Starting phenix.real_space_refine on Sat Apr 6 13:28:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zf1_14694/04_2024/7zf1_14694.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zf1_14694/04_2024/7zf1_14694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zf1_14694/04_2024/7zf1_14694.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zf1_14694/04_2024/7zf1_14694.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zf1_14694/04_2024/7zf1_14694.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zf1_14694/04_2024/7zf1_14694.pdb" } resolution = 4.14 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= 0.002 sd= 0.032 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 19129 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: 6 Type Number sf(0) Gaussians P 54 5.49 5 S 103 5.16 5 C 12311 2.51 5 N 3264 2.21 5 O 3726 1.98 5 H 19431 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 425": "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-5288/modules/chem_data/mon_lib" Total number of atoms: 38889 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 16846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 16846 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 34, 'TRANS': 1007} Chain breaks: 9 Chain: "B" Number of atoms: 19103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1179, 19103 Classifications: {'peptide': 1179} Link IDs: {'PTRANS': 41, 'TRANS': 1137} Chain breaks: 10 Chain: "C" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1228 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "S" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 860 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "T" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 852 Classifications: {'DNA': 27} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 26} Time building chain proxies: 13.12, per 1000 atoms: 0.34 Number of scatterers: 38889 At special positions: 0 Unit cell: (111.507, 130.944, 167.772, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 103 16.00 P 54 15.00 O 3726 8.00 N 3264 7.00 C 12311 6.00 H 19431 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: 25.59 Conformation dependent library (CDL) restraints added in 3.2 seconds 4506 Ramachandran restraints generated. 2253 Oldfield, 0 Emsley, 2253 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4436 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 6 sheets defined 78.9% alpha, 1.9% beta 24 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 13.65 Creating SS restraints... Processing helix chain 'A' and resid 172 through 182 Processing helix chain 'A' and resid 187 through 205 removed outlier: 4.123A pdb=" N GLU A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 Processing helix chain 'A' and resid 225 through 249 removed outlier: 3.735A pdb=" N VAL A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 282 removed outlier: 3.852A pdb=" N GLU A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N HIS A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 293 removed outlier: 3.806A pdb=" N GLY A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 319 removed outlier: 3.540A pdb=" N ILE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 346 Processing helix chain 'A' and resid 347 through 354 removed outlier: 4.066A pdb=" N GLN A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 371 removed outlier: 3.673A pdb=" N LEU A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 393 removed outlier: 4.231A pdb=" N GLN A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY A 381 " --> pdb=" O HIS A 377 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 411 through 433 removed outlier: 3.767A pdb=" N HIS A 417 " --> pdb=" O MET A 413 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 449 removed outlier: 4.256A pdb=" N LEU A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLU A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 Processing helix chain 'A' and resid 472 through 477 removed outlier: 3.987A pdb=" N SER A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS A 477 " --> pdb=" O VAL A 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 472 through 477' Processing helix chain 'A' and resid 477 through 486 removed outlier: 3.674A pdb=" N ASP A 486 " --> pdb=" O THR A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 491 removed outlier: 4.009A pdb=" N LEU A 491 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 503 removed outlier: 3.627A pdb=" N ARG A 498 " --> pdb=" O GLN A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 510 through 525 Processing helix chain 'A' and resid 529 through 547 Processing helix chain 'A' and resid 576 through 596 removed outlier: 4.438A pdb=" N SER A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 616 removed outlier: 4.301A pdb=" N TYR A 610 " --> pdb=" O TYR A 606 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASP A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 633 removed outlier: 4.336A pdb=" N GLN A 625 " --> pdb=" O ASN A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 650 Processing helix chain 'A' and resid 663 through 686 removed outlier: 4.656A pdb=" N ILE A 683 " --> pdb=" O LYS A 679 " (cutoff:3.500A) Proline residue: A 684 - end of helix Processing helix chain 'A' and resid 696 through 716 removed outlier: 4.026A pdb=" N GLU A 700 " --> pdb=" O GLU A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 722 removed outlier: 4.067A pdb=" N PHE A 721 " --> pdb=" O GLU A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 762 removed outlier: 4.630A pdb=" N SER A 762 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 790 Processing helix chain 'A' and resid 806 through 819 Processing helix chain 'A' and resid 822 through 834 removed outlier: 3.884A pdb=" N