Starting phenix.real_space_refine on Sun Feb 25 07:49:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbx_17587/02_2024/8pbx_17587.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbx_17587/02_2024/8pbx_17587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbx_17587/02_2024/8pbx_17587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbx_17587/02_2024/8pbx_17587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbx_17587/02_2024/8pbx_17587.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pbx_17587/02_2024/8pbx_17587.pdb" } resolution = 3.3 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= 0.077 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 16861 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 10715 2.51 5 N 2864 2.21 5 O 3394 1.98 5 H 16455 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 84": "OD1" <-> "OD2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 539": "OD1" <-> "OD2" Residue "A TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 560": "OD1" <-> "OD2" Residue "A PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 661": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 666": "OD1" <-> "OD2" Residue "A PHE 735": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 785": "OE1" <-> "OE2" Residue "A ASP 836": "OD1" <-> "OD2" Residue "A PHE 879": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 909": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 925": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B ASP 386": "OD1" <-> "OD2" Residue "B TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 648": "OD1" <-> "OD2" Residue "B PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 712": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 726": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 757": "OD1" <-> "OD2" Residue "B ASP 931": "OD1" <-> "OD2" Residue "B ASP 1051": "OD1" <-> "OD2" Residue "B ASP 1202": "OD1" <-> "OD2" Residue "B PHE 1279": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1295": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1307": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33448 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 13661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 13661 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 40, 'TRANS': 861} Chain breaks: 2 Chain: "B" Number of atoms: 19787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1285, 19787 Classifications: {'peptide': 1285} Link IDs: {'PTRANS': 80, 'TRANS': 1204} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 14.69, per 1000 atoms: 0.44 Number of scatterers: 33448 At special positions: 0 Unit cell: (91.35, 128.1, 135.45, 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 3394 8.00 N 2864 7.00 C 10715 6.00 H 16455 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: 27.54 Conformation dependent library (CDL) restraints added in 3.8 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: 72 helices and 37 sheets defined 23.0% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 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 148 removed outlier: 3.923A pdb=" N GLN A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 3.902A 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 Processing helix chain 'A' and resid 243 through 252 Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.664A pdb=" N ILE A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 349 through 358 Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 490 through 495 removed outlier: 4.455A pdb=" N SER A 494 " --> pdb=" O ASP A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 522 Processing helix chain 'A' and resid 548 through 561 removed outlier: 4.219A pdb=" N SER A 554 " --> pdb=" O ASN A 550 " (cutoff:3.500A) 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 removed outlier: 3.532A pdb=" N THR A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 694 through 696 No H-bonds generated for 'chain 'A' and resid 694 through 696' 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 removed outlier: 3.578A pdb=" N THR A 754 " --> pdb=" O GLN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 821 removed outlier: 3.588A pdb=" N SER A 818 " --> pdb=" O GLN A 814 " (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 Processing helix chain 'B' and resid 110 through 126 removed outlier: 3.874A pdb=" N GLY B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN B 125 " --> pdb=" O TYR B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.830A pdb=" N GLU B 254 " --> pdb=" O LYS B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 297 No H-bonds generated for 'chain 'B' and resid 295 through 297' Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 326 through 333 Processing helix chain 'B' and resid 334 through 337 removed outlier: 3.589A pdb=" N GLY B 337 " --> pdb=" O LYS B 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 334 through 337' Processing helix chain 'B' and resid 363 through 368 Processing helix chain 'B' and resid 369 through 370 No H-bonds generated