cc_start: 0.6940 (ttp-170) cc_final: 0.6690 (ttp-170) REVERT: F 347 THR cc_start: 0.6854 (OUTLIER) cc_final: 0.6640 (m) REVERT: F 398 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8577 (tp40) REVERT: G 46 GLU cc_start: 0.7374 (tt0) cc_final: 0.6569 (tt0) REVERT: G 55 ILE cc_start: 0.8236 (mt) cc_final: 0.7886 (tp) REVERT: G 74 MET cc_start: 0.7531 (mtm) cc_final: 0.7307 (mtp) REVERT: G 153 LYS cc_start: 0.4184 (OUTLIER) cc_final: 0.3469 (tptt) REVERT: H 178 LYS cc_start: 0.7337 (mmtp) cc_final: 0.6864 (mtpt) REVERT: H 184 ARG cc_start: 0.7471 (mmm-85) cc_final: 0.7070 (mtp85) REVERT: f 238 LYS cc_start: 0.8258 (mtpt) cc_final: 0.7844 (mtmt) REVERT: f 249 ASP cc_start: 0.7882 (m-30) cc_final: 0.7543 (m-30) REVERT: f 340 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7785 (tt) REVERT: f 389 LYS cc_start: 0.8273 (mtpt) cc_final: 0.7697 (ttmt) outliers start: 81 outliers final: 57 residues processed: 331 average time/residue: 0.3457 time to fit residues: 171.2399 Evaluate side-chains 336 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 265 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 416 TRP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 743 PHE Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 851 ASP Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 942 MET Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1019 LYS Chi-restraints excluded: chain A residue 1023 TRP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain F residue 327 TRP Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain f residue 253 TYR Chi-restraints excluded: chain f residue 270 ASN Chi-restraints excluded: chain f residue 272 VAL Chi-restraints excluded: chain f residue 326 HIS Chi-restraints excluded: chain f residue 340 ILE Chi-restraints excluded: chain f residue 347 THR Chi-restraints excluded: chain f residue 391 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 chunk 195 optimal weight: 0.4980 chunk 129 optimal weight: 0.5980 chunk 231 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 141 optimal weight: 0.4980 chunk 106 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 HIS ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 916 ASN G 53 HIS f 214 HIS f 254 GLN ** f 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21182 Z= 0.233 Angle : 0.555 7.928 29061 Z= 0.296 Chirality : 0.040 0.171 3241 Planarity : 0.004 0.060 3397 Dihedral : 17.843 150.661 3534 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.28 % Allowed : 17.17 % Favored : 78.55 % 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: 0.40 (0.18), residues: 2300 helix: 1.40 (0.16), residues: 1123 sheet: -0.08 (0.31), residues: 271 loop : -1.05 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 932 HIS 0.008 0.001 HIS B 137 PHE 0.023 0.001 PHE G 130 TYR 0.016 0.001 TYR F 281 ARG 0.007 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 272 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.6863 (tp30) REVERT: A 639 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7306 (pp) REVERT: A 692 MET cc_start: 0.7869 (mtp) cc_final: 0.7297 (mtm) REVERT: A 744 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6856 (tt0) REVERT: A 745 ASN cc_start: 0.7933 (OUTLIER) cc_final: 0.7327 (p0) REVERT: A 1058 HIS cc_start: 0.6064 (OUTLIER) cc_final: 0.5381 (t70) REVERT: A 1165 LEU cc_start: -0.3442 (OUTLIER) cc_final: -0.3683 (tt) REVERT: B 41 GLN cc_start: 0.7582 (mp10) cc_final: 0.7362 (mp10) REVERT: B 71 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6736 (ttt-90) REVERT: B 120 ASP cc_start: 0.7213 (m-30) cc_final: 0.6486 (m-30) REVERT: B 145 LYS cc_start: 0.8112 (mttt) cc_final: 0.7472 (mtpp) REVERT: B 212 MET cc_start: 