Starting phenix.real_space_refine on Mon Mar 25 17:18:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pby_17588/03_2024/8pby_17588.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pby_17588/03_2024/8pby_17588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pby_17588/03_2024/8pby_17588.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pby_17588/03_2024/8pby_17588.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pby_17588/03_2024/8pby_17588.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pby_17588/03_2024/8pby_17588.pdb" } resolution = 3.7 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= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16866 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 20 5.16 5 C 10723 2.51 5 N 2866 2.21 5 O 3397 1.98 5 H 16474 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 735": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 843": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 933": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 724": "OD1" <-> "OD2" Residue "B PHE 761": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1022": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33480 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 13658 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 902, 13658 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 40, 'TRANS': 861} Chain breaks: 2 Chain: "B" Number of atoms: 19822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1285, 19822 Classifications: {'peptide': 1285} Link IDs: {'PTRANS': 80, 'TRANS': 1204} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N BARG A 834 " occ=0.50 ... (22 atoms not shown) pdb="HH22BARG A 834 " occ=0.50 Time building chain proxies: 13.94, per 1000 atoms: 0.42 Number of scatterers: 33480 At special positions: 0 Unit cell: (90.3, 128.1, 140.7, 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 20 16.00 O 3397 8.00 N 2866 7.00 C 10723 6.00 H 16474 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 28.68 Conformation dependent library (CDL) restraints added in 3.9 seconds 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4066 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 33 sheets defined 20.9% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.86 Creating SS restraints... Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 101 through 104 Processing helix chain 'A' and resid 138 through 147 removed outlier: 4.005A pdb=" N ASN A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 236 through 243 removed outlier: 3.612A pdb=" N THR A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 252 Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 349 through 359 removed outlier: 3.891A pdb=" N GLN A 359 " --> pdb=" O PHE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 489 through 496 removed outlier: 4.354A pdb=" N SER A 494 " --> pdb=" O ASP A 491 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 496 " --> pdb=" O LYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 522 Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 596 through 600 Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 717 through 719 No H-bonds generated for 'chain 'A' and resid 717 through 719' Processing helix chain 'A' and resid 750 through 754 Processing helix chain 'A' and resid 812 through 820 removed outlier: 4.277A pdb=" N SER A 818 " --> pdb=" O GLN A 814 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 852 Processing helix chain 'A' and resid 858 through 864 Processing helix chain 'A' and resid 865 through 870 Processing helix chain 'B' and resid 99 through 103 removed outlier: 3.695A pdb=" N VAL B 103 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 124 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 212 through 216 Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 326 through 333 Processing helix chain 'B' and resid 362 through 369 removed outlier: 3.958A pdb=" N MET B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 411 through 416 removed outlier: 3.736A pdb=" N LYS B 415 " --> pdb=" O GLY B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 453 Processing helix chain 'B' and resid 471 through 475 Processing helix chain 'B' and resid 504 through 510 removed outlier: 3.590A pdb=" N LEU B 508 " --> pdb=" O PRO B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 583 Processing helix chain 'B' and resid 604 through 612 removed outlier: 4.527A pdb=" N LEU B 609 " --> pdb=" O GLY B 606 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLN B 610 " --> pdb=" O ALA B 607 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP B 611 " --> pdb=" O TRP B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 633 through 641 Processing helix chain 'B' and resid 661 through 670 Processing helix chain 'B' and resid 699 through 706 Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 721 through 726 Processing helix chain 'B' and resid 740 through 744 Processing helix chain 'B' and resid 758 through 768 removed outlier: 3.859A pdb=" N ASP B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 810 No H-bonds generated