for 'chain 'B' and resid 369 through 370' Processing helix chain 'B' and resid 371 through 376 Processing helix chain 'B' and resid 383 through 394 Processing helix chain 'B' and resid 405 through 409 removed outlier: 3.726A pdb=" N TRP B 408 " --> pdb=" O HIS B 405 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 409 " --> pdb=" O PRO B 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 409' Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 446 through 453 Processing helix chain 'B' and resid 505 through 510 Processing helix chain 'B' and resid 574 through 583 Processing helix chain 'B' and resid 604 through 608 Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.565A pdb=" N ILE B 628 " --> pdb=" O ASN B 625 " (cutoff:3.500A) 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 721 through 727 removed outlier: 4.292A pdb=" N ASN B 727 " --> pdb=" O ALA B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 745 removed outlier: 4.180A pdb=" N ASN B 745 " --> pdb=" O ARG B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 768 removed outlier: 3.962A 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 838 through 842 removed outlier: 3.585A pdb=" N LYS B 842 " --> pdb=" O ALA B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 917 removed outlier: 3.510A pdb=" N GLN B 909 " --> pdb=" O PRO B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 944 removed outlier: 3.726A pdb=" N THR B 944 " --> pdb=" O TRP B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 950 Processing helix chain 'B' and resid 961 through 970 Processing helix chain 'B' and resid 1051 through 1056 Processing helix chain 'B' and resid 1059 through 1062 Processing helix chain 'B' and resid 1130 through 1136 removed outlier: 4.304A pdb=" N ALA B1134 " --> pdb=" O THR B1131 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR B1135 " --> pdb=" O SER B1132 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1142 Processing helix chain 'B' and resid 1145 through 1154 removed outlier: 3.583A pdb=" N ILE B1149 " --> pdb=" O THR B1145 " (cutoff:3.500A) Processing helix chain 'B' and resid 1157 through 1161 Processing helix chain 'B' and resid 1192 through 1203 Processing helix chain 'B' and resid 1204 through 1211 removed outlier: 4.224A pdb=" N LYS B1208 " --> pdb=" O GLN B1205 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N SER B1209 " --> pdb=" O ASN B1206 " (cutoff:3.500A) Processing helix chain 'B' and resid 1245 through 1249 Processing helix chain 'B' and resid 1255 through 1259 Processing helix chain 'B' and resid 1260 through 1266 Processing helix chain 'B' and resid 1268 through 1273 removed outlier: 3.906A pdb=" N PHE B1273 " --> pdb=" O VAL B1269 " (cutoff:3.500A) Processing helix chain 'B' and resid 1281 through 1287 Proline residue: B1286 - end of helix Processing helix chain 'B' and resid 1296 through 1298 No H-bonds generated for 'chain 'B' and resid 1296 through 1298' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 71 removed outlier: 6.516A pdb=" N LEU A 79 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLN A 69 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE A 77 " --> pdb=" O GLN A 69 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 128 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N THR A 115 " --> pdb=" O MET A 126 " (cutoff:3.500A) removed outlier: 5.817A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 225 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 304 removed outlier: 3.513A pdb=" N MET A 312 " --> pdb=" O LYS A 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 345 Processing sheet with id=AA9, first strand: chain 'A' and resid 383 through 391 removed outlier: 5.028A pdb=" N ILE A 385 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE A 400 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ILE A 541 " --> pdb=" O LYS A 401 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 424 through 425 removed outlier: 3.949A pdb=" N GLY A 406 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 458 through 459 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.792A pdb=" N GLY A 477 " --> pdb=" O THR A 474 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 626 through 633 removed outlier: 5.536A pdb=" N GLY A 628 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU A 651 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 649 " --> pdb=" O LYS A 630 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 698 through 704 removed outlier: 5.582A pdb=" N PHE A 698 " --> pdb=" O ASP A 715 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASP A 715 " --> pdb=" O PHE A 698 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 700 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 709 " --> pdb=" O ASN A 704 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 740 " --> pdb=" O TRP A 710 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ILE A 769 " --> pdb=" O VAL A 737 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR A 739 " --> pdb=" O SER A 767 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N