0.8437 (mtt) cc_final: 0.8164 (mtt) REVERT: B 262 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7807 (mtm) REVERT: B 295 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7566 (mt) REVERT: B 437 HIS cc_start: 0.7458 (t-90) cc_final: 0.6650 (m90) REVERT: B 520 LYS cc_start: 0.8475 (tttt) cc_final: 0.8093 (ttmm) REVERT: B 683 ASP cc_start: 0.7752 (m-30) cc_final: 0.7196 (m-30) REVERT: B 785 ARG cc_start: 0.8543 (mtm180) cc_final: 0.8243 (mtm-85) REVERT: B 798 MET cc_start: 0.7436 (mmm) cc_final: 0.6960 (mtp) REVERT: B 892 GLU cc_start: 0.8202 (tt0) cc_final: 0.7810 (mt-10) REVERT: B 916 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.8252 (p0) REVERT: F 219 GLU cc_start: 0.5595 (OUTLIER) cc_final: 0.4647 (pp20) REVERT: F 252 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7494 (tt) REVERT: F 281 TYR cc_start: 0.7333 (m-80) cc_final: 0.7090 (m-80) REVERT: F 287 LYS cc_start: 0.8786 (tptp) cc_final: 0.8256 (ttmt) REVERT: F 295 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7600 (pp) REVERT: F 335 ARG cc_start: 0.7012 (ttp-170) cc_final: 0.6752 (ttp-170) REVERT: F 347 THR cc_start: 0.6827 (OUTLIER) cc_final: 0.6521 (m) REVERT: F 398 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8583 (tp40) REVERT: F 421 ASP cc_start: 0.7801 (p0) cc_final: 0.7374 (p0) REVERT: G 46 GLU cc_start: 0.7401 (tt0) cc_final: 0.6586 (tt0) REVERT: G 55 ILE cc_start: 0.8265 (mt) cc_final: 0.7903 (tp) REVERT: G 74 MET cc_start: 0.7526 (mtm) cc_final: 0.7274 (mtp) REVERT: G 153 LYS cc_start: 0.4197 (OUTLIER) cc_final: 0.3486 (tptt) REVERT: H 178 LYS cc_start: 0.7335 (mmtp) cc_final: 0.6858 (mtpt) REVERT: f 238 LYS cc_start: 0.8260 (mtpt) cc_final: 0.7842 (mtmt) REVERT: f 249 ASP cc_start: 0.7877 (m-30) cc_final: 0.7531 (m-30) REVERT: f 340 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7820 (tt) REVERT: f 389 LYS cc_start: 0.8276 (mtpt) cc_final: 0.7663 (ttmm) outliers start: 87 outliers final: 64 residues processed: 339 average time/residue: 0.3601 time to fit residues: 184.7715 Evaluate side-chains 344 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 265 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 416 TRP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 743 PHE Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 851 ASP Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 942 MET Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 1019 LYS Chi-restraints excluded: chain A residue 1023 TRP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 945 CYS Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain f residue 253 TYR Chi-restraints excluded: chain f residue 270 ASN Chi-restraints excluded: chain f residue 272 VAL Chi-restraints excluded: chain f residue 326 HIS Chi-restraints excluded: chain f residue 337 VAL Chi-restraints excluded: chain f residue 340 ILE Chi-restraints excluded: chain f residue 347 THR Chi-restraints excluded: chain f residue 391 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 138 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 157 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 HIS ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 916 ASN ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 HIS ** G 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 214 HIS ** f 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 21182 Z= 0.346 Angle : 0.606 9.946 29061 Z= 0.321 Chirality : 0.043 0.178 3241 Planarity : 0.004 0.048 3397 Dihedral : 17.936 150.891 3534 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.33 % Allowed : 16.92 % Favored : 78.75 % 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: 0.26 (0.17), residues: 2300 helix: 1.26 (0.16), residues: 