for 'chain 'B' and resid 808 through 810' Processing helix chain 'B' and resid 903 through 917 Processing helix chain 'B' and resid 946 through 950 removed outlier: 3.589A pdb=" N GLY B 949 " --> pdb=" O THR B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 970 Processing helix chain 'B' and resid 1051 through 1057 Processing helix chain 'B' and resid 1080 through 1084 Processing helix chain 'B' and resid 1134 through 1136 No H-bonds generated for 'chain 'B' and resid 1134 through 1136' Processing helix chain 'B' and resid 1137 through 1143 removed outlier: 3.738A pdb=" N LEU B1143 " --> pdb=" O SER B1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 1145 through 1154 Processing helix chain 'B' and resid 1157 through 1161 removed outlier: 3.778A pdb=" N SER B1160 " --> pdb=" O THR B1157 " (cutoff:3.500A) Processing helix chain 'B' and resid 1192 through 1205 Processing helix chain 'B' and resid 1207 through 1212 removed outlier: 3.646A pdb=" N ILE B1211 " --> pdb=" O ASN B1207 " (cutoff:3.500A) Processing helix chain 'B' and resid 1255 through 1259 Processing helix chain 'B' and resid 1281 through 1285 removed outlier: 3.897A pdb=" N VAL B1285 " --> pdb=" O ASP B1282 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.699A pdb=" N VAL A 30 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A 38 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 71 removed outlier: 6.742A pdb=" N LEU A 79 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLN A 69 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE A 77 " --> pdb=" O GLN A 69 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LEU A 76 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE A 114 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 78 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR A 110 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS A 128 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N THR A 115 " --> pdb=" O MET A 126 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N MET A 126 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 213 through 215 removed outlier: 3.909A pdb=" N ILE A 149 " --> pdb=" O SER A 500 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 225 removed outlier: 3.657A pdb=" N GLU A 224 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 269 " --> pdb=" O GLU A 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 302 removed outlier: 3.745A pdb=" N VAL A 325 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA9, first strand: chain 'A' and resid 383 through 391 removed outlier: 7.063A pdb=" N SER A 398 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE A 388 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE A 396 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER A 390 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N GLN A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE A 395 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A 397 " --> pdb=" O GLY A 545 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 545 " --> pdb=" O PHE A 397 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE A 541 " --> pdb=" O LYS A 401 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 648 through 650 removed outlier: 3.561A pdb=" N VAL A 657 " --> pdb=" O VAL A 650 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A 658 " --> pdb=" O SER A 682 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER A 682 " --> pdb=" O ARG A 658 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 698 through 701 removed outlier: 5.851A pdb=" N PHE A 698 " --> pdb=" O ASP A 715 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASP A 715 " --> pdb=" O PHE A 698 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU A 700 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N PHE A 735 " --> pdb=" O ILE A 769 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE A 769 " --> pdb=" O PHE A 735 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N VAL A 737 " --> pdb=" O SER A 767 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 767 " --> pdb=" O VAL A 737 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A 741 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 763 " --> pdb=" O SER A 741 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR A 743 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER A 761 " --> pdb=" O THR A 743 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 775 through 780 removed outlier: 6.780A pdb=" N ILE A 790 " --> pdb=" O THR A 777 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N VAL A 779 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA A 788 " --> pdb=" O VAL A 779 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 840 through 843 Processing sheet with id=AB5, first strand: chain 'A' and resid 884 through 887 removed outlier: 3.775A pdb=" N VAL A 887 " --> pdb=" O SER A 899 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER A 899 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 895 through 897 removed outlier: 3.607A pdb=" N PHE A 930 " --> pdb=" O LEU A 896 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 