SER A 828 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL A 831 " --> pdb=" O GLU A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 856 removed outlier: 3.890A pdb=" N MET A 839 " --> pdb=" O SER A 835 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 843 " --> pdb=" O MET A 839 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU A 855 " --> pdb=" O GLN A 851 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 856 " --> pdb=" O GLN A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 888 removed outlier: 3.648A pdb=" N ILE A 870 " --> pdb=" O ASN A 866 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 877 " --> pdb=" O ASN A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 893 Processing helix chain 'A' and resid 896 through 901 removed outlier: 4.231A pdb=" N GLY A 901 " --> pdb=" O LYS A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 923 removed outlier: 4.671A pdb=" N GLN A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN A 921 " --> pdb=" O SER A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 935 removed outlier: 3.640A pdb=" N ASP A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 971 removed outlier: 3.963A pdb=" N PHE A 957 " --> pdb=" O GLN A 953 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN A 958 " --> pdb=" O ARG A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 994 removed outlier: 3.790A pdb=" N LYS A 994 " --> pdb=" O THR A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1017 removed outlier: 3.826A pdb=" N VAL A1004 " --> pdb=" O SER A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1040 removed outlier: 3.817A pdb=" N SER A1038 " --> pdb=" O SER A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1058 removed outlier: 3.527A pdb=" N GLN A1051 " --> pdb=" O ARG A1047 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP A1052 " --> pdb=" O ASP A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1113 removed outlier: 3.558A pdb=" N LEU A1087 " --> pdb=" O THR A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1150 removed outlier: 4.234A pdb=" N VAL A1130 " --> pdb=" O PRO A1126 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLN A1150 " --> pdb=" O HIS A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1188 removed outlier: 3.777A pdb=" N ASP A1160 " --> pdb=" O GLY A1156 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A1182 " --> pdb=" O ARG A1178 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A1183 " --> pdb=" O TYR A1179 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A1185 " --> pdb=" O LEU A1181 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER A1186 " --> pdb=" O GLN A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1205 removed outlier: 3.671A pdb=" N LYS A1196 " --> pdb=" O LYS A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1219 removed outlier: 3.665A pdb=" N TYR A1210 " --> pdb=" O THR A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1246 removed outlier: 3.773A pdb=" N ARG A1242 " --> pdb=" O THR A1238 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1272 removed outlier: 3.698A pdb=" N ILE A1254 " --> pdb=" O ILE A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1274 through 1278 Processing helix chain 'A' and resid 1290 through 1302 Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 71 through 86 Processing helix chain 'B' and resid 88 through 104 Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.552A pdb=" N ILE B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 157 Processing helix chain 'B' and resid 159 through 167 removed outlier: 4.350A pdb=" N GLU B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 165 " --> pdb=" O PHE B 161 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN B 166 " --> pdb=" O PHE B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 181 Processing helix chain 'B' and resid 188 through 203 Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 214 through 219 Processing helix chain 'B' and resid 223 through 238 Processing helix chain 'B' and resid 241 through 252 Processing helix chain 'B' and resid 255 through 270 removed outlier: 4.222A pdb=" N LYS B 261 " --> pdb=" O ASN B 257 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 262 " --> pdb=" O PHE B 258 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 273 No H-bonds generated for 'chain 'B' and resid 271 through 273' Processing helix chain 'B' and resid 277 through 287 removed outlier: 3.962A pdb=" N ILE B 281 " --> pdb=" O ASP B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 337 through 357 removed outlier: 4.275A pdb=" N TYR B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 372 removed outlier: 3.507A pdb=" N ILE B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 392 Processing helix chain 'B' and resid 395 through 410 Processing helix chain 'B' and resid 414 through 424 removed outlier: 3.668A pdb=" N GLN B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 429 removed outlier: 3.654A pdb=" N LYS B 429 " --> pdb=" O TYR B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 445 removed outlier: 3.871A pdb=" N HIS B 444 " --> pdb=" O GLN B 440 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 465 Processing helix chain 'B' and resid 466 through 484 removed outlier: 3.822A pdb=" N VAL B 474 " --> pdb=" O GLN B 470 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 479 " --> pdb=" O GLY B 475 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY B 484 " --> pdb=" O HIS B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 503 Processing helix chain 'B' and resid 503 through 510 removed outlier: 3.671A pdb=" N MET B 507 " --> pdb=" O ASN B 503 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN B 510 " --> pdb=" O ALA B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 