SER A 767 " --> pdb=" O THR A 739 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N SER A 741 " --> pdb=" O VAL A 765 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL A 765 " --> pdb=" O SER A 741 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 775 through 780 removed outlier: 5.094A pdb=" N LEU A 776 " --> pdb=" O LYS A 792 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LYS A 792 " --> pdb=" O LEU A 776 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A 800 " --> pdb=" O VAL A 789 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 808 " --> pdb=" O ASN A 805 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 840 through 843 Processing sheet with id=AB8, first strand: chain 'A' and resid 884 through 892 removed outlier: 6.157A pdb=" N SER A 895 " --> pdb=" O GLN A 891 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 884 through 892 removed outlier: 6.157A pdb=" N SER A 895 " --> pdb=" O GLN A 891 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 915 through 916 removed outlier: 3.623A pdb=" N VAL A 919 " --> pdb=" O ILE A 916 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 79 through 80 removed outlier: 6.762A pdb=" N ARG B 132 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 164 through 165 Processing sheet with id=AC4, first strand: chain 'B' and resid 187 through 193 removed outlier: 6.553A pdb=" N LEU B 204 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL B 191 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE B 202 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLN B 193 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU B 200 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL B 340 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL B 358 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N SER B 342 " --> pdb=" O GLY B 356 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 246 through 247 Processing sheet with id=AC6, first strand: chain 'B' and resid 270 through 271 removed outlier: 3.551A pdb=" N LYS B 876 " --> pdb=" O VAL B 868 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 277 through 279 removed outlier: 3.596A pdb=" N LEU B 277 " --> pdb=" O VAL B 653 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 281 through 282 removed outlier: 3.797A pdb=" N LYS B 292 " --> pdb=" O GLU B 282 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 457 through 460 removed outlier: 3.554A pdb=" N LYS B 497 " --> pdb=" O THR B 492 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 537 through 545 removed outlier: 5.160A pdb=" N VAL B 539 " --> pdb=" O THR B 554 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR B 554 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU B 549 " --> pdb=" O LEU B 698 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA B 695 " --> pdb=" O PHE B 750 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE B 750 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE B 697 " --> pdb=" O GLN B 748 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 804 through 806 Processing sheet with id=AD3, first strand: chain 'B' and resid 845 through 846 Processing sheet with id=AD4, first strand: chain 'B' and resid 921 through 923 Processing sheet with id=AD5, first strand: chain 'B' and resid 1009 through 1014 removed outlier: 5.288A pdb=" N GLN B1023 " --> pdb=" O GLY B1010 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU B1012 " --> pdb=" O GLY B1021 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY B1021 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B1020 " --> pdb=" O PHE B1031 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1064 through 1069 removed outlier: 4.900A pdb=" N GLY B1066 " --> pdb=" O LEU B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1228 through 1230 Processing sheet with id=AD8, first strand: chain 'B' and resid 1252 through 1253 removed outlier: 3.600A pdb=" N SER B1252 " --> pdb=" O ASN B1290 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1300 through 1307 removed outlier: 6.920A pdb=" N ILE B1300 " --> pdb=" O LYS B1321 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LYS B1321 " --> pdb=" O ILE B1300 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU B1302 " --> pdb=" O GLU B1319 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU B1319 " --> pdb=" O LEU B1302 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL B1304 " --> pdb=" O ARG B1317 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ARG B1317 " --> pdb=" O VAL B1304 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1300 through 1307 removed outlier: 6.920A pdb=" N ILE B1300 " --> pdb=" O LYS B1321 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LYS B1321 " --> pdb=" O ILE B1300 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU B1302 " --> pdb=" O GLU B1319 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU B1319 " --> pdb=" O LEU B1302 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL B1304 " --> pdb=" O ARG B1317 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ARG