915 through 916 Processing sheet with id=AB8, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.592A pdb=" N ALA B 129 " --> pdb=" O VAL B 91 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 164 through 165 Processing sheet with id=AC1, first strand: chain 'B' and resid 186 through 194 removed outlier: 6.527A pdb=" N VAL B 206 " --> pdb=" O PRO B 188 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 190 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU B 200 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 340 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL B 358 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N SER B 342 " --> pdb=" O GLY B 356 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 245 through 247 Processing sheet with id=AC3, first strand: chain 'B' and resid 292 through 293 removed outlier: 4.645A pdb=" N LYS B 292 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 282 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 653 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 458 through 460 removed outlier: 3.576A pdb=" N LYS B 490 " --> pdb=" O SER B 499 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 499 " --> pdb=" O LYS B 490 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 537 through 539 removed outlier: 3.554A pdb=" N SER B 692 " --> pdb=" O LEU B 555 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA B 695 " --> pdb=" O PHE B 750 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE B 750 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE B 697 " --> pdb=" O GLN B 748 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 558 through 559 removed outlier: 4.384A pdb=" N GLU B 685 " --> pdb=" O ASP B 559 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 804 through 806 removed outlier: 3.567A pdb=" N ILE B 828 " --> pdb=" O SER B 805 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 845 through 846 Processing sheet with id=AC9, first strand: chain 'B' and resid 867 through 868 Processing sheet with id=AD1, first strand: chain 'B' and resid 921 through 923 removed outlier: 3.557A pdb=" N VAL B 921 " --> pdb=" O VAL B 998 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 996 " --> pdb=" O ILE B 923 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1021 through 1024 removed outlier: 3.530A pdb=" N PHE B1022 " --> pdb=" O ILE B1029 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1067 through 1068 removed outlier: 3.673A pdb=" N TYR B1068 " --> pdb=" O LYS B1076 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1228 through 1229 Processing sheet with id=AD5, first strand: chain 'B' and resid 1301 through 1306 removed outlier: 6.911A pdb=" N GLY B1315 " --> pdb=" O ILE B1305 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1301 through 1306 removed outlier: 6.911A pdb=" N GLY B1315 " --> pdb=" O ILE B1305 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B1316 " --> pdb=" O THR B1341 " (cutoff:3.500A) 375 hydrogen bonds defined for protein. 924 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.53 Time building geometry restraints manager: 29.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16474 1.03 - 1.22: 4 1.22 - 1.42: 7399 1.42 - 1.61: 9961 1.61 - 1.81: 40 Bond restraints: 33878 Sorted by residual: bond pdb=" C ASN B 150 " pdb=" O ASN B 150 " ideal model delta sigma weight residual 1.235 1.228 0.007 4.70e-03 4.53e+04 2.26e+00 bond pdb=" CA PRO B 371 " pdb=" C PRO B 371 " ideal model delta sigma weight residual 1.514 1.507 0.007 5.50e-03 3.31e+04 1.66e+00 bond pdb=" CH2 TRP A 240 " pdb=" HH2 TRP A 240 " ideal model delta sigma weight residual 0.930 0.908 0.022 2.00e-02 2.50e+03 1.16e+00 bond pdb=" CD GLN B 590 " pdb=" NE2 GLN B 590 " ideal model delta sigma weight residual 1.328 1.306 0.022 2.10e-02 2.27e+03 1.14e+00 bond pdb=" CA GLN B 590 " pdb=" CB GLN B 590 " ideal model delta sigma weight residual 1.526 1.509 0.017 1.70e-02 3.46e+03 1.04e+00 ... (remaining 33873 not shown) Histogram of bond angle deviations from ideal: 100.23 - 107.01: 741 107.01 - 113.78: 39960 113.78 - 120.55: 10785 120.55 - 127.32: 9409 127.32 - 134.09: 206 Bond angle restraints: 61101 Sorted by residual: angle pdb=" CA GLN B 590 " pdb=" CB GLN B 590 " pdb=" CG GLN B 590 " ideal model delta sigma weight residual 114.10 122.14 -8.04 2.00e+00 2.50e-01 1.62e+01 angle pdb=" N GLN B 590 " pdb=" CA GLN B 590 " pdb=" CB GLN B 590 " ideal model delta sigma weight residual 110.87 105.55 5.32 1.63e+00 3.76e-01 1.07e+01 angle pdb=" N ASN A 119 " pdb=" CA ASN A 119 " pdb=" C ASN A 119 " ideal model delta sigma weight residual 112.97 109.55 3.42 1.06e+00 8.90e-01 1.04e+01 angle pdb=" N ASN B 855 " pdb=" CA ASN B 855 " pdb=" C ASN B 855 " ideal model delta sigma weight residual 112.97 109.76 3.21 1.06e+00 8.90e-01 9.18e+00 angle pdb=" C GLN B 590 " pdb=" CA GLN B 590 " pdb=" CB GLN B 590 " ideal model delta sigma weight residual 111.17 115.52 -4.35 1.54e+00 4.22e-01 7.99e+00 ... (remaining 61096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 14530 17.59 - 35.18: 1247 35.18 - 52.77: 338 52.77 - 70.37: 78 70.37 - 87.96: 12 Dihedral angle restraints: 16205 sinusoidal: 8739 harmonic: 7466 Sorted by residual: dihedral pdb=" CA LEU B 589 " pdb=" C LEU B 589 " pdb=" N GLN B 590 " pdb=" CA GLN B 590 " ideal model delta harmonic sigma weight residual -180.00 -145.26 -34.74 0 5.00e+00 4.00e-02 4.83e+01 dihedral pdb=" CA TRP B1061 " pdb=" C TRP B1061 " pdb=" N THR B1062 " pdb=" CA THR B1062 " ideal model delta harmonic sigma weight residual 180.00 152.77 27.23 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA GLN A 152 " pdb=" C GLN A 152 " pdb=" N PRO A 153 " pdb=" CA PRO A 153 " ideal model delta harmonic sigma weight residual -180.00 -152.93 -27.07 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 16202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1634 0.031 - 0.061: 690 0.061 - 0.092: 147 0.092 - 0.122: 140 0.122 - 0.153: 18 Chirality restraints: 2629 Sorted by residual: chirality pdb=" CA ILE A 309 " pdb=" N ILE A 309 " pdb=" C ILE A 309 " pdb=" CB ILE A 309 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA ILE B 489 " pdb=" N ILE B 489 " pdb=" C ILE B 489 " pdb=" CB ILE B 489 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA GLU B 638 " pdb=" N GLU B 638 " pdb=" C GLU B 638 " pdb=" CB GLU B 638 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 2626 not shown) Planarity restraints: 5173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 220 " 0.022 2.00e-02 2.50e+03 1.21e-02 5.89e+00 pdb=" CG TRP A 220 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 220 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 220 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 220 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 220 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 220 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 220 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 220 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP A 220 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 TRP A 220 " 0.007 2.00e-02 2.50e+03 pdb=" HE1 TRP A 220 " 0.004 2.00e-02 2.50e+03 pdb=" HE3 TRP A 220 " -0.007 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 220 " 0.006 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 220 " 0.006 2.00e-02 2.50e+03 pdb=" HH2 TRP A 220 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 45 " 0.037 5.00e-02 4.00e+02 5.64e-02 5.08e+00 pdb=" N PRO A 46 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 46 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 46 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 197 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.76e+00 pdb=" N PRO B 198 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 198 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 198 " 0.030 5.00e-02 4.00e+02 ... (remaining 5170 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.86: 272 1.86 - 2.55: 33685 2.55 - 3.23: 109045 3.23 - 3.92: 138620 3.92 - 4.60: 217181 Nonbonded interactions: 498803 Sorted by model distance: nonbonded pdb=" O ASN A 530 " pdb="HD21 ASN A 530 " model vdw 1.179 1.850 nonbonded pdb=" OD1 ASN B 903 " pdb=" H GLN B 906 " model vdw 1.425 1.850 nonbonded pdb=" HE2 HIS B 405 " pdb=" O ASN B 686 " model vdw 1.486 1.850 nonbonded pdb="HD22 ASN B 369 " pdb=" O GLY B 502 " model vdw 1.488 1.850 nonbonded pdb=" H PHE B1253 " pdb=" O ALA B1334 " model vdw 1.509 1.850 ... (remaining 498798 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.300 Construct map_model_manager: 0.500 Extract box with map and model: 7.580 Check model and map are aligned: 0.480 Set scattering table: 0.280 Process input model: 109.100 Find NCS groups from input model: 0.540 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6021 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17404 Z= 0.180 Angle : 0.565 8.040 23686 Z= 0.304 Chirality : 0.041 0.153 2629 Planarity : 0.005 0.056 3111 Dihedral : 13.884 87.957 6296 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.37 % Favored : 91.40 % Rotamer: Outliers : 0.05 % Allowed : 0.26 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.20 (0.17), residues: 2177 helix: -0.76 (0.29), residues: 332 sheet: -1.47 (0.30), residues: 282 loop : -1.73 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 220 HIS 0.004 0.001 HIS B 967 PHE 0.014 0.001 PHE B 761 TYR 0.021 0.001 TYR A 486 ARG 0.005 0.001 ARG A 537 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 321 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 320 time to evaluate : 2.