520 removed outlier: 3.564A pdb=" N TYR B 520 " --> pdb=" O GLY B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 542 removed outlier: 4.116A pdb=" N LYS B 531 " --> pdb=" O GLN B 527 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 533 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TYR B 534 " --> pdb=" O ARG B 530 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 565 removed outlier: 4.055A pdb=" N ASP B 554 " --> pdb=" O HIS B 550 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N MET B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 587 removed outlier: 3.581A pdb=" N THR B 580 " --> pdb=" O ILE B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 621 Processing helix chain 'B' and resid 624 through 642 Processing helix chain 'B' and resid 645 through 664 Processing helix chain 'B' and resid 698 through 708 Processing helix chain 'B' and resid 726 through 728 No H-bonds generated for 'chain 'B' and resid 726 through 728' Processing helix chain 'B' and resid 729 through 746 removed outlier: 3.907A pdb=" N TYR B 733 " --> pdb=" O CYS B 729 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU B 742 " --> pdb=" O ARG B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 758 removed outlier: 3.513A pdb=" N CYS B 758 " --> pdb=" O GLY B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 771 removed outlier: 3.516A pdb=" N LYS B 770 " --> pdb=" O PRO B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 801 removed outlier: 3.719A pdb=" N ILE B 786 " --> pdb=" O MET B 782 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE B 787 " --> pdb=" O CYS B 783 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU B 788 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 797 " --> pdb=" O PHE B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 833 removed outlier: 3.510A pdb=" N VAL B 812 " --> pdb=" O MET B 808 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU B 821 " --> pdb=" O LYS B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 925 removed outlier: 4.094A pdb=" N HIS B 922 " --> pdb=" O LEU B 918 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA B 923 " --> pdb=" O HIS B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 938 Processing helix chain 'B' and resid 961 through 981 Processing helix chain 'B' and resid 1008 through 1019 removed outlier: 3.832A pdb=" N ILE B1012 " --> pdb=" O SER B1008 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL B1013 " --> pdb=" O ALA B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1038 removed outlier: 3.602A pdb=" N MET B1023 " --> pdb=" O LEU B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1053 through 1074 Processing helix chain 'B' and resid 1075 through 1079 Processing helix chain 'B' and resid 1080 through 1082 No H-bonds generated for 'chain 'B' and resid 1080 through 1082' Processing helix chain 'B' and resid 1083 through 1099 removed outlier: 4.367A pdb=" N VAL B1093 " --> pdb=" O SER B1089 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU B1094 " --> pdb=" O ALA B1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 1106 through 1120 Processing helix chain 'B' and resid 1121 through 1124 Processing helix chain 'B' and resid 1127 through 1144 removed outlier: 4.091A pdb=" N ALA B1131 " --> pdb=" O SER B1127 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B1132 " --> pdb=" O PHE B1128 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR B1133 " --> pdb=" O GLN B1129 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS B1144 " --> pdb=" O VAL B1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 1147 through 1165 Processing helix chain 'B' and resid 1178 through 1193 removed outlier: 3.615A pdb=" N LEU B1182 " --> pdb=" O SER B1178 " (cutoff:3.500A) Processing helix chain 'B' and resid 1195 through 1214 Proline residue: B1209 - end of helix Processing helix chain 'B' and resid 1230 through 1249 removed outlier: 3.793A pdb=" N ILE B1249 " --> pdb=" O THR B1245 " (cutoff:3.500A) Processing helix chain 'B' and resid 1257 through 1280 removed outlier: 4.242A pdb=" N GLU B1263 " --> pdb=" O GLN B1259 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS B1264 " --> pdb=" O ILE B1260 " (cutoff:3.500A) Processing helix chain 'B' and resid 1287 through 1316 removed outlier: 3.619A pdb=" N LEU B1291 " --> pdb=" O SER B1287 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B1296 " --> pdb=" O HIS B1292 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET B1310 " --> pdb=" O LEU B1306 " (cutoff:3.500A) Proline residue: B1311 - end of helix Processing helix chain 'B' and resid 1320 through 1348 Processing helix chain 'B' and resid 1350 through 1356 removed outlier: 4.492A pdb=" N HIS B1356 " --> pdb=" O ARG B1352 " (cutoff:3.500A) Processing helix chain 'B' and resid 1356 through 1378 removed outlier: 3.793A pdb=" N LEU B1360 " --> pdb=" O HIS B1356 " (cutoff:3.500A) Processing helix chain 'B' and resid 1380 through 1382 No H-bonds generated for 'chain 'B' and resid 1380 through 1382' Processing helix chain 'C' and resid 8 through 10 No H-bonds generated for 'chain 'C' and resid 8 through 10' Processing helix chain 'C' and resid 22 through 35 Processing sheet with id=AA1, first strand: chain 'A' and resid 651 through 654 removed outlier: 3.701A pdb=" N SER A 659 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN A 654 " --> pdb=" O LYS A 657 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 657 " --> pdb=" O GLN A 654 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1284 through 1289 removed outlier: 4.605A pdb=" N SER A1284 " --> pdb=" O LEU B1389 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 57 through 58 Processing sheet with id=AA4, first strand: chain 'B' and resid 665 through 666 Processing sheet with id=AA5, first strand: chain 'B' and resid 681 through 683 Processing sheet with id=AA6, first strand: chain 'C' and resid 12 through 16 removed outlier: 4.113A pdb=" N SER C 65 " --> pdb=" O GLN C 2 " (cutoff:3.500A) 1241 hydrogen bonds defined for protein. 