B1317 " --> pdb=" O VAL B1304 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1131 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: 16.80 Time building geometry restraints manager: 28.46 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: 16455 1.03 - 1.23: 6 1.23 - 1.42: 7395 1.42 - 1.61: 9950 1.61 - 1.81: 40 Bond restraints: 33846 Sorted by residual: bond pdb=" C VAL B 653 " pdb=" N TYR B 654 " ideal model delta sigma weight residual 1.329 1.290 0.038 1.60e-02 3.91e+03 5.77e+00 bond pdb=" N GLN B 59 " pdb=" CA GLN B 59 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N THR A 27 " pdb=" CA THR A 27 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.67e+00 bond pdb=" N THR A 27 " pdb=" H THR A 27 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" N GLN B 59 " pdb=" H GLN B 59 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.31e+00 ... (remaining 33841 not shown) Histogram of bond angle deviations from ideal: 98.76 - 105.81: 404 105.81 - 112.85: 38956 112.85 - 119.90: 8942 119.90 - 126.95: 12495 126.95 - 134.00: 234 Bond angle restraints: 61031 Sorted by residual: angle pdb=" N VAL A 604 " pdb=" CA VAL A 604 " pdb=" C VAL A 604 " ideal model delta sigma weight residual 113.53 109.82 3.71 9.80e-01 1.04e+00 1.44e+01 angle pdb=" N GLY B 383 " pdb=" CA GLY B 383 " pdb=" C GLY B 383 " ideal model delta sigma weight residual 111.35 115.46 -4.11 1.20e+00 6.94e-01 1.18e+01 angle pdb=" N ILE A 868 " pdb=" CA ILE A 868 " pdb=" C ILE A 868 " ideal model delta sigma weight residual 112.35 108.35 4.00 1.41e+00 5.03e-01 8.04e+00 angle pdb=" CB MET A 141 " pdb=" CG MET A 141 " pdb=" SD MET A 141 " ideal model delta sigma weight residual 112.70 120.93 -8.23 3.00e+00 1.11e-01 7.52e+00 angle pdb=" N VAL B 189 " pdb=" CA VAL B 189 " pdb=" C VAL B 189 " ideal model delta sigma weight residual 113.71 111.13 2.58 9.50e-01 1.11e+00 7.40e+00 ... (remaining 61026 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14346 17.99 - 35.98: 1294 35.98 - 53.97: 405 53.97 - 71.96: 112 71.96 - 89.95: 36 Dihedral angle restraints: 16193 sinusoidal: 8727 harmonic: 7466 Sorted by residual: dihedral pdb=" CA SER A 367 " pdb=" C SER A 367 " pdb=" N THR A 368 " pdb=" CA THR A 368 " ideal model delta harmonic sigma weight residual 180.00 158.37 21.63 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA ASN B 668 " pdb=" C ASN B 668 " pdb=" N TRP B 669 " pdb=" CA TRP B 669 " ideal model delta harmonic sigma weight residual -180.00 -159.74 -20.26 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PHE B 451 " pdb=" C PHE B 451 " pdb=" N ALA B 452 " pdb=" CA ALA B 452 " ideal model delta harmonic sigma weight residual 180.00 160.18 19.82 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 16190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2236 0.056 - 0.111: 333 0.111 - 0.167: 57 0.167 - 0.223: 0 0.223 - 0.279: 1 Chirality restraints: 2627 Sorted by residual: chirality pdb=" CB VAL A 443 " pdb=" CA VAL A 443 " pdb=" CG1 VAL A 443 " pdb=" CG2 VAL A 443 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA ILE A 790 " pdb=" N ILE A 790 " pdb=" C ILE A 790 " pdb=" CB ILE A 790 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE B 603 " pdb=" N ILE B 603 " pdb=" C ILE B 603 " pdb=" CB ILE B 603 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 2624 not shown) Planarity restraints: 5172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 669 " 0.027 2.00e-02 2.50e+03 1.76e-02 1.24e+01 pdb=" CG TRP B 669 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP B 669 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 669 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 669 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 669 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 669 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 669 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 669 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 669 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TRP B 669 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 TRP B 669 " 0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP B 669 " -0.003 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 669 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 669 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP B 669 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 625 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO B 626 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 626 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 626 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 600 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO B 601 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 601 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 601 " -0.025 5.00e-02 4.00e+02 ... (remaining 5169 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.12: 1349 2.12 - 2.74: 63188 2.74 - 3.36: 99958 3.36 - 3.98: 131274 3.98 - 4.60: 203908 Nonbonded interactions: 499677 Sorted by model distance: nonbonded