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8039 (ttpp) cc_final: 0.7714 (tttp) REVERT: A 152 GLN cc_start: 0.7643 (pt0) cc_final: 0.7326 (pt0) REVERT: A 165 LYS cc_start: 0.7252 (ptmm) cc_final: 0.6498 (ptmm) REVERT: A 582 TYR cc_start: 0.7349 (p90) cc_final: 0.7141 (p90) REVERT: A 789 VAL cc_start: 0.6481 (t) cc_final: 0.6238 (t) REVERT: B 168 LYS cc_start: 0.7482 (tppt) cc_final: 0.7202 (ttmt) REVERT: B 333 GLU cc_start: 0.7700 (tp30) cc_final: 0.7051 (tp30) REVERT: B 402 PRO cc_start: 0.7611 (Cg_endo) cc_final: 0.6776 (Cg_exo) REVERT: B 409 PHE cc_start: 0.7165 (m-80) cc_final: 0.6520 (m-80) REVERT: B 630 ASP cc_start: 0.6463 (m-30) cc_final: 0.6139 (m-30) REVERT: B 685 GLU cc_start: 0.6397 (tm-30) cc_final: 0.6114 (tm-30) REVERT: B 707 SER cc_start: 0.8190 (t) cc_final: 0.7986 (t) REVERT: B 1327 GLN cc_start: 0.6346 (tt0) cc_final: 0.6104 (tt0) outliers start: 1 outliers final: 0 residues processed: 321 average time/residue: 0.6251 time to fit residues: 309.3684 Evaluate side-chains 235 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN A 817 ASN B 97 ASN B 155 GLN ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN ** B 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN B1023 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17404 Z= 0.352 Angle : 0.646 6.541 23686 Z= 0.344 Chirality : 0.043 0.194 2629 Planarity : 0.006 0.063 3111 Dihedral : 5.459 28.151 2301 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 24.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.87 % Favored : 87.90 % Rotamer: Outliers : 0.84 % Allowed : 8.05 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.17), residues: 2177 helix: -0.78 (0.29), residues: 329 sheet: -1.49 (0.29), residues: 308 loop : -2.04 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 220 HIS 0.006 0.001 HIS B 967 PHE 0.022 0.002 PHE B 694 TYR 0.019 0.002 TYR A 577 ARG 0.004 0.001 ARG B 907 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 249 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 233 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8161 (ttpp) cc_final: 0.7815 (tttp) REVERT: A 789 VAL cc_start: 0.6905 (t) cc_final: 0.6673 (t) REVERT: A 840 LYS cc_start: 0.4370 (mmmm) cc_final: 0.3132 (tmtt) REVERT: B 333 GLU cc_start: 0.7817 (tp30) cc_final: 0.7105 (tp30) REVERT: B 402 PRO cc_start: 0.7730 (Cg_endo) cc_final: 0.6863 (Cg_exo) REVERT: B 409 PHE cc_start: 0.7456 (m-80) cc_final: 0.6758 (m-80) REVERT: B 630 ASP cc_start: 0.6482 (m-30) cc_final: 0.6233 (m-30) REVERT: B 748 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7779 (tm-30) outliers start: 16 outliers final: 10 residues processed: 242 average time/residue: 0.6382 time to fit residues: 242.3970 Evaluate side-chains 225 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 215 time to evaluate : 3.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 1035 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 chunk 214 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 196 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN ** B 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 ASN B1327 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6227 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 17404 Z= 0.376 Angle : 0.653 6.943 23686 Z= 0.350 Chirality : 0.043 0.180 2629 Planarity : 0.006 0.074 3111 Dihedral : 5.775 27.706 2301 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 27.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.87 % Favored : 87.86 % Rotamer: Outliers : 1.36 % Allowed : 12.64 % Favored : 86.00 % 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: -2.88 (0.16), residues: 2177 helix: -1.25 (0.27), residues: 348 sheet: -1.71 (0.29), residues: 313 loop : -2.27 (0.14), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 220 HIS 0.009 0.002 HIS B 967 PHE 0.024 0.002 PHE B 682 TYR 0.020 0.002 TYR A 577 ARG 0.009 0.001 ARG B1301 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 248 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 222 time to evaluate : 2.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8167 (ttpp) cc_final: 0.7749 (tttp) REVERT: A 317 LEU cc_start: 0.8272 (pt) cc_final: 0.8027 (pp) REVERT: A 789 VAL cc_start: 0.7013 (t) cc_final: 0.6794 (t) REVERT: B 402 PRO cc_start: 0.7772 (Cg_endo) cc_final: 0.6833 (Cg_exo) REVERT: B 409 PHE cc_start: 0.7686 (m-80) cc_final: 0.6928 (m-80) REVERT: B 748 GLN cc_start: 0.7988 (tm-30) cc_final: 0.7740 (tm-30) REVERT: B 1301 ARG cc_start: 0.7371 (mmt90) cc_final: 0.7139 (mmm160) outliers start: 26 outliers final: 22 residues processed: 236 average time/residue: 0.5912 time to fit residues: 220.9665 Evaluate side-chains 236 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 214 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 892 ASP Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1035 ILE Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1341 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 195 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 199 optimal weight: 0.0470 chunk 210 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 909 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17404 Z= 0.201 Angle : 0.559 5.332 23686 Z= 0.292 Chirality : 0.041 0.182 2629 Planarity : 0.005 0.061 3111 Dihedral : 5.321 28.689 2301 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.43 % Favored : 90.29 % Rotamer: Outliers : 0.84 % Allowed : 14.42 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.50 (0.17), residues: 2177 helix: -0.79 (0.28), residues: 336 sheet: -1.55 (0.29), residues: 305 loop : -2.02 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1061 HIS 0.006 0.001 HIS B 967 PHE 0.018 0.001 PHE B 343 TYR 0.016 0.001 TYR A 40 ARG 0.003 0.000 