3660 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 63 hydrogen bonds 126 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 12.92 Time building geometry restraints manager: 27.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 19380 1.03 - 1.23: 119 1.23 - 1.42: 7995 1.42 - 1.62: 11688 1.62 - 1.81: 155 Bond restraints: 39337 Sorted by residual: bond pdb=" C GLU A1258 " pdb=" O GLU A1258 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.19e-02 7.06e+03 9.12e+00 bond pdb=" N SER B1095 " pdb=" CA SER B1095 " ideal model delta sigma weight residual 1.459 1.424 0.035 1.19e-02 7.06e+03 8.82e+00 bond pdb=" CB SER B1095 " pdb=" OG SER B1095 " ideal model delta sigma weight residual 1.417 1.362 0.055 2.00e-02 2.50e+03 7.61e+00 bond pdb=" C ASN A 580 " pdb=" O ASN A 580 " ideal model delta sigma weight residual 1.236 1.205 0.031 1.15e-02 7.56e+03 7.36e+00 bond pdb=" C ASN B1085 " pdb=" O ASN B1085 " ideal model delta sigma weight residual 1.236 1.203 0.033 1.25e-02 6.40e+03 6.95e+00 ... (remaining 39332 not shown) Histogram of bond angle deviations from ideal: 98.95 - 106.01: 639 106.01 - 113.07: 47082 113.07 - 120.14: 12712 120.14 - 127.20: 10710 127.20 - 134.27: 269 Bond angle restraints: 71412 Sorted by residual: angle pdb=" N ASN A 304 " pdb=" CA ASN A 304 " pdb=" C ASN A 304 " ideal model delta sigma weight residual 111.82 106.71 5.11 1.16e+00 7.43e-01 1.94e+01 angle pdb=" N SER A 917 " pdb=" CA SER A 917 " pdb=" C SER A 917 " ideal model delta sigma weight residual 112.90 107.67 5.23 1.31e+00 5.83e-01 1.60e+01 angle pdb=" N ASN A 711 " pdb=" CA ASN A 711 " pdb=" C ASN A 711 " ideal model delta sigma weight residual 111.07 115.20 -4.13 1.07e+00 8.73e-01 1.49e+01 angle pdb=" N ARG A1285 " pdb=" CA ARG A1285 " pdb=" C ARG A1285 " ideal model delta sigma weight residual 110.42 116.25 -5.83 1.55e+00 4.16e-01 1.42e+01 angle pdb=" N ASN B 798 " pdb=" CA ASN B 798 " pdb=" C ASN B 798 " ideal model delta sigma weight residual 111.36 107.29 4.07 1.09e+00 8.42e-01 1.39e+01 ... (remaining 71407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 16050 17.31 - 34.63: 1465 34.63 - 51.94: 437 51.94 - 69.26: 161 69.26 - 86.57: 23 Dihedral angle restraints: 18136 sinusoidal: 10310 harmonic: 7826 Sorted by residual: dihedral pdb=" CA ASP B 277 " pdb=" C ASP B 277 " pdb=" N LEU B 278 " pdb=" CA LEU B 278 " ideal model delta harmonic sigma weight residual -180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA HIS A1204 " pdb=" C HIS A1204 " pdb=" N LEU A1205 " pdb=" CA LEU A1205 " ideal model delta harmonic sigma weight residual -180.00 -157.97 -22.03 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA LEU B 739 " pdb=" C LEU B 739 " pdb=" N CYS B 740 " pdb=" CA CYS B 740 " ideal model delta harmonic sigma weight residual -180.00 -158.37 -21.63 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 18133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2745 0.059 - 0.119: 403 0.119 - 0.178: 47 0.178 - 0.238: 4 0.238 - 0.297: 1 Chirality restraints: 3200 Sorted by residual: chirality pdb=" CA THR A1151 " pdb=" N THR A1151 " pdb=" C THR A1151 " pdb=" CB THR A1151 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA GLN A 504 " pdb=" N GLN A 504 " pdb=" C GLN A 504 " pdb=" CB GLN A 504 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE C 3 " pdb=" N ILE C 3 " pdb=" C ILE C 3 " pdb=" CB ILE C 3 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 3197 not shown) Planarity restraints: 5459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B1138 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.88e+00 pdb=" C LEU B1138 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU B1138 " 0.019 2.00e-02 2.50e+03 pdb=" N MET B1139 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 816 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.49e+00 pdb=" C LEU B 816 " 0.044 2.00e-02 2.50e+03 pdb=" O LEU B 816 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS B 817 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 210 " 0.042 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO A 211 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 211 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 211 " 0.034 5.00e-02 4.00e+02 ... (remaining 5456 not shown) Histogram of nonbonded interaction distances: 1.30 - 1.96: 126 1.96 - 2.62: 46371 2.62 - 3.28: 119484 3.28 - 3.94: 144979 3.94 - 4.60: 226724 Nonbonded interactions: 537684 Sorted by model distance: nonbonded pdb=" NZ LYS A 523 " pdb=" C GLY C 76 " model vdw 1.299 3.250 nonbonded pdb=" O LYS B 811 " pdb=" HG1 THR B 814 " model vdw 1.618 1.850 nonbonded pdb=" OE2 GLU A1131 " pdb=" HH TYR A1180 " model vdw 1.671 1.850 nonbonded pdb=" O LEU C 8 " pdb=" HG1 THR C 9 " model vdw 1.688 1.850 nonbonded pdb=" O LEU A1148 " pdb=" HG1 THR A1151 " model vdw 1.693 1.850 ... (remaining 537679 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.280 Construct map_model_manager: 0.410 Extract box with map and model: 7.740 Check model and map are aligned: 0.440 Set scattering table: 0.330 Process input model: 108.600 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.090 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:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 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 0.069 19906 Z= 0.303 Angle : 0.810 10.680 27120 Z= 0.439 Chirality : 0.042 0.297 3200 Planarity : 0.006 0.062 3217 Dihedral : 16.565 86.574 7582 Min Nonbonded Distance : 1.299 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.17), residues: 2253 helix: 0.90 (0.12), residues: 1591 sheet: -0.62 (0.95), residues: 20 loop : -0.22 (0.27), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 364 HIS 0.010 0.001 HIS B 550 PHE 0.021 0.002 PHE A1144 TYR 0.012 0.001 TYR B1297 ARG 0.007 0.000 ARG A 884 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4506 Ramachandran restraints generated. 