1122 sheet: -0.11 (0.31), residues: 270 loop : -1.09 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 327 HIS 0.008 0.001 HIS B 137 PHE 0.023 0.002 PHE B 190 TYR 0.015 0.001 TYR F 374 ARG 0.009 0.001 ARG H 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 262 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6856 (tp30) REVERT: A 639 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7266 (pp) REVERT: A 744 GLU cc_start: 0.7135 (tm-30) cc_final: 0.6855 (tt0) REVERT: A 745 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.7320 (p0) REVERT: A 1058 HIS cc_start: 0.6113 (OUTLIER) cc_final: 0.5391 (t70) REVERT: A 1165 LEU cc_start: -0.3435 (OUTLIER) cc_final: -0.3669 (tt) REVERT: B 41 GLN cc_start: 0.7586 (mp10) cc_final: 0.7358 (mp10) REVERT: B 71 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6702 (ttt-90) REVERT: B 120 ASP cc_start: 0.7428 (m-30) cc_final: 0.6767 (m-30) REVERT: B 145 LYS cc_start: 0.8180 (mttt) cc_final: 0.7538 (mtpp) REVERT: B 212 MET cc_start: 0.8435 (mtt) cc_final: 0.8173 (mtt) REVERT: B 262 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7859 (mtm) REVERT: B 295 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7587 (mt) REVERT: B 298 ARG cc_start: 0.8015 (mmm-85) cc_final: 0.7597 (mmt-90) REVERT: B 362 MET cc_start: 0.8676 (tpp) cc_final: 0.8437 (tpp) REVERT: B 520 LYS cc_start: 0.8459 (tttt) cc_final: 0.8090 (ttmm) REVERT: B 582 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7474 (mm-30) REVERT: B 683 ASP cc_start: 0.7757 (m-30) cc_final: 0.7225 (m-30) REVERT: B 785 ARG cc_start: 0.8558 (mtm180) cc_final: 0.8260 (mtm-85) REVERT: B 798 MET cc_start: 0.7484 (mmm) cc_final: 0.6947 (mtp) REVERT: B 892 GLU cc_start: 0.8220 (tt0) cc_final: 0.7834 (mt-10) REVERT: B 916 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8252 (p0) REVERT: F 219 GLU cc_start: 0.5626 (OUTLIER) cc_final: 0.4643 (pp20) REVERT: F 252 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7552 (tt) REVERT: F 281 TYR cc_start: 0.7394 (m-80) cc_final: 0.7138 (m-80) REVERT: F 287 LYS cc_start: 0.8812 (tptp) cc_final: 0.8212 (ttmt) REVERT: F 295 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7601 (pp) REVERT: F 335 ARG cc_start: 0.6986 (ttp-170) cc_final: 0.6744 (ttp-170) REVERT: F 398 GLN cc_start: 0.8926 (mm-40) cc_final: 0.8605 (tp40) REVERT: G 46 GLU cc_start: 0.7453 (tt0) cc_final: 0.6610 (tt0) REVERT: G 55 ILE cc_start: 0.8365 (mt) cc_final: 0.8011 (tp) REVERT: G 153 LYS cc_start: 0.4240 (OUTLIER) cc_final: 0.3512 (tptt) REVERT: H 178 LYS cc_start: 0.7342 (mmtp) cc_final: 0.6884 (mtpt) REVERT: f 238 LYS cc_start: 0.8272 (mtpt) cc_final: 0.7826 (mtmt) REVERT: f 340 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7877 (tt) REVERT: f 389 LYS cc_start: 0.8320 (mtpt) cc_final: 0.7696 (ttmm) REVERT: f 402 ARG cc_start: 0.7218 (tmm-80) cc_final: 0.6695 (tmm-80) REVERT: f 421 ASP cc_start: 0.7555 (p0) cc_final: 0.7039 (t0) outliers start: 88 outliers final: 64 residues processed: 332 average time/residue: 0.3612 time to fit residues: 180.6947 Evaluate side-chains 336 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 258 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 416 TRP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 743 PHE Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 851 ASP Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 942 MET Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 1023 TRP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 611 GLU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain F residue 219 GLU Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain f residue 220 GLN Chi-restraints excluded: chain f residue 253 TYR