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 246 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 230 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8091 (ttpp) cc_final: 0.7705 (tttp) REVERT: A 317 LEU cc_start: 0.8052 (pt) cc_final: 0.7835 (pp) REVERT: A 789 VAL cc_start: 0.6899 (t) cc_final: 0.6696 (t) REVERT: A 904 PHE cc_start: 0.6220 (t80) cc_final: 0.5644 (t80) REVERT: B 333 GLU cc_start: 0.7326 (tp30) cc_final: 0.6935 (tp30) REVERT: B 402 PRO cc_start: 0.7741 (Cg_endo) cc_final: 0.6790 (Cg_exo) REVERT: B 409 PHE cc_start: 0.7495 (m-80) cc_final: 0.6748 (m-80) REVERT: B 909 GLN cc_start: 0.7976 (mt0) cc_final: 0.7314 (mt0) REVERT: B 1301 ARG cc_start: 0.7668 (mmt90) cc_final: 0.7180 (mmm160) outliers start: 16 outliers final: 13 residues processed: 238 average time/residue: 0.5909 time to fit residues: 221.8403 Evaluate side-chains 229 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 216 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 667 PHE Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 892 ASP Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 1078 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 175 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 107 optimal weight: 0.0050 chunk 189 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 17404 Z= 0.368 Angle : 0.634 6.759 23686 Z= 0.338 Chirality : 0.043 0.177 2629 Planarity : 0.006 0.068 3111 Dihedral : 5.626 28.381 2301 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 28.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.20 % Favored : 86.57 % Rotamer: Outliers : 1.67 % Allowed : 15.83 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.17), residues: 2177 helix: -1.08 (0.27), residues: 343 sheet: -1.60 (0.30), residues: 309 loop : -2.27 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 838 HIS 0.008 0.002 HIS B 967 PHE 0.023 0.002 PHE B 694 TYR 0.018 0.002 TYR A 295 ARG 0.004 0.001 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 252 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 220 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8162 (ttpp) cc_final: 0.7743 (tttp) REVERT: A 317 LEU cc_start: 0.8251 (pt) cc_final: 0.7992 (pp) REVERT: A 840 LYS cc_start: 0.4783 (mmmm) cc_final: 0.3670 (tttm) REVERT: A 904 PHE cc_start: 0.6333 (t80) cc_final: 0.5704 (t80) REVERT: B 333 GLU cc_start: 0.7431 (tp30) cc_final: 0.6825 (tp30) REVERT: B 402 PRO cc_start: 0.7770 (Cg_endo) cc_final: 0.6838 (Cg_exo) REVERT: B 409 PHE cc_start: 0.7681 (m-80) cc_final: 0.6881 (m-80) REVERT: B 748 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7791 (tm-30) REVERT: B 1301 ARG cc_start: 0.7734 (mmt90) cc_final: 0.7165 (mmm160) outliers start: 32 outliers final: 25 residues processed: 238 average time/residue: 0.5950 time to fit residues: 222.1240 Evaluate side-chains 233 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 208 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 892 ASP Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1035 ILE Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1341 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 70 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 210 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6197 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17404 Z= 0.270 Angle : 0.586 5.734 23686 Z= 0.308 Chirality : 0.042 0.178 2629 Planarity : 0.005 0.065 3111 Dihedral : 5.475 29.480 2301 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 24.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.53 % Favored : 89.24 % Rotamer: Outliers : 1.67 % Allowed : 17.19 % Favored : 81.14 % 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: -2.60 (0.17), residues: 2177 helix: -0.73 (0.28), residues: 329 sheet: -1.61 (0.29), residues: 309 loop : -2.12 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B1061 HIS 0.007 0.001 HIS B 967 PHE 0.019 0.002 PHE B 343 TYR 0.020 0.001 TYR B 133 ARG 0.004 0.001 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 248 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 216 time to evaluate : 2.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7766 (tttp) REVERT: A 317 LEU cc_start: 0.8243 (pt) cc_final: 0.8005 (pp) REVERT: A 840 LYS cc_start: 0.4715 (mmmm) cc_final: 0.3734 (tttm) REVERT: A 904 PHE cc_start: 0.6337 (t80) cc_final: 0.5684 (t80) REVERT: B 333 GLU cc_start: 0.7334 (tp30) cc_final: 0.6738 (tp30) REVERT: B 402 PRO cc_start: 0.7775 (Cg_endo) cc_final: 0.6814 (Cg_exo) REVERT: B 409 PHE cc_start: 0.7631 (m-80) cc_final: 0.6845 (m-80) REVERT: B 457 MET cc_start: 0.3334 (OUTLIER) cc_final: 0.2976 (ppp) REVERT: B 748 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7794 (tm-30) REVERT: B 1301 ARG cc_start: 0.7944 (mmt90) cc_final: 0.7376 (mmm160) outliers start: 32 outliers final: 26 residues processed: 233 average time/residue: 0.6161 time to fit residues: 226.3084 Evaluate side-chains 239 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 212 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 667 PHE Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain B residue 892 