2253 Oldfield, 0 Emsley, 2253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4506 Ramachandran restraints generated. 2253 Oldfield, 0 Emsley, 2253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 523 is missing expected H atoms. Skipping. Evaluate side-chains 505 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 505 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 206 ASN cc_start: 0.7895 (m-40) cc_final: 0.7489 (t0) REVERT: A 511 MET cc_start: 0.7509 (ppp) cc_final: 0.7289 (ppp) REVERT: A 586 GLU cc_start: 0.8714 (pt0) cc_final: 0.8203 (pt0) REVERT: A 589 ASP cc_start: 0.8461 (t0) cc_final: 0.8216 (t0) REVERT: A 613 LEU cc_start: 0.9285 (tt) cc_final: 0.8938 (tt) REVERT: A 841 TYR cc_start: 0.9020 (t80) cc_final: 0.8803 (t80) REVERT: A 923 TYR cc_start: 0.8023 (m-80) cc_final: 0.7763 (m-80) REVERT: A 1017 ASN cc_start: 0.8047 (m-40) cc_final: 0.7769 (m110) REVERT: A 1148 LEU cc_start: 0.8550 (pp) cc_final: 0.7937 (tp) REVERT: B 205 GLU cc_start: 0.6118 (tm-30) cc_final: 0.5860 (tm-30) REVERT: B 631 TYR cc_start: 0.8563 (t80) cc_final: 0.7975 (t80) REVERT: B 698 ASN cc_start: 0.8578 (p0) cc_final: 0.8287 (p0) REVERT: B 734 PHE cc_start: 0.8509 (t80) cc_final: 0.8161 (t80) REVERT: B 761 PHE cc_start: 0.7779 (p90) cc_final: 0.7506 (p90) REVERT: B 970 GLU cc_start: 0.8862 (tt0) cc_final: 0.8242 (tt0) REVERT: B 1206 VAL cc_start: 0.8249 (m) cc_final: 0.7846 (p) REVERT: B 1310 MET cc_start: 0.8331 (mmm) cc_final: 0.8116 (mmm) REVERT: C 32 ASP cc_start: 0.8629 (t70) cc_final: 0.8410 (t70) REVERT: C 49 GLN cc_start: 0.7908 (tp40) cc_final: 0.7600 (tp40) outliers start: 0 outliers final: 0 residues processed: 505 average time/residue: 0.5398 time to fit residues: 429.0566 Evaluate side-chains 343 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 343 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.0670 chunk 175 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 210 optimal weight: 0.7980 overall best weight: 0.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 GLN B1113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19906 Z= 0.212 Angle : 0.559 7.020 27120 Z= 0.310 Chirality : 0.035 0.150 3200 Planarity : 0.005 0.065 3217 Dihedral : 13.028 59.923 2989 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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: 1.46 (0.18), residues: 2253 helix: 1.44 (0.13), residues: 1603 sheet: -0.02 (1.04), residues: 20 loop : -0.06 (0.27), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 677 HIS 0.005 0.001 HIS B 550 PHE 0.030 0.001 PHE A 609 TYR 0.023 0.001 TYR B1033 ARG 0.007 0.000 ARG B 263 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4506 Ramachandran restraints generated. 2253 Oldfield, 0 Emsley, 2253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4506 Ramachandran restraints generated. 2253 Oldfield, 0 Emsley, 2253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 523 is missing expected H atoms. Skipping. Evaluate side-chains 422 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 2.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 206 ASN cc_start: 0.7953 (m-40) cc_final: 0.7635 (t0) REVERT: A 511 MET cc_start: 0.7479 (ppp) cc_final: 0.7182 (ppp) REVERT: A 586 GLU cc_start: 0.8690 (pt0) cc_final: 0.8202 (pt0) REVERT: A 589 ASP cc_start: 0.8445 (t0) cc_final: 0.8234 (t0) REVERT: A 604 MET cc_start: 0.8922 (tpt) cc_final: 0.8628 (tpp) REVERT: A 841 TYR cc_start: 0.8964 (t80) cc_final: 0.8744 (t80) REVERT: A 978 ASN cc_start: 0.8543 (m-40) cc_final: 0.8341 (m-40) REVERT: A 1087 LEU cc_start: 0.8690 (tt) cc_final: 0.8453 (tt) REVERT: A 1147 GLU cc_start: 0.7632 (tp30) cc_final: 0.7253 (tp30) REVERT: B 560 ARG cc_start: 0.9341 (mtp180) cc_final: 0.9125 (ttp80) REVERT: B 581 MET cc_start: 0.8685 (ttp) cc_final: 0.8418 (tmm) REVERT: B 631 TYR cc_start: 0.8703 (t80) cc_final: 0.8446 (t80) REVERT: B 675 ASP cc_start: 0.8049 (t70) cc_final: 0.7819 (t0) REVERT: B 734 PHE cc_start: 0.8737 (t80) cc_final: 0.8335 (t80) REVERT: B 761 PHE cc_start: 0.7843 (p90) cc_final: 0.7497 (p90) REVERT: B 970 GLU cc_start: 0.8830 (tt0) cc_final: 0.8279 (tt0) REVERT: B 977 GLU cc_start: 0.8505 (tp30) cc_final: 0.8273 (mm-30) REVERT: B 1206 VAL cc_start: 0.8236 (m) cc_final: 0.7864 (p) REVERT: B 1239 MET cc_start: 0.8140 (mmm) cc_final: 0.7694 (mmp) REVERT: C 32 ASP cc_start: 0.8633 (t70) cc_final: 0.8421 (t70) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.5177 time to fit residues: 347.4607 Evaluate side-chains 325 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 211 optimal weight: 0.9980 chunk 228 optimal weight: 10.0000 chunk 187 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1332 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19906 Z= 0.197 Angle : 0.527 6.544 27120 Z= 0.292 Chirality : 0.035 0.154 3200 Planarity : 0.004 0.063 3217 Dihedral : 13.284 59.923 2989 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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: 1.55 (0.18), residues: 2253 helix: 1.57 (0.13), residues: 1613 sheet: 0.24 (1.12), residues: 20 loop : -0.26 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 677 HIS 0.006 0.001 HIS B 550 PHE 0.030 0.001 PHE A 609 TYR 0.010 0.001 TYR B1297 ARG 0.005 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4506 Ramachandran restraints generated. 2253 Oldfield, 0 Emsley, 2253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4506 Ramachandran restraints generated. 