pdb=" OE1 GLN A 380 " pdb=" H ALA A 382 " model vdw 1.505 1.850 nonbonded pdb=" OE1 GLU B 83 " pdb=" H GLU B 83 " model vdw 1.529 1.850 nonbonded pdb=" HE1 TRP B 374 " pdb=" O PHE B 531 " model vdw 1.541 1.850 nonbonded pdb="HE21 GLN B 906 " pdb=" O ASN B 958 " model vdw 1.545 1.850 nonbonded pdb=" O GLY B 917 " pdb=" HG SER B1000 " model vdw 1.545 1.850 ... (remaining 499672 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.310 Construct map_model_manager: 0.500 Extract box with map and model: 7.580 Check model and map are aligned: 0.520 Set scattering table: 0.290 Process input model: 108.870 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.100 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 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 : 0.005 0.038 17391 Z= 0.307 Angle : 0.591 8.227 23670 Z= 0.323 Chirality : 0.043 0.279 2627 Planarity : 0.004 0.052 3110 Dihedral : 15.134 89.593 6286 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.52 % Favored : 93.43 % Rotamer: Outliers : 0.26 % Allowed : 16.03 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.18), residues: 2177 helix: -0.35 (0.28), residues: 353 sheet: 0.06 (0.28), residues: 330 loop : -0.56 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP B 669 HIS 0.006 0.001 HIS B 352 PHE 0.022 0.002 PHE B 451 TYR 0.014 0.002 TYR A 296 ARG 0.006 0.001 ARG A 742 *********************** 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 VAL 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. 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: 5 poor density : 239 time to evaluate : 2.730 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: B 411 GLU cc_start: 0.6409 (tt0) cc_final: 0.6194 (tt0) outliers start: 5 outliers final: 4 residues processed: 241 average time/residue: 0.5862 time to fit residues: 224.1697 Evaluate side-chains 238 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 234 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 760 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 170 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 127 optimal weight: 0.4980 chunk 197 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 ASN ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 ASN ** B1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.0436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17391 Z= 0.199 Angle : 0.525 4.497 23670 Z= 0.276 Chirality : 0.042 0.186 2627 Planarity : 0.004 0.048 3110 Dihedral : 5.046 41.637 2311 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.33 % Favored : 94.63 % Rotamer: Outliers : 0.94 % Allowed : 15.35 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.18), residues: 2177 helix: -0.22 (0.29), residues: 348 sheet: 0.15 (0.28), residues: 336 loop : -0.48 (0.17), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 669 HIS 0.005 0.001 HIS B 352 PHE 0.017 0.001 PHE B 451 TYR 0.009 0.001 TYR A 296 ARG 0.003 0.000 ARG A 742 *********************** 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 VAL 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 260 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 242 time to evaluate : 2.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 GLU cc_start: 0.7430 (tm-30) cc_final: 0.7200 (tm-30) REVERT: A 586 GLU cc_start: 0.8082 (tp30) cc_final: 0.7836 (tm-30) REVERT: B 453 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7830 (t0) REVERT: B 1312 GLN cc_start: 0.7319 (mt0) cc_final: 0.7046 (mm-40) outliers start: 18 outliers final: 12 residues processed: 253 average time/residue: 0.5611 time to fit residues: 228.6412 Evaluate side-chains 245 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 232 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 453 ASN Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 1289 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 110 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 214 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 ASN B 823 ASN ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 17391 Z= 0.394 Angle : 0.577 4.963 23670 Z= 0.305 Chirality : 0.044 0.180 2627 Planarity : 0.004 0.056 3110 Dihedral : 5.209 38.268 2308 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.35 % Favored : 92.56 % Rotamer: Outliers : 1.73 % Allowed : 15.72 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.18), residues: 2177 helix: -0.56 (0.28), residues: 348 sheet: -0.40 (0.27), residues: 364 loop : -0.76 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 669 HIS 0.006 0.001 HIS B 352 PHE 0.023 0.002 PHE B 451 TYR 0.017 0.002 TYR A 296 ARG 0.004 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 VAL 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 264 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 231 time to evaluate : 2.641 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: A 247 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7180 (tm-30) REVERT: A 556 LYS cc_start: 0.8601 (tptt) cc_final: 0.8384 (tptt) REVERT: A 582 TYR cc_start: 0.8239 (p90) cc_final: 0.7999 (p90) REVERT: A 586 GLU cc_start: 0.8357 (tp30) cc_final: 0.8107 (tm-30) REVERT: B 201 TYR cc_start: 0.6840 (m-80) cc_final: 0.6533 (m-80) REVERT: B 453 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8095 (t0) REVERT: B 662 TYR cc_start: 0.7609 (t80) cc_final: 0.7127 (t80) REVERT: B 1312 GLN cc_start: 0.7524 (mt0) cc_final: 0.7075 (mm-40) outliers start: 33 outliers final: 27 residues processed: 251 average time/residue: 0.5581 time to fit residues: 225.1508 Evaluate side-chains 253 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 225 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 453 ASN Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 646 ASN Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 1044 ILE Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1300 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 195 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 chunk 210 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 ASN ** B1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17391 Z= 0.292 Angle : 0.544 4.702 23670 Z= 0.286 Chirality : 0.042 0.181 2627 Planarity : 0.004 0.056 3110 Dihedral : 5.147 37.240 2308 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.43 % Favored : 93.48 % Rotamer: Outliers : 1.57 % Allowed : 16.29 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.18), residues: 2177 helix: -0.51 (0.28), residues: 348 sheet: -0.44 (0.27), residues: 353 loop : -0.77 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 669 HIS 0.005 0.001 HIS B 352 PHE 0.020 0.001 PHE B 451 TYR 0.013 0.001 TYR A 296 ARG 0.004 0.000 ARG B 565 *********************** 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 VAL 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 262 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 232 time to evaluate : 2.868 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: A 247 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7107 (tm-30) REVERT: A 582 TYR cc_start: 0.8250 (p90) cc_final: 0.7902 (p90) REVERT: B 201 TYR cc_start: 0.6804 (m-80) cc_final: 0.6397 (m-80) REVERT: B 453 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.8027 (t0) REVERT: B 1312 GLN cc_start: 0.7500 (mt0) cc_final: 0.7066 (mm-40) outliers start: 30 outliers final: 22 residues processed: 251 average time/residue: 0.5775 time to fit residues: 232.6287 Evaluate side-chains 251 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 228 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 453 ASN Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 1289 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 175 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17391 Z= 0.273 Angle : 0.529 5.626 23670 Z= 0.276 Chirality : 0.042 0.182 2627 Planarity : 0.004 0.055 3110 Dihedral : 5.052 35.922 2308 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.17 % Favored : 92.79 % Rotamer: Outliers : 1.94 % Allowed : 16.66 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.18), residues: 2177 helix: -0.42 (0.28), residues: 348 sheet: -0.50 (0.27), residues: 353 loop : -0.75 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 669 HIS 0.005 0.001 HIS B 352 PHE 0.019 0.001 PHE B 451 TYR 0.013 0.001 TYR A 296 ARG 0.003 0.000 ARG B1301 *********************** 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 VAL 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 273 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 236 time to evaluate : 2.859 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: A 247 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7072 (tm-30) REVERT: A 582 TYR cc_start: 0.8241 (p90) cc_final: 0.7813 (p90) REVERT: B 119 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7394 (mm-30) REVERT: B 201 TYR cc_start: 0.6927 (m-80) cc_final: 0.6556 (m-80) REVERT: B 453 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.8001 (t0) REVERT: B 1312 GLN cc_start: 0.7470 (mt0) cc_final: 0.7047 (mm-40) outliers start: 37 outliers final: 26 residues processed: 262 average time/residue: 0.5834 time to fit residues: 245.3149 Evaluate side-chains 255 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 227 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 453 ASN Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1289 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 70 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 210 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 17391 Z= 0.363 Angle : 0.561 4.958 23670 Z= 0.295 Chirality : 0.043 0.196 2627 Planarity : 0.004 0.058 3110 Dihedral : 5.194 33.454 2308 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.90 % Favored : 92.01 % Rotamer: Outliers : 2.04 % Allowed : 17.23 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.18), residues: 2177 helix: -0.59 (0.28), residues: 348 sheet: -0.68 (0.27), residues: 359 loop : -0.90 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 669 HIS 0.005 0.001 HIS B 352 PHE 0.023 0.002 PHE B 451 TYR 0.017 0.002 TYR A 296 ARG 0.004 0.000 ARG B 565 *********************** 