ASP Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1078 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 203 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 117 optimal weight: 0.8980 chunk 210 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 17404 Z= 0.415 Angle : 0.661 7.374 23686 Z= 0.353 Chirality : 0.044 0.175 2629 Planarity : 0.006 0.072 3111 Dihedral : 5.797 29.881 2301 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 31.36 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.75 % Favored : 86.02 % Rotamer: Outliers : 2.56 % Allowed : 17.40 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.17), residues: 2177 helix: -1.03 (0.27), residues: 335 sheet: -1.87 (0.30), residues: 297 loop : -2.29 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 838 HIS 0.009 0.002 HIS B 967 PHE 0.017 0.002 PHE B 343 TYR 0.020 0.002 TYR A 295 ARG 0.005 0.001 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 252 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 203 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8282 (ttpp) cc_final: 0.7870 (tttp) REVERT: A 840 LYS cc_start: 0.4935 (mmmm) cc_final: 0.3792 (tttm) REVERT: B 333 GLU cc_start: 0.7464 (tp30) cc_final: 0.6875 (tp30) REVERT: B 457 MET cc_start: 0.3582 (OUTLIER) cc_final: 0.3097 (ppp) REVERT: B 748 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7810 (tm-30) outliers start: 49 outliers final: 40 residues processed: 231 average time/residue: 0.5936 time to fit residues: 215.6956 Evaluate side-chains 242 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 201 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 749 GLN Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 531 PHE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 701 ASP Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain B residue 892 ASP Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 906 GLN Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1035 ILE Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain B residue 1322 ASP Chi-restraints excluded: chain B residue 1341 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 129 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 103 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6179 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17404 Z= 0.213 Angle : 0.571 6.741 23686 Z= 0.297 Chirality : 0.042 0.182 2629 Planarity : 0.005 0.064 3111 Dihedral : 5.435 30.659 2301 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 23.54 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.94 % Favored : 89.83 % Rotamer: Outliers : 1.41 % Allowed : 18.55 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.53 (0.17), residues: 2177 helix: -0.65 (0.28), residues: 329 sheet: -1.56 (0.31), residues: 290 loop : -2.08 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B1061 HIS 0.006 0.001 HIS B 967 PHE 0.022 0.002 PHE B 343 TYR 0.011 0.001 TYR A 439 ARG 0.004 0.000 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 243 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 216 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8199 (ttpp) cc_final: 0.7840 (tttp) REVERT: A 427 TRP cc_start: 0.8463 (p90) cc_final: 0.8263 (p90) REVERT: A 840 LYS cc_start: 0.4795 (mmmm) cc_final: 0.3668 (tttm) REVERT: A 904 PHE cc_start: 0.6329 (t80) cc_final: 0.5543 (t80) REVERT: B 333 GLU cc_start: 0.7369 (tp30) cc_final: 0.6780 (tp30) REVERT: B 402 PRO cc_start: 0.7759 (Cg_endo) cc_final: 0.7502 (Cg_exo) REVERT: B 457 MET cc_start: 0.3418 (OUTLIER) cc_final: 0.2973 (ppp) REVERT: B 748 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7690 (tm-30) REVERT: B 1301 ARG cc_start: 0.7862 (mmt90) cc_final: 0.6971 (mmm160) outliers start: 27 outliers final: 22 residues processed: 227 average time/residue: 0.6021 time to fit residues: 214.5390 Evaluate side-chains 233 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 210 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain B residue 892 ASP Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 906 GLN Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1341 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 191 optimal weight: 0.5980 chunk 201 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 153 optimal weight: 0.1980 chunk 60 optimal weight: 0.7980 chunk 176 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17404 Z= 0.183 Angle : 0.549 6.726 23686 Z= 0.283 Chirality : 0.041 0.180 2629 Planarity : 0.005 0.062 3111 Dihedral : 5.106 28.765 2301 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.66 % Favored : 90.11 % Rotamer: Outliers : 1.52 % Allowed : 18.55 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.30 (0.17), residues: 2177 helix: -0.39 (0.29), residues: 329 sheet: -1.43 (0.31), residues: 287 loop : -1.94 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1061 HIS 0.004 0.001 HIS B 810 PHE 0.022 0.001 PHE B 343 TYR 0.012 0.001 TYR A 486 ARG 0.003 0.000 ARG B1036 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 254 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 225 time to evaluate : 2.