2253 Oldfield, 0 Emsley, 2253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 523 is missing expected H atoms. Skipping. Evaluate side-chains 402 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 206 ASN cc_start: 0.7931 (m-40) cc_final: 0.7602 (t0) REVERT: A 511 MET cc_start: 0.7527 (ppp) cc_final: 0.7231 (ppp) REVERT: A 586 GLU cc_start: 0.8677 (pt0) cc_final: 0.8209 (pt0) REVERT: A 589 ASP cc_start: 0.8649 (t0) cc_final: 0.8290 (t0) REVERT: A 604 MET cc_start: 0.8989 (tpt) cc_final: 0.8702 (tpp) REVERT: A 650 CYS cc_start: 0.6494 (t) cc_final: 0.6010 (t) REVERT: A 664 LEU cc_start: 0.8511 (mm) cc_final: 0.7966 (mm) REVERT: A 841 TYR cc_start: 0.9037 (t80) cc_final: 0.8820 (t80) REVERT: A 1147 GLU cc_start: 0.7655 (tp30) cc_final: 0.7426 (tp30) REVERT: B 560 ARG cc_start: 0.9342 (mtp180) cc_final: 0.9131 (ttp80) REVERT: B 581 MET cc_start: 0.8734 (ttp) cc_final: 0.8368 (tmm) REVERT: B 631 TYR cc_start: 0.8716 (t80) cc_final: 0.8486 (t80) REVERT: B 675 ASP cc_start: 0.8127 (t70) cc_final: 0.7897 (t0) REVERT: B 734 PHE cc_start: 0.8701 (t80) cc_final: 0.8226 (t80) REVERT: B 761 PHE cc_start: 0.7884 (p90) cc_final: 0.7484 (p90) REVERT: B 970 GLU cc_start: 0.8813 (tt0) cc_final: 0.8288 (tt0) REVERT: C 32 ASP cc_start: 0.8637 (t70) cc_final: 0.8421 (t70) outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.5215 time to fit residues: 333.5457 Evaluate side-chains 327 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 211 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1332 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19906 Z= 0.186 Angle : 0.516 7.556 27120 Z= 0.286 Chirality : 0.035 0.200 3200 Planarity : 0.004 0.061 3217 Dihedral : 13.440 59.989 2989 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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: 1.60 (0.18), residues: 2253 helix: 1.61 (0.13), residues: 1626 sheet: 0.57 (1.16), residues: 20 loop : -0.31 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 677 HIS 0.006 0.001 HIS C 68 PHE 0.017 0.001 PHE A 609 TYR 0.018 0.001 TYR A 923 ARG 0.005 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4506 Ramachandran restraints generated. 2253 Oldfield, 0 Emsley, 2253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4506 Ramachandran restraints generated. 2253 Oldfield, 0 Emsley, 2253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 523 is missing expected H atoms. Skipping. Evaluate side-chains 390 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 2.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 206 ASN cc_start: 0.7993 (m-40) cc_final: 0.7719 (m-40) REVERT: A 287 ARG cc_start: 0.7951 (ttm110) cc_final: 0.7729 (ttp-110) REVERT: A 511 MET cc_start: 0.7616 (ppp) cc_final: 0.7339 (ppp) REVERT: A 586 GLU cc_start: 0.8667 (pt0) cc_final: 0.8210 (pt0) REVERT: A 604 MET cc_start: 0.9046 (tpt) cc_final: 0.8728 (tpp) REVERT: A 650 CYS cc_start: 0.6484 (t) cc_final: 0.6025 (t) REVERT: A 664 LEU cc_start: 0.8405 (mm) cc_final: 0.7752 (mm) REVERT: A 978 ASN cc_start: 0.8597 (m-40) cc_final: 0.8392 (m-40) REVERT: B 205 GLU cc_start: 0.6317 (tm-30) cc_final: 0.6115 (tm-30) REVERT: B 401 ARG cc_start: 0.8141 (mtm110) cc_final: 0.7937 (mtm110) REVERT: B 539 LEU cc_start: 0.8647 (pp) cc_final: 0.8446 (pp) REVERT: B 560 ARG cc_start: 0.9344 (mtp180) cc_final: 0.9135 (ttp80) REVERT: B 581 MET cc_start: 0.8739 (ttp) cc_final: 0.8317 (tmm) REVERT: B 631 TYR cc_start: 0.8734 (t80) cc_final: 0.8147 (t80) REVERT: B 675 ASP cc_start: 0.8178 (t70) cc_final: 0.7947 (t0) REVERT: B 734 PHE cc_start: 0.8714 (t80) cc_final: 0.8317 (t80) REVERT: B 761 PHE cc_start: 0.7907 (p90) cc_final: 0.7457 (p90) REVERT: C 32 ASP cc_start: 0.8648 (t70) cc_final: 0.8422 (t70) REVERT: C 51 GLU cc_start: 0.8167 (tp30) cc_final: 0.7754 (tp30) outliers start: 0 outliers final: 0 residues processed: 390 average time/residue: 0.5224 time to fit residues: 323.5320 Evaluate side-chains 316 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 191 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 HIS ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 GLN ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 166 ASN ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 959 GLN ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1192 HIS ** B1258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1332 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 19906 Z= 0.402 Angle : 0.677 8.498 27120 Z= 0.384 Chirality : 0.038 0.157 3200 Planarity : 0.005 0.055 3217 Dihedral : 13.774 59.896 2989 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2253 helix: 0.70 (0.12), residues: 1616 sheet: 0.31 (1.14), residues: 20 loop : -0.77 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 677 HIS 0.012 0.002 HIS B1339 PHE 0.046 0.002 PHE B1162 TYR 0.027 0.002 TYR B 103 ARG 0.008 0.001 ARG B1228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4506 Ramachandran restraints generated. 2253 Oldfield, 0 Emsley, 2253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4506 Ramachandran restraints generated. 