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 VAL 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 271 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 232 time to evaluate : 4.054 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: A 582 TYR cc_start: 0.8302 (p90) cc_final: 0.7760 (p90) REVERT: B 119 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7412 (mm-30) REVERT: B 201 TYR cc_start: 0.7017 (m-80) cc_final: 0.6561 (m-80) REVERT: B 453 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8009 (t0) REVERT: B 1312 GLN cc_start: 0.7416 (mt0) cc_final: 0.7109 (mm-40) outliers start: 39 outliers final: 30 residues processed: 258 average time/residue: 0.6224 time to fit residues: 257.3082 Evaluate side-chains 258 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 226 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 453 ASN Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 1044 ILE Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1300 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 203 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 210 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17391 Z= 0.409 Angle : 0.582 4.882 23670 Z= 0.308 Chirality : 0.044 0.190 2627 Planarity : 0.004 0.059 3110 Dihedral : 5.240 31.367 2305 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.50 % Favored : 91.41 % Rotamer: Outliers : 2.25 % Allowed : 17.44 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.17), residues: 2177 helix: -0.76 (0.28), residues: 348 sheet: -0.79 (0.27), residues: 357 loop : -1.06 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 669 HIS 0.006 0.001 HIS B 381 PHE 0.024 0.002 PHE B 451 TYR 0.019 0.002 TYR A 296 ARG 0.004 0.001 ARG B 565 *********************** 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 VAL 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 224 time to evaluate : 2.882 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: A 582 TYR cc_start: 0.8369 (p90) cc_final: 0.7787 (p90) REVERT: B 119 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7436 (mm-30) REVERT: B 201 TYR cc_start: 0.7042 (m-80) cc_final: 0.6579 (m-80) REVERT: B 453 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.7972 (t0) REVERT: B 817 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6869 (tpt-90) REVERT: B 1312 GLN cc_start: 0.7349 (mt0) cc_final: 0.7074 (mm-40) outliers start: 43 outliers final: 36 residues processed: 253 average time/residue: 0.5964 time to fit residues: 240.6840 Evaluate side-chains 259 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 220 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 453 ASN Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 817 ARG Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 1044 ILE Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1300 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 129 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17391 Z= 0.311 Angle : 0.549 4.605 23670 Z= 0.288 Chirality : 0.043 0.187 2627 Planarity : 0.004 0.057 3110 Dihedral : 5.146 30.695 2305 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.90 % Favored : 92.01 % Rotamer: Outliers : 2.10 % Allowed : 17.81 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.18), residues: 2177 helix: -0.63 (0.28), residues: 348 sheet: -0.75 (0.28), residues: 338 loop : -1.00 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 669 HIS 0.004 0.001 HIS B 381 PHE 0.021 0.002 PHE B 451 TYR 0.014 0.002 TYR B 880 ARG 0.003 0.000 ARG B 565 *********************** 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 VAL 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 260 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 220 time to evaluate : 2.857 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: A 582 TYR cc_start: 0.8378 (p90) cc_final: 0.7764 (p90) REVERT: B 119 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7399 (mm-30) REVERT: B 201 TYR cc_start: 0.7010 (m-80) cc_final: 0.6548 (m-80) REVERT: B 453 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.7952 (t0) REVERT: B 817 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.6851 (tpt-90) REVERT: B 1210 GLU cc_start: 0.7981 (tt0) cc_final: 0.7766 (tt0) REVERT: B 1312 GLN cc_start: 0.7340 (mt0) cc_final: 0.7073 (mm-40) outliers start: 40 outliers final: 32 residues processed: 245 average time/residue: 0.6490 time to fit residues: 252.7984 Evaluate side-chains 252 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 217 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 453 ASN Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 662 TYR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 817 ARG Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1289 VAL Chi-restraints excluded: chain B residue 1300 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 191 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 185 optimal weight: 0.6980 chunk 128 optimal weight: 0.4980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17391 Z= 0.215 Angle : 0.522 4.439 23670 Z= 0.272 Chirality : 0.042 