Chi-restraints excluded: chain f residue 270 ASN Chi-restraints excluded: chain f residue 272 VAL Chi-restraints excluded: chain f residue 326 HIS Chi-restraints excluded: chain f residue 337 VAL Chi-restraints excluded: chain f residue 340 ILE Chi-restraints excluded: chain f residue 347 THR Chi-restraints excluded: chain f residue 391 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 6.9990 chunk 221 optimal weight: 0.8980 chunk 202 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 129 optimal weight: 0.0980 chunk 93 optimal weight: 0.5980 chunk 169 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 194 optimal weight: 0.8980 chunk 203 optimal weight: 0.0970 chunk 214 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 916 ASN ** F 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 HIS ** G 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 214 HIS ** f 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21182 Z= 0.240 Angle : 0.579 11.980 29061 Z= 0.306 Chirality : 0.041 0.170 3241 Planarity : 0.004 0.046 3397 Dihedral : 17.866 150.725 3534 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.84 % Allowed : 17.17 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.18), residues: 2300 helix: 1.39 (0.16), residues: 1123 sheet: -0.06 (0.31), residues: 270 loop : -1.03 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 327 HIS 0.007 0.001 HIS B 454 PHE 0.022 0.001 PHE B 190 TYR 0.018 0.001 TYR F 374 ARG 0.011 0.000 ARG A1233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 262 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7118 (tp30) REVERT: A 639 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7375 (pp) REVERT: A 692 MET cc_start: 0.7873 (mtp) cc_final: 0.7290 (mtm) REVERT: A 744 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6797 (tt0) REVERT: A 745 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.7302 (p0) REVERT: A 1058 HIS cc_start: 0.6153 (OUTLIER) cc_final: 0.5439 (t70) REVERT: A 1165 LEU cc_start: -0.3400 (OUTLIER) cc_final: -0.3646 (tt) REVERT: B 41 GLN cc_start: 0.7583 (mp10) cc_final: 0.7354 (mp10) REVERT: B 71 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6731 (ttt-90) REVERT: B 120 ASP cc_start: 0.7379 (m-30) cc_final: 0.6640 (m-30) REVERT: B 145 LYS cc_start: 0.8099 (mttt) cc_final: 0.7479 (mtpp) REVERT: B 212 MET cc_start: 0.8434 (mtt) cc_final: 0.8162 (mtt) REVERT: B 262 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7705 (mtm) REVERT: B 295 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7505 (mt) REVERT: B 362 MET cc_start: 0.8675 (tpp) cc_final: 0.8434 (tpp) REVERT: B 520 LYS cc_start: 0.8461 (tttt) cc_final: 0.8095 (ttmm) REVERT: B 683 ASP cc_start: 0.7740 (m-30) cc_final: 0.7211 (m-30) REVERT: B 785 ARG cc_start: 0.8543 (mtm180) cc_final: 0.8245 (mtm-85) REVERT: B 798 MET cc_start: 0.7452 (mmm) cc_final: 0.6955 (mtp) REVERT: B 879 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7338 (mm-30) REVERT: B 892 GLU cc_start: 0.8198 (tt0) cc_final: 0.7792 (mt-10) REVERT: B 916 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8140 (p0) REVERT: F 252 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7562 (tt) REVERT: F 281 TYR cc_start: 0.7392 (m-80) cc_final: 0.7146 (m-80) REVERT: F 287 LYS cc_start: 0.8816 (tptp) cc_final: 0.8252 (ttmt) REVERT: F 295 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7569 (pp) REVERT: F 335 ARG cc_start: 0.6962 (ttp-170) cc_final: 0.6739 (ttp-170) REVERT: F 398 GLN cc_start: 0.8926 (mm-40) cc_final: 0.8606 (tp40) REVERT: G 46 GLU cc_start: 0.7450 (tt0) cc_final: 0.6608 (tt0) REVERT: G 55 ILE cc_start: 0.8354 (mt) cc_final: 0.7999 (tp) REVERT: G 74 MET cc_start: 0.7578 (mtm) cc_final: 0.7315 (mtp) REVERT: G 153 LYS cc_start: 0.4172 (OUTLIER) cc_final: 0.3478 (tptt) REVERT: H 178 LYS cc_start: 0.7298 (mmtp) cc_final: 0.6846 (mtpt) REVERT: f 238 LYS cc_start: 0.8304 (mtpt) cc_final: 0.7894 (mtmt) REVERT: f 340 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7785 (tt) REVERT: f 389 LYS cc_start: 0.8263 (mtpt) cc_final: 0.7661 (ttmm) REVERT: f 421 ASP cc_start: 0.7488 (p0) cc_final: 0.7026 (t0) outliers start: 78 outliers final: 62 residues processed: 324 average time/residue: 0.3464 time to fit residues: 168.7142 Evaluate side-chains 336 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 261 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 416 TRP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 743 PHE Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 851 ASP Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 942 MET Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 1023 TRP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain f residue 220 GLN Chi-restraints excluded: chain f residue 253 TYR Chi-restraints excluded: chain f residue 270 ASN Chi-restraints excluded: chain f residue 272 VAL Chi-restraints excluded: chain f residue 326 HIS Chi-restraints excluded: chain f residue 337 VAL Chi-restraints excluded: chain f residue 340 ILE Chi-restraints excluded: chain f residue 347 THR Chi-restraints excluded: chain f residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.6980 chunk 227 optimal weight: 0.5980 chunk 139 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 chunk 239 optimal weight: 10.0000 chunk 220 optimal weight: 0.6980 chunk 190 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 916 ASN ** F 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 HIS ** G 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 214 HIS ** f 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 21182 Z= 0.294 Angle : 0.599 12.184 29061 Z= 0.316 Chirality : 0.042 0.176 3241 Planarity : 0.004 0.044 3397 Dihedral : 17.851 150.856 3534 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.89 % Allowed : 17.27 % Favored : 78.85 % 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: 0.38 (0.18), residues: 2300 helix: 1.34 (0.16), residues: 1124 sheet: -0.06 (0.31), residues: 270 loop : -1.02 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 327 HIS 0.008 0.001 HIS B 454 PHE 0.023 0.001 PHE B 190 TYR 0.019 0.001 TYR F 374 ARG 0.011 0.000 ARG A1233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 261 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7098 (tp30) REVERT: A 639 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7242 (pp) REVERT: A 744 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6852 (tt0) REVERT: A 745 ASN cc_start: 0.7938 (OUTLIER) cc_final: 0.7314 (p0) REVERT: A 1058 HIS cc_start: 0.6187 (OUTLIER) cc_final: 0.5471 (t70) REVERT: A 1165 LEU cc_start: -0.3413 (OUTLIER) cc_final: -0.3653 (tt) REVERT: B 41 GLN cc_start: 0.7581 (mp10) cc_final: 0.7351 (mp10) REVERT: B 71 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6676 (ttt90) REVERT: B 120 ASP cc_start: 0.7580 (m-30) cc_final: 0.6921 (m-30) REVERT: B 145 LYS cc_start: 0.8115 (mttt) cc_final: 0.7496 (mtpp) REVERT: B 212 MET cc_start: 0.8437 (mtt) cc_final: 0.8162 (mtt) REVERT: B 262 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7694 (mtm) REVERT: B 295 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7498 (mt) REVERT: B 520 LYS cc_start: 0.8473 (tttt) cc_final: 0.8100 (ttmm) REVERT: B 683 ASP cc_start: 0.7744 (m-30) cc_final: 0.7213 (m-30) REVERT: B 785 ARG cc_start: 0.8548 (mtm180) cc_final: 0.8249 (mtm-85) REVERT: B 798 MET cc_start: 0.7472 (mmm) cc_final: 0.6955 (mtp) REVERT: B 879 