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8221 (ttpp) cc_final: 0.7888 (tttp) REVERT: A 840 LYS cc_start: 0.4782 (mmmm) cc_final: 0.3676 (tttm) REVERT: A 872 PHE cc_start: 0.6164 (m-10) cc_final: 0.5935 (m-80) REVERT: A 904 PHE cc_start: 0.6262 (t80) cc_final: 0.5550 (t80) REVERT: B 333 GLU cc_start: 0.7348 (tp30) cc_final: 0.6736 (tp30) REVERT: B 402 PRO cc_start: 0.7714 (Cg_endo) cc_final: 0.6769 (Cg_exo) REVERT: B 409 PHE cc_start: 0.7511 (m-80) cc_final: 0.6752 (m-80) REVERT: B 457 MET cc_start: 0.3324 (OUTLIER) cc_final: 0.2880 (ppp) REVERT: B 814 GLU cc_start: 0.6346 (mp0) cc_final: 0.6057 (mp0) REVERT: B 1301 ARG cc_start: 0.7938 (mmt90) cc_final: 0.7085 (mmm160) outliers start: 29 outliers final: 24 residues processed: 238 average time/residue: 0.6267 time to fit residues: 234.0430 Evaluate side-chains 243 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 218 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 667 PHE Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 892 ASP Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 906 GLN Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1341 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 207 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 106 optimal weight: 0.0050 chunk 137 optimal weight: 4.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6224 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17404 Z= 0.310 Angle : 0.611 6.963 23686 Z= 0.320 Chirality : 0.042 0.175 2629 Planarity : 0.005 0.075 3111 Dihedral : 5.380 28.730 2301 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 26.61 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.73 % Favored : 87.99 % Rotamer: Outliers : 1.57 % Allowed : 18.81 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.17), residues: 2177 helix: -0.67 (0.28), residues: 335 sheet: -1.72 (0.30), residues: 302 loop : -2.08 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 838 HIS 0.006 0.001 HIS B 967 PHE 0.018 0.002 PHE B1320 TYR 0.017 0.002 TYR A 295 ARG 0.005 0.001 ARG B 138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4354 Ramachandran restraints generated. 2177 Oldfield, 0 Emsley, 2177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 244 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 214 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8237 (ttpp) cc_final: 0.7884 (tttp) REVERT: A 840 LYS cc_start: 0.4823 (mmmm) cc_final: 0.3709 (tttm) REVERT: A 872 PHE cc_start: 0.6311 (m-10) cc_final: 0.6083 (m-80) REVERT: A 904 PHE cc_start: 0.6278 (t80) cc_final: 0.5492 (t80) REVERT: B 333 GLU cc_start: 0.7434 (tp30) cc_final: 0.6837 (tp30) REVERT: B 336 MET cc_start: 0.6345 (mmt) cc_final: 0.6096 (mmt) REVERT: B 402 PRO cc_start: 0.7766 (Cg_endo) cc_final: 0.7513 (Cg_exo) REVERT: B 457 MET cc_start: 0.3507 (OUTLIER) cc_final: 0.3036 (ppp) REVERT: B 557 MET cc_start: 0.7015 (mtt) cc_final: 0.6575 (mmt) REVERT: B 748 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7754 (tm-30) outliers start: 30 outliers final: 28 residues processed: 225 average time/residue: 0.5992 time to fit residues: 212.0283 Evaluate side-chains 238 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 209 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain B residue 202 PHE Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 667 PHE Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 814 GLU Chi-restraints excluded: chain B residue 892 ASP Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 906 GLN Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1213 ILE Chi-restraints excluded: chain B residue 1341 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 159 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 21 optimal weight: 0.0870 chunk 31 optimal weight: 5.9990 chunk 152 optimal weight: 0.6980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.183789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.159696 restraints weight = 95444.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.166441 restraints weight = 43151.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.170435 restraints weight = 23684.907| |-----------------------------------------------------------------------------| r_work (final): 0.4505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4505 r_free = 0.4505 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4503 r_free = 0.4503 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17404 Z= 0.179 Angle : 0.549 7.898 23686 Z= 0.284 Chirality : 0.041 0.178 2629 Planarity : 0.005 0.062 3111 Dihedral : 5.094 28.870 2301 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.83 % Favored : 90.94 % Rotamer: Outliers : 1.46 % Allowed : 18.91 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.17), residues: 2177 helix: -0.35 (0.29), residues: 329 sheet: -1.52 (0.31), residues: 287 loop : -1.93 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B1061 HIS 0.004 0.001 HIS B 810 PHE 0.022 0.002 PHE B 343 TYR 0.020 0.001 TYR A 486 ARG 0.003 0.000 ARG B1036 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6499.82 seconds wall clock time: 117 minutes 9.66 seconds (7029.66 seconds total)