0.209 2627 Planarity : 0.004 0.053 3110 Dihedral : 4.967 30.593 2305 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.89 % Favored : 93.02 % Rotamer: Outliers : 1.41 % Allowed : 18.44 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.18), residues: 2177 helix: -0.43 (0.28), residues: 355 sheet: -0.68 (0.28), residues: 335 loop : -0.88 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B 669 HIS 0.004 0.001 HIS B 352 PHE 0.021 0.001 PHE B 451 TYR 0.011 0.001 TYR A 157 ARG 0.004 0.000 ARG B1301 *********************** 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 VAL 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 256 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 229 time to evaluate : 2.966 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: A 111 VAL cc_start: 0.8693 (t) cc_final: 0.8427 (p) REVERT: A 582 TYR cc_start: 0.8323 (p90) cc_final: 0.7724 (p90) REVERT: B 119 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7389 (mm-30) REVERT: B 201 TYR cc_start: 0.7024 (m-80) cc_final: 0.6559 (m-80) REVERT: B 453 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.7945 (t0) REVERT: B 817 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.6839 (tpt-90) outliers start: 27 outliers final: 23 residues processed: 248 average time/residue: 0.5829 time to fit residues: 230.6408 Evaluate side-chains 250 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 224 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 453 ASN Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 662 TYR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 817 ARG Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1289 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 207 optimal weight: 4.9990 chunk 126 optimal weight: 0.0970 chunk 98 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 217 optimal weight: 0.4980 chunk 199 optimal weight: 6.9990 chunk 172 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17391 Z= 0.177 Angle : 0.509 4.314 23670 Z= 0.263 Chirality : 0.041 0.193 2627 Planarity : 0.004 0.051 3110 Dihedral : 4.787 30.414 2305 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.83 % Favored : 94.12 % Rotamer: Outliers : 1.31 % Allowed : 18.75 % 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: -0.99 (0.18), residues: 2177 helix: -0.12 (0.29), residues: 351 sheet: -0.71 (0.27), residues: 350 loop : -0.77 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP B 669 HIS 0.004 0.001 HIS B 352 PHE 0.019 0.001 PHE A 355 TYR 0.015 0.001 TYR A 157 ARG 0.002 0.000 ARG A 742 ********************** 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 VAL 227 is missing expected H atoms. Skipping. Residue LYS 228 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue SER 789 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 236 time to evaluate : 3.205 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: A 111 VAL cc_start: 0.8544 (t) cc_final: 0.8264 (p) REVERT: A 582 TYR cc_start: 0.8309 (p90) cc_final: 0.7794 (p90) REVERT: B 119 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7222 (mm-30) REVERT: B 201 TYR cc_start: 0.6977 (m-80) cc_final: 0.6463 (m-80) REVERT: B 453 ASN cc_start: 0.8400 (OUTLIER) cc_final: 0.8030 (t0) REVERT: B 817 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6761 (tpt-90) REVERT: B 1271 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7885 (mp0) outliers start: 25 outliers final: 18 residues processed: 251 average time/residue: 0.5923 time to fit residues: 236.2747 Evaluate side-chains 251 residues out of total 1916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 230 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 453 ASN Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 662 TYR Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 817 ARG Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1231 THR Chi-restraints excluded: chain B residue 1289 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 159 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1240 GLN ** 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 = 0.3979 r_free = 0.3979 target = 0.148644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.121211 restraints weight = 71596.398| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.22 r_work: 0.3530 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17391 Z= 0.279 Angle : 0.529 4.528 23670 Z= 0.276 Chirality : 0.042 0.194 2627 Planarity : 0.004 0.051 3110 Dihedral : 4.857 29.080 2305 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.30 % Favored : 92.60 % Rotamer: Outliers : 1.31 % Allowed : 18.86 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.18), residues: 2177 helix: -0.27 (0.28), residues: 355 sheet: -0.73 (0.27), residues: 345 loop : -0.84 (0.16), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP B 669 HIS 0.006 0.001 HIS B 352 PHE 0.025 0.001 PHE B 451 TYR 0.015 0.001 TYR A 157 ARG 0.003 0.000 ARG B 565 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6977.98 seconds wall clock time: 128 minutes 8.37 seconds (7688.37 seconds total)