2253 Oldfield, 0 Emsley, 2253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 523 is missing expected H atoms. Skipping. Evaluate side-chains 352 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 275 ILE cc_start: 0.9474 (pt) cc_final: 0.9215 (tt) REVERT: A 511 MET cc_start: 0.7858 (ppp) cc_final: 0.7554 (ppp) REVERT: A 664 LEU cc_start: 0.8481 (mm) cc_final: 0.8060 (mm) REVERT: A 902 LYS cc_start: 0.8247 (mptt) cc_final: 0.7826 (mmtm) REVERT: A 1147 GLU cc_start: 0.8081 (tp30) cc_final: 0.7839 (tp30) REVERT: A 1246 GLU cc_start: 0.8310 (pp20) cc_final: 0.7958 (pp20) REVERT: B 581 MET cc_start: 0.8755 (ttp) cc_final: 0.8404 (tmm) REVERT: B 631 TYR cc_start: 0.8824 (t80) cc_final: 0.8499 (t80) REVERT: B 675 ASP cc_start: 0.8189 (t70) cc_final: 0.7925 (t0) REVERT: B 761 PHE cc_start: 0.7973 (p90) cc_final: 0.7520 (p90) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.5334 time to fit residues: 297.9740 Evaluate side-chains 287 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 186 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19906 Z= 0.184 Angle : 0.534 5.900 27120 Z= 0.291 Chirality : 0.035 0.140 3200 Planarity : 0.004 0.059 3217 Dihedral : 13.830 59.923 2989 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: 1.20 (0.17), residues: 2253 helix: 1.33 (0.13), residues: 1616 sheet: 0.30 (1.13), residues: 20 loop : -0.50 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 677 HIS 0.006 0.001 HIS C 68 PHE 0.032 0.002 PHE B 380 TYR 0.015 0.001 TYR B1297 ARG 0.005 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4506 Ramachandran restraints generated. 2253 Oldfield, 0 Emsley, 2253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4506 Ramachandran restraints generated. 2253 Oldfield, 0 Emsley, 2253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 523 is missing expected H atoms. Skipping. Evaluate side-chains 368 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 511 MET cc_start: 0.7712 (ppp) cc_final: 0.7467 (ppp) REVERT: A 586 GLU cc_start: 0.8570 (pt0) cc_final: 0.8087 (pt0) REVERT: A 664 LEU cc_start: 0.8368 (mm) cc_final: 0.7642 (mm) REVERT: A 902 LYS cc_start: 0.8218 (mptt) cc_final: 0.7752 (mmtm) REVERT: A 1147 GLU cc_start: 0.7715 (tp30) cc_final: 0.7256 (tp30) REVERT: B 205 GLU cc_start: 0.6195 (tm-30) cc_final: 0.5987 (tm-30) REVERT: B 581 MET cc_start: 0.8641 (ttp) cc_final: 0.8303 (tmm) REVERT: B 631 TYR cc_start: 0.8780 (t80) cc_final: 0.8484 (t80) REVERT: B 675 ASP cc_start: 0.8289 (t70) cc_final: 0.8063 (t0) REVERT: B 761 PHE cc_start: 0.7937 (p90) cc_final: 0.7481 (p90) REVERT: B 769 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8346 (mm-30) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.5349 time to fit residues: 315.5498 Evaluate side-chains 295 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 chunk 188 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 GLN ** A 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 19906 Z= 0.253 Angle : 0.550 5.790 27120 Z= 0.306 Chirality : 0.035 0.164 3200 Planarity : 0.004 0.059 3217 Dihedral : 13.952 59.989 2989 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % 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: 1.15 (0.18), residues: 2253 helix: 1.30 (0.13), residues: 1618 sheet: 0.38 (1.13), residues: 20 loop : -0.52 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 677 HIS 0.006 0.001 HIS C 68 PHE 0.034 0.002 PHE B1162 TYR 0.017 0.002 TYR B 103 ARG 0.008 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4506 Ramachandran restraints generated. 2253 Oldfield, 0 Emsley, 2253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4506 Ramachandran restraints generated. 2253 Oldfield, 0 Emsley, 2253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 523 is missing expected H atoms. Skipping. Evaluate side-chains 357 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 391 ASP cc_start: 0.9169 (p0) cc_final: 0.8925 (p0) REVERT: A 511 MET cc_start: 0.7861 (ppp) cc_final: 0.7487 (ppp) REVERT: A 586 GLU cc_start: 0.8605 (pt0) cc_final: 0.8160 (pt0) REVERT: A 664 LEU cc_start: 0.8433 (mm) cc_final: 0.7785 (mm) REVERT: A 902 LYS cc_start: 0.8181 (mptt) cc_final: 0.7716 (mmtm) REVERT: A 1006 MET cc_start: 0.8623 (tpp) cc_final: 0.8327 (tmm) REVERT: B 581 MET cc_start: 0.8558 (ttp) cc_final: 0.8296 (tmm) REVERT: B 631 TYR cc_start: 0.8835 (t80) cc_final: 0.8509 (t80) REVERT: B 675 ASP cc_start: 0.8336 (t70) cc_final: 0.8106 (t0) REVERT: B 761 PHE cc_start: 0.7986 (p90) cc_final: 0.7512 (p90) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.5184 time to fit residues: 294.6114 Evaluate side-chains 293 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1150 GLN ** A1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19906 Z= 0.228 Angle : 0.540 6.114 27120 Z= 0.299 Chirality : 0.035 0.135 3200 Planarity : 0.004 0.063 3217 Dihedral : 14.043 60.370 2989 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.05 % Allowed : 0.57 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.17), residues: 2253 helix: 1.34 (0.13), residues: 1609 sheet: 0.47 (1.15), residues: 20 loop : -0.47 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 677 HIS 0.007 0.001 HIS C 68 PHE 0.025 0.002 PHE B 380 TYR 0.016 0.002 TYR B 733 ARG 0.008 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4506 Ramachandran restraints generated. 2253 Oldfield, 0 Emsley, 2253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4506 Ramachandran restraints generated. 2253 Oldfield, 0 Emsley, 2253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 523 is missing expected H atoms. Skipping. Evaluate side-chains 356 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 355 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 391 ASP cc_start: 0.9144 (p0) cc_final: 0.8871 (p0) REVERT: A 511 MET cc_start: 0.7827 (ppp) cc_final: 0.7444 (ppp) REVERT: A 586 GLU cc_start: 0.8588 (pt0) cc_final: 0.8122 (pt0) REVERT: A 664 LEU cc_start: 0.8416 (mm) cc_final: 0.7740 (mm) REVERT: A 902 LYS cc_start: 0.8171 (mptt) cc_final: 0.7723 (mmtm) REVERT: A 1006 MET cc_start: 0.8603 (tpp) cc_final: 0.8285 (tmm) REVERT: B 205 GLU cc_start: 0.6241 (tm-30) cc_final: 0.6004 (tm-30) REVERT: B 581 MET cc_start: 0.8510 (ttp) cc_final: 0.8260 (tmm) REVERT: B 631 TYR cc_start: 0.8813 (t80) cc_final: 0.8456 (t80) REVERT: B 675 ASP cc_start: 0.8200 (t70) cc_final: 0.7961 (t0) REVERT: B 761 PHE cc_start: 0.8002 (p90) cc_final: 0.7506 (p90) REVERT: B 769 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8347 (mm-30) outliers start: 1 outliers final: 0 residues processed: 356 average time/residue: 0.5134 time to fit residues: 292.6624 Evaluate side-chains 292 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.7980 chunk 208 optimal weight: 4.9990 chunk 214 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 90 optimal weight: 0.0870 chunk 163 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19906 Z= 0.182 Angle : 0.515 5.498 27120 Z= 0.282 Chirality : 0.035 0.179 3200 Planarity : 0.004 0.058 3217 Dihedral : 14.099 60.671 2989 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: 1.50 (0.18), residues: 2253 helix: 1.56 (0.13), residues: 1610 sheet: 0.60 (1.16), residues: 20 loop : -0.37 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 364 HIS 0.008 0.001 HIS A1146 PHE 0.033 0.001 PHE B 380 TYR 0.014 0.001 TYR B1297 ARG 0.009 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4506 Ramachandran restraints generated. 2253 Oldfield, 0 Emsley, 2253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4506 Ramachandran restraints generated. 2253 Oldfield, 0 Emsley, 2253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 523 is missing expected H atoms. Skipping. Evaluate side-chains 360 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 349 PHE cc_start: 0.8287 (t80) cc_final: 0.7965 (t80) REVERT: A 391 ASP cc_start: 0.9111 (p0) cc_final: 0.8849 (p0) REVERT: A 511 MET cc_start: 0.7825 (ppp) cc_final: 0.7447 (ppp) REVERT: A 586 GLU cc_start: 0.8572 (pt0) cc_final: 0.8058 (pt0) REVERT: A 664 LEU cc_start: 0.8410 (mm) cc_final: 0.7720 (mm) REVERT: A 682 VAL cc_start: 0.8817 (t) cc_final: 0.8585 (t) REVERT: A 902 LYS cc_start: 0.8136 (mptt) cc_final: 0.7686 (mmtm) REVERT: A 1006 MET cc_start: 0.8530 (tpp) cc_final: 0.8268 (tmm) REVERT: A 1147 GLU cc_start: 0.7854 (tp30) cc_final: 0.7537 (tp30) REVERT: B 205 GLU cc_start: 0.6238 (tm-30) cc_final: 0.6011 (tm-30) REVERT: B 581 MET cc_start: 0.8487 (ttp) cc_final: 0.8239 (tmm) REVERT: B 631 TYR cc_start: 0.8757 (t80) cc_final: 0.8451 (t80) REVERT: B 675 ASP cc_start: 0.8274 (t70) cc_final: 0.8049 (t0) REVERT: B 761 PHE cc_start: 0.7995 (p90) cc_final: 0.7501 (p90) REVERT: B 769 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8404 (mm-30) REVERT: B 1162 PHE cc_start: 0.8175 (m-80) cc_final: 0.7872 (m-10) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.5197 time to fit residues: 303.2752 Evaluate side-chains 298 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 231 optimal weight: 10.0000 chunk 212 optimal weight: 0.2980 chunk 184 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 146 optimal weight: 0.2980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19906 Z= 0.179 Angle : 0.513 5.563 27120 Z= 0.280 Chirality : 0.034 0.135 3200 Planarity : 0.004 0.058 3217 Dihedral : 14.140 60.490 2989 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.18), residues: 2253 helix: 1.63 (0.13), residues: 1603 sheet: 0.67 (1.18), residues: 20 loop : -0.37 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 677 HIS 0.007 0.001 HIS A1146 PHE 0.023 0.001 PHE A 609 TYR 0.023 0.001 TYR B1189 ARG 0.004 0.000 ARG B 404 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4506 Ramachandran restraints generated. 2253 Oldfield, 0 Emsley, 2253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4506 Ramachandran restraints generated. 2253 Oldfield, 0 Emsley, 2253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 523 is missing expected H atoms. Skipping. Evaluate side-chains 362 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 391 ASP cc_start: 0.9093 (p0) cc_final: 0.8852 (p0) REVERT: A 511 MET cc_start: 0.7819 (ppp) cc_final: 0.7456 (ppp) REVERT: A 586 GLU cc_start: 0.8579 (pt0) cc_final: 0.8058 (pt0) REVERT: A 664 LEU cc_start: 0.8366 (mm) cc_final: 0.7715 (mm) REVERT: A 682 VAL cc_start: 0.8806 (t) cc_final: 0.8572 (t) REVERT: A 902 LYS cc_start: 0.8119 (mptt) cc_final: 0.7668 (mmtm) REVERT: A 1006 MET cc_start: 0.8501 (tpp) cc_final: 0.8290 (tmm) REVERT: A 1147 GLU cc_start: 0.7810 (tp30) cc_final: 0.7564 (tp30) REVERT: B 205 GLU cc_start: 0.6265 (tm-30) cc_final: 0.6012 (tm-30) REVERT: B 581 MET cc_start: 0.8543 (ttp) cc_final: 0.8241 (tmm) REVERT: B 675 ASP cc_start: 0.8248 (t70) cc_final: 0.8021 (t0) REVERT: B 761 PHE cc_start: 0.7968 (p90) cc_final: 0.7505 (p90) REVERT: B 769 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8239 (mm-30) REVERT: B 1162 PHE cc_start: 0.8060 (m-80) cc_final: 0.7823 (m-10) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.5223 time to fit residues: 302.3048 Evaluate side-chains 296 residues out of total 2114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 184 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 189 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1217 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 = 0.4022 r_free = 0.4022 target = 0.124859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.091263 restraints weight = 162054.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.094881 restraints weight = 76778.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.097149 restraints weight = 48171.845| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19906 Z= 0.169 Angle : 0.510 6.236 27120 Z= 0.276 Chirality : 0.035 0.197 3200 Planarity : 0.004 0.057 3217 Dihedral : 14.160 60.289 2989 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 1.66 (0.18), residues: 2253 helix: 1.67 (0.13), residues: 1607 sheet: 0.57 (1.18), residues: 20 loop : -0.28 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B1385 HIS 0.007 0.001 HIS C 68 PHE 0.022 0.001 PHE B 380 TYR 0.018 0.001 TYR B 733 ARG 0.006 0.000 ARG A 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7042.31 seconds wall clock time: 122 minutes 31.31 seconds (7351.31 seconds total)