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7366 (mm-30) REVERT: B 892 GLU cc_start: 0.8150 (tt0) cc_final: 0.7796 (mt-10) REVERT: B 916 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8232 (p0) REVERT: F 252 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7585 (tt) REVERT: F 281 TYR cc_start: 0.7404 (m-80) cc_final: 0.7155 (m-80) REVERT: F 287 LYS cc_start: 0.8823 (tptp) cc_final: 0.8222 (ttmt) REVERT: F 295 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7572 (pp) REVERT: F 335 ARG cc_start: 0.6974 (ttp-170) cc_final: 0.6735 (ttp-170) REVERT: F 398 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8618 (tp40) REVERT: G 46 GLU cc_start: 0.7458 (tt0) cc_final: 0.6611 (tt0) REVERT: G 55 ILE cc_start: 0.8354 (mt) cc_final: 0.7897 (tp) REVERT: G 153 LYS cc_start: 0.4176 (OUTLIER) cc_final: 0.3493 (tptt) REVERT: H 178 LYS cc_start: 0.7309 (mmtp) cc_final: 0.6899 (mtpt) REVERT: f 238 LYS cc_start: 0.8325 (mtpt) cc_final: 0.7905 (mtmt) REVERT: f 340 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7803 (tt) REVERT: f 389 LYS cc_start: 0.8308 (mtpt) cc_final: 0.7711 (ttmm) REVERT: f 421 ASP cc_start: 0.7528 (p0) cc_final: 0.7058 (t0) outliers start: 79 outliers final: 63 residues processed: 324 average time/residue: 0.3664 time to fit residues: 179.5940 Evaluate side-chains 334 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 258 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 416 TRP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 743 PHE Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 851 ASP Chi-restraints excluded: chain A residue 925 ASP Chi-restraints excluded: chain A residue 942 MET Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 970 ASN Chi-restraints excluded: chain A residue 1023 TRP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 788 LYS Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 945 CYS Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 326 HIS Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain f residue 220 GLN Chi-restraints excluded: chain f residue 253 TYR Chi-restraints excluded: chain f residue 270 ASN Chi-restraints excluded: chain f residue 272 VAL Chi-restraints excluded: chain f residue 326 HIS Chi-restraints excluded: chain f residue 337 VAL Chi-restraints excluded: chain f residue 340 ILE Chi-restraints excluded: chain f residue 347 THR Chi-restraints excluded: chain f residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.2980 chunk 202 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 190 optimal weight: 0.0980 chunk 79 optimal weight: 0.6980 chunk 195 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 916 ASN ** F 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 214 HIS ** f 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.163822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.111654 restraints weight = 28252.491| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.54 r_work: 0.3002 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21182 Z= 0.246 Angle : 0.583 12.411 29061 Z= 0.308 Chirality : 0.041 0.170 3241 Planarity : 0.004 0.044 3397 Dihedral : 17.812 150.779 3534 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.89 % Allowed : 17.41 % Favored : 78.70 % 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: 0.44 (0.18), residues: 2300 helix: 1.41 (0.16), residues: 1124 sheet: -0.04 (0.31), residues: 270 loop : -0.99 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 327 HIS 0.009 0.001 HIS B 137 PHE 0.022 0.001 PHE F 344 TYR 0.019 0.001 TYR F 374 ARG 0.010 0.000 ARG A1233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5513.96 seconds wall clock time: 100 